Horizontal gene transfer facilitated the evolution of
plant parasitic mechanisms in the oomycetes
Thomas A. Richardsa,b,1, Darren M. Soanesa, Meredith D. M. Jonesa,b, Olga Vasievac, Guy Leonarda,b,
Konrad Paszkiewicza, Peter G. Fosterb, Neil Hallc, and Nicholas J. Talbota
a
Biosciences, University of Exeter, Exeter EX4 4QD, United Kingdom; bDepartment of Zoology, Natural History Museum, London SW7 5BD, United Kingdom;
and cSchool of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
Horizontal gene transfer (HGT) can radically alter the genomes of
microorganisms, providing the capacity to adapt to new lifestyles,
environments, and hosts. However, the extent of HGT between
eukaryotes is unclear. Using whole-genome, gene-by-gene phylogenetic analysis we demonstrate an extensive pattern of crosskingdom HGT between fungi and oomycetes. Comparative
genomics, including the de novo genome sequence of Hyphochytrium catenoides, a free-living sister of the oomycetes, shows that
these transfers largely converge within the radiation of oomycetes
that colonize plant tissues. The repertoire of HGTs includes a large
number of putatively secreted proteins; for example, 7.6% of the
secreted proteome of the sudden oak death parasite Phytophthora ramorum has been acquired from fungi by HGT. Transfers
include gene products with the capacity to break down plant cell
walls and acquire sugars, nucleic acids, nitrogen, and phosphate
sources from the environment. Predicted HGTs also include proteins implicated in resisting plant defense mechanisms and effector proteins for attacking plant cells. These data are consistent
with the hypothesis that some oomycetes became successful plant
parasites by multiple acquisitions of genes from fungi.
osmotrophy
| pseudofungi | lateral gene transfer
H
orizontal gene transfer (HGT) involves the transfer of genetic material between reproductively isolated lineages (1,
2) and has been an important factor in prokaryotic evolution (3–
5). By contrast, the role of HGT between eukaryotic genomes is
less clear (2, 6) and seems to have occurred at a lower frequency,
with some reports suggesting that HGT between eukaryotic
kingdoms is rare (7). Conversely, HGTs originating from prokaryotic genomes constitute a significant, but relatively small,
proportion of the total inventory of genes in phagotrophic protists (8–12) and some osmotrophic fungi (13).
Fungi branch with animals on the tree of life (14) and encompass an extremely diverse group of organisms, including
species adapted to forming intimate relationships with plants,
including mutualistic and parasitic associations, as well as saprophytic growth (15–17). To explore the frequency of HGT between distinct eukaryotic groups that form parasitic associations
with plants, we previously used the predicted protein-encoding
sequences from the genome of a fungal plant parasite, Magnaporthe oryzae (18), as a BLASTp search seed and identified four
HGTs from fungi to oomycetes with strong phylogenetic support
(19). The oomycetes are distant relatives of fungi and branch
within the stramenopile radiation, which includes a diversity of
photosynthetic microbes possessing plastid organelles of secondary endosymbiotic ancestry (20). Oomycetes, however, are
not photosynthetic and display filamentous growth, closely resembling fungi in many aspects of their biology. Both fungi and
oomycetes, for instance, feed exclusively by osmotrophy, secreting depolymerizing enzymes to break down complex biological
materials in the extracellular environment, followed by transport
of broken-down metabolic units into the cell. Fungi and oomycetes also cause many of the world’s most serious plant diseases.
Sudden oak death is caused by the oomycete Phytophthora
www.pnas.org/cgi/doi/10.1073/pnas.1105100108
ramorum, for example, whereas the Irish potato famine of the
19th century was caused by the late blight parasite Phytophthora
infestans. Important crop diseases caused by fungi include the
devastating rice blast disease caused by M. oryzae and the rusts,
smuts, and mildews that affect wheat, barley, and maize. In this
study we report that HGT between fungi and oomycetes has
occurred to a far greater degree than hitherto recognized (19).
Our previous analysis suggested four strongly supported cases of
HGT, but by using a whole-genome, gene-by-gene phylogenetic
analysis we now reveal a pattern of 34 transfers and propose that
these transfers have been fundamental to the evolution of plant
parasitic traits within the oomycetes.
Results and Discussion
Identifying and Testing the Pattern of HGT Between Fungi and
Oomycetes. Among the best methods for identifying HGT is to
identify a gene phylogeny that places a taxonomic group (recipient) within the branches of a distantly related group (donor)
in direct contradiction to the known phylogenetic relationships
of the respective taxa (2, 6). To identify all potential gene transfers between fungi and oomycetes, we selected the predicted
proteomes of the oomycete species Phytophthora ramorum, Phytophthora sojae, Phytophthora infestans, and Hyaloperonospora
parasitica (also named Hyaloperonospora arabidopsidis) (21–23).
We processed each proteome separately, first excluding all putative transposable elements (SI Materials and Methods). Then
we clustered the genes from each genome into closely related
cluster groups (24) (SI Materials and Methods). Cluster groups
that BLASTp demonstrated were exclusively found only in the
oomycete genomes were then removed (SI Materials and Methods). This process left 3,014, 3,018, 3,233, and 2,169 cluster groups
from P. ramorum, P. sojae, P. infestans, and H. parasitica, respectively, totaling 11,434 gene clusters (Table 1). We then used
a gene-by-gene phylogeny pipeline (7) to generate fast maximumlikelihood trees for all 11,434 gene family groups, using a database of 795 (173 eukaryotic and 622 prokaryotic) genomes (Table
S1). These data were searched manually for trees that demonstrated putative fungi/oomycete gene transfer. Gene families that
produced unresolved tree topologies were reprocessed by running
the tree-building pipeline again but using different gathering
thresholds (SI Materials and Methods).
Author contributions: T.A.R., N.H., and N.J.T. designed research; T.A.R., D.M.S., M.D.M.J.,
O.V., and N.H. performed research; P.G.F. contributed new reagents/analytic tools; T.A.R.,
D.M.S., O.V., G.L., K.P., P.G.F., and N.H. analyzed data; and T.A.R., N.H., and N.J.T. wrote
the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
Data deposition: The genome sequence data reported in this paper (Hyphochytrium) have
been submitted to Sequence Read Archive for the raw data (SRP004821), and the assembled genome has been archived at the European Bioinformatics Institute (Genome Project: 61035).
1
To whom correspondence should be addressed. E-mail: [email protected].
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.
1073/pnas.1105100108/-/DCSupplemental.
PNAS Early Edition | 1 of 6
EVOLUTION
Edited by W. Ford Doolittle, Dalhousie University, Halifax, Canada, and approved July 27, 2011 (received for review March 31, 2011)
Table 1. Comparative gene-by-gene phylogenomic analysis and identified HGTs
Species
P. ramorum
P. sojae
P. infestans
H. parasitica
15,743
6,871
3,014
19
11
143
1,326
521
101
7.61
19.38
19,027
6,079
3,018
17
10
117
1,586
630
89
5.61
14.13
22,658
7,093
3,233
11
7
48
1,123
351
30
2.67
8.55
13,240
3,365
2,169
4
5
21
411
121
13
3.16
10.74
Total no. of predicted proteins
Total proteins used in phylogenetic analysis
No. of gene cluster groups used for phylogenetic analyses [after OrthoMCL (24) clustering]
No. of HGT gene families strongly supported by all methods
No. of “gray zone” HGT gene families (Table 2 and Table S3)
Total putative ORFs from fungal-derived HGTs
Total secreted proteins in genome identified by both WoLFPSORT and SignalP
Total no. of proteins analyzed with phylogeny predicted to be secreted
No. of fungal HGT-derived proteins with N-terminal secretion motif
% Total predicted secretome derived from fungi by HGT
% Proteins analyzed that are predicted to be secreted and are derived by HGT
All of the predicted fungi/oomycete HGTs were subject to
reevaluation of taxon sampling using additional database searches
and manual alignment improvement, followed by recalculation of
the phylogenetic tree, combined with bootstrap analyses (see SI
Materials and Methods and Table S2 for details of phylogenetic
analysis). These analyses identified multiple cases in which
oomycete genes (the recipient group) branched within a clade of
fungal genes (the donor group) and a single case demonstrating
the opposite relationship. To confirm the results of these phylogenetic analyses, we used alternative topology tests to test
whether it was possible to reject monophyly of the donor group.
Where taxon sampling allowed, we used a variety of different
topology constraints, corresponding to different relationships
within the fungi (15, 25). This approach enabled us to partially
polarize the ancestry of the HGT event relative to the donor
group (Table S3). Taken together, our analyses identified 20 gene
families predicted to have been transferred from within the fungi
to the oomycetes and one case in which the transfer occurred
from the oomycetes to the fungi (Fig. 1 and Figs. S1.1–S1.21).
Our pipeline analysis also identified four gene families that
were exclusively found in oomycete and fungal genomes and
not present in any additional taxonomic groups analyzed. We
checked to confirm that the taxon sampling was robust by comparison with the GenBank nr database, using both BLASTp and
psi-BLAST with five iterations (26), and by interrogating the
GenBank EST and the Taxonomically Broad EST database using tBLASTn (27). Because of the taxon distribution it was not
possible to perform phylogenetic analysis to test an HGT hypothesis directly, because the taxon sampling included only
oomycetes and fungi. However, punctate taxon distribution of
a gene family can be used to suggest HGT because alternative
explanations involving ancient acquisition of a gene in the last
common ancestor, coupled to gene loss, are less parsimonious
(see ref. 6 for description of different HGT scenarios). On the
basis of these criteria, we have included the additional four gene
families among the putative fungi–oomycete HGTs (Table 2 and
Table S3).
Our analysis also identified an additional nine gene families
that demonstrated phylogenetic support for the oomycete gene
branching within the fungi to the exclusion of all other taxa,
but the approximately unbiased (AU) alternative topology tests
proved inconclusive, suggesting that the case for HGT is not definitive given available data (Table S3). In four of these cases
(Figs. S1.22–S1.24 and S1.30) our analyses demonstrated that the
gene family was present in a mosaic scattering of prokaryote,
fungi, and oomycete taxa, with the oomycetes branching within
the fungal clade but with weak bootstrap support. These data sets
implicate HGT (on the basis of taxonomic distribution of the gene
family with phylogenetic analyses suggesting fungi-to-oomycete
HGT), but alternative topology tests proved inconclusive. The
remaining five gene families also suggested fungi-to-oomycete
HGT, placing the oomycete gene within the fungi, separate from
other eukaryotic taxa, with moderate to strong bootstrap support
but with alternative topology tests again proving inconclusive
(Figs. S1.25–S1.29 and Table S3). We therefore find strong evidence for 21 gene transfers and tentative evidence for a further
13 transfers, suggesting an important and pervasive pattern of
HGT between these distantly related groups (Table S3).
Theoretically, the presence of conserved introns in both recipient and donor taxa would suggest that any HGT is the
Rise of fungal cell wall
Dependance on osmotrophy
Loss of phagotrophy
2
5
4
9
6
11
7
3
12
21
1
16
18
8
10
17
13
19
14
20
Loss of phagotrophy
Dependance on osmotrophy
Rise of plant pathogenesis
2 of 6 | www.pnas.org/cgi/doi/10.1073/pnas.1105100108
15
Saccharomycotina
Fungi
Pezizomycotina
Unikonts
other fungi
Metazoa
Amoebozoa
Archaeplastida
Alveolata
Blastocystis hominis
Diatoms
Ectocarpus siliculosus
Aureococcus anophagefferens
Hyphochytrium catenoides
Saprolegnia parasitica
Albugo laibachii
Phytophthora ramorum
Phytophthora sojae
Phytophthora infestans
Hyaloperonospora parastica
Fig. 1. Pattern of HGTs between fungi and oomycetes, demonstrating that the majority of the fungal-derived gene transfers are into/or retained by
the plant parasitic oomycetes. Using the results of
the phylogenetic analysis in combination with alternative topology tests, it was possible to estimate
the earliest point of transfer for each of the 21
strongly supported HGTs (Table S3). By comparing
the taxonomic distribution of the HGTs it was then
possible to identify the putative primary point of
acquisition. Incomplete phylogenetic resolution and
incomplete taxon sampling may cause these estimates to misplace the HGT events. We also note that
the figure is a based on a hypothetical cladogram
and does not identify the pattern of transfer relative
to either phylogenetic distance or time. Additional
genome sampling will enable improved resolution
of these transfers. The number labels on each
transfer event refer to phylogenetic data in Figs.
S1.1–S1.21. Major events in cell evolution are
marked to polarize HGTs in relation to evolutionary
history of these microbes.
Richards et al.
Table 2. Summary of support for each HGT and gene annotation in brief
HGT ID 1–34
GenBank accession
no./Joint Genome Institute
database protein ID
1 (Fig. S1.1)
EEY57756
2 (Fig. S1.2)
82760 (P. ramorum)
P, B, Ct
3 (Fig. S1.3)
4 (Fig. S1.4)
AAM48174.1
71178 (P. ramorum)
P, B, Ct
P, B, Ct, Td
5 (Fig. S1.5)
EEY56552
6 (Fig. S1.6)
72257 (P. ramorum)
7 (Fig. S1.7)
EEY52979
8 (Fig. S1.8)
9 (Fig. S1.9)
EEY63463
EEY64355
P, B, AU test
is borderline
P, B, Ct
P, B, Ct
10 (Fig. S1.10)
EEY59160
P, B, Ct
11 (Fig. S1.11)
12 (Fig. S1.12)
83543 (P. ramorum)
85044 (P. ramorum)
13 (Fig. S1.13)
P, B, Ct, Td
Conserved introns
between donors
and recipients
(Table S4)
1 shared intron
P, B, Ct
P, B, Ct, Td
P, B, Ct
P, B, Ct, Td
1 shared intron
EEY53137
P, B, Ct
1 shared intron
14 (Fig. S1.14)
133521 (P. sojae)
P, B, Ct
15 (Fig. S1.15)
142730 (P. sojae)
P, B, Ct
16 (Fig. S1.16)
EEY68514
P, B, Ct
17 (Fig. S1.17)
EEY55544
P, B, Ct, Td
18 (Fig. S1.18)
EEY59913
P, B, Ct, Td
19 (Fig. S1.19)
141189 (P. sojae)
20 (Fig. S1.20)
EEY58144
P, B, Ct, Td
21 (Fig. S1.21)
EEY64154
P, B, Ct, Td
22 (Fig. S1.22)
23 (Fig. S1.23)
24 (Fig. S1.24)
EEY62062
EEY67135
ABB22031
P, Td
P, Td
P, Td
25 (Fig. S1.25)
EEY67552
P, B
1 shared intron
26 (Fig. S1.26)
EEY65395
P, B
2 shared intron
27 (Fig. S1.27)
75147 (P. ramorum)
P, B
28 (Fig. S1.28)
EEY56384
P, B
Richards et al.
1 shared intron
2 shared introns
P, B, Ct
1 shared intron
Annotation of putative
function
MFS transporters similar
to saccharide monomer
transporters
Extracellular esterase/lipase
Aldose 1-epimerase
α-ketoglutarate dependent
xanthine dioxygenase (XanA)
Dehydrogenase/reductase
family protein
Extracellular quercetin 2,
3-dioxygenase
Extracellular α-L-rhamnosidase
(glycosyl hydrolase 78)
Lactonohydrolase/gluconolactonase
Extracellular glucooligosaccharide
oxidase
Extracellular unsaturated
rhamnogalacturonyl hydrolase
(glycosyl hydrolase 88)
Transcription factor
3-octaprenyl-4-hydroxybenzoate
carboxy-lyase/Phenylphosphate
carboxylase family
Phosphatidylinositol transfer
protein
Extracellular protein similar to
prokaryote lipases
Esterase/lipase protein
domain family
Xylitol dehydrogenase/sorbitol
dehydrogenase
Extracellular arabinan-endo-1,
5-α-L-arabinosidase
(glycosyl hydrolase 43)
Transporter for purines
and pyrimidines
Extracellular protein with
an esterase/lipase domain
Putative member of the NPP1
(necrosis and ethylene-inducing
peptide 1 proteins)
Conserved hypothetical protein
with similarity to a prokaryotic
antibiotic biosynthesis
monooxygenase
Pectate lyase
Extracellular intradiol dioxygenase
Extracellular endoglucanase
(glycosyl hydrolase 12)
Extracellular histidine
phosphatase domain protein
Extracellular endo-1,4-β-xylanase
(glycosyl hydrolase 10)
Member of Zinc metalloprotease
proteins which include
archaemetzincin
Extracellular arabinogalactan
endo-1,4-β-galactosidase (glycosyl
hydrolase 53)
Reported by
Richards et al. (19)
Yes (named AraJ)
Yes (named esterase/lipase
(ref. 19, Fig. S3B)
Yes (named GalM)
EVOLUTION
Support for HGT:
phylogeny (P),
bootstrap analysis
(B), topology
comparison tests
(Ct), and/or taxon
distribution (Td)
Yes (named CodB)
Yes (named PcaH)
PNAS Early Edition | 3 of 6
Table 2. Cont.
Support for HGT:
phylogeny (P),
bootstrap analysis
(B), topology
comparison tests
(Ct), and/or taxon
distribution (Td)
HGT ID 1–34
GenBank accession
no./Joint Genome Institute
database protein ID
29 (Fig. S1.29)
30 (Fig. S1.30)
77558 (P. ramorum)
EEY68947
P, B
P, Td
31
32
76863 (P. ramorum)
EEY55495
Td
Td
33
134308 (P. sojae)
Td
34
EEY58177
Td
Conserved introns
between donors
and recipients
(Table S4)
Annotation of putative
function
Reported by
Richards et al. (19)
Aliphatic nitrilase (CN hydrolase family)
Extracellular α-L-rhamnosidase
(glycosyl hydrolase 78)
LysM domain protein
Extracellular conserved
hypothetical protein
NmrA, a negative transcriptional
regulator
Conserved hypothetical protein
Sequences for P. ramorum and P. sojae are available from the Department of Energy, Joint Genome Institute website. Protein sequences can be obtained
using the protein ID and searching at http://genome.jgi-psf.org/pages/search-for-genes.jsf?organism=Phyra1_1 for P. ramorum and http://genome.jgi-psf.org/
pages/search-for-genes.jsf?organism=Physo1_1 for P. sojae.
product of a direct eukaryotic-to-eukaryotic transfer. To test for
evidence of such a pattern, we searched all 30 HGT gene families
supported by phylogenetic analysis (Figs. S1.1–S1.30) for evidence of a conserved intron present in the donor and recipient
taxa. We found eight such cases (Table 2 and Table S4), providing additional data to support the hypothesis that in these
cases the transfers are eukaryotic-to-eukaryotic HGT events.
Distribution of HGTs Relative to Evolution of Parasitic Traits in the
Oomycetes. To provide additional data for polarizing the ancestry
of these HGT events, we sequenced the genome of Hyphochytrium
catenoides using a combination of DNA and RNA (transcribed as
cDNA) sequencing using both the Roche 454 GS FLX titanium
and Illumina GAIIx paired-end methods (SI Materials and Methods). H. catenoides forms a sister branch to the oomycetes and, like
the oomycetes, was originally classified as a fungus because of its
fungal-like morphology and osmotrophic feeding habit (20, 28).
However, molecular phylogenetics have since demonstrated that
oomycetes and hyphochytriomycetes are sister groups and branch
separately from fungi within the stramenopile radiation (20, 28).
Analysis of this draft genome assembly revealed that all of the 34
oomycete/fungi HGTs are absent from the Hyphochytrium genome
(SI Materials and Methods). Of the 34 putative HGTs identified,
we noted that only 2 were present in the genome assembly of the
oomycete fish parasite Saprolegnia parasitica (Figs. S1.1 and S1.21),
one of which is an HGT from the oomycete lineage to the fungi
(Fig. 1). To further test this pattern we compared the 34 HGTs
with 13,807 proteins from the oomycete Albugo laibachii genome
available in GenBank (29). Albugo forms a deeper branch sister
to the Phytophthora/Hyaloperonospora clade and possesses a distinct repertoire of effector proteins compared with other
oomycete plant pathogens (29). Comparative analysis suggests
that only one of the HGTs was present in the Albugo assembly
(HGT 34; Table 2 and Table S3). However, all 34 HGTs were
present in one or more of the Phytophthora/Hyaloperonospora
plant parasitic oomycete species. The majority of the HGTs
therefore seem to have been acquired specifically within the
oomycete plant parasite clade, although this result will need
retesting as more oomycete genomes become available.
In 2006 Richards et al. (19) provided preliminary evidence of
a pattern of HGT between fungi and oomycetes. These data were
based on a BLAST survey of a single fungal genome and provided
strong evidence for four gene transfers from fungi to oomycetes,
with an additional four candidates for which the tree topologies
could not be resolved but could potentially indicate HGT. We
used these data to propose that HGT led to transfer of osmo4 of 6 | www.pnas.org/cgi/doi/10.1073/pnas.1105100108
trophic characteristics from fungi to oomycetes and was an important step in the evolution of the fungal-like biology of
oomycetes and possibly their sisters (e.g., hyphochytridiomycetes),
which together form the “Pseudofungi” (20). The data reported
here were based on a comprehensive gene-by-gene phylogeny
approach and confirmed five of these HGTs [including the four
strongly supported HGTs reported previously (19); Table 2 and
Table S5]. The remaining three HGTs, which were listed as tentative in the 2006 article, are not supported by this analysis (Table
S5). Using additional genome sampling including a de novo assembly of H. cateniodes, we were then able to test the hypothesis
that fungal-to-oomycete HGTs were important for the transition
from a phagotrophic algal form to an osmotrophic filamentous
form deep within the oomycete/hyphochytrium clade. Contrary to
our previous suggestion (19), the results of this study support an
alternative hypothesis, with the pattern of HGT seeming to have
occurred much later, with the majority of the HGTs specifically
retained by oomycete plant parasites, a pattern consistent with the
putative function of these proteins, discussed below (Fig. 2, Table
2, and Table S5). Furthermore, the pattern demonstrates that the
HGTs occurred after the last common ancestor of the oomycetes
and the hyphochytriomycetes had lost the capacity for phagotrophy and had instead evolved an osmotrophic/filamentous lifestyle (Fig. 1), demonstrating that the absence of phagotrophy, at
least for the oomycetes, is not a barrier to HGT.
The pattern of fungal-derived HGTs implicates the gene
acquisitions as being important in the evolution of plant parasitism. To test this idea, we examined the HGTs in detail. First,
we found that of the 34 HGTs, 21 demonstrated evidence of
gene duplication after transfer. In some cases the number of
gene duplication events was extensive, such that the 33 fungito-oomycete HGTs contributed a total of 329 predicted genes,
including 143 genes to P. ramorum, 117 to P. sojae, 48 to
P. infestans, and 21 to H. parasitica (Table 1).
Putative Function of HGTs in the Oomycetes. We set out to determine the proportion of the HGT candidates that were predicted to encode secreted proteins (SI Materials and Methods).
Both fungi and oomycetes secrete large numbers of proteins,
including plant cell wall-degrading enzymes, attachment factors,
and effector proteins to subvert host defenses. We used a combination of SignalP and WolfPSORT to identify HGT-derived
genes that putatively encoded proteins with N-terminal secretion
signals (Table S5). This analysis showed that between 62% and
76% of all the HGT-derived genes in each of the four oomycete
genomes investigated possess putative N-terminal secretion sigRichards et al.
tively degrade plant-specific structural components, including
lignin, hemicellulose, pectin, and suberin. These structural
compounds include key components of plant cell walls (e.g.,
hemicellulose and pectin) and the waxy epidermis (cutin), which
together constitute the first barrier to plant infection (Fig. 2).
Consequently, any acquisition of enzymes used to break down
these structures would be advantageous to a plant parasite.
Additional HGTs include several gene products predicted to
be involved in nutrient acquisition including a nucleotide transporter, which putatively functions in purine and/or pyrimidine
uptake (Table S5). Potentially coupled to this adaptation, the
fungal-derived HGTs include a putative xanthine dioxygenase
involved in hydroxylation of the purine xanthine to uric acid (30,
31) (Fig. 2). A putative monosaccharide transporter gene was
identified that would enable the cell to traffic sugar monomers
(Fig. 2), whereas two additional fungal-derived HGT acquisitions
were also identified that putatively function to process monosaccharides within the cell (Fig. 2). A nitrilase is present among
the putative HGTs, predicted to break down toxic nitriles to
carboxylic acids and ammonia. Such enzymes in plant parasites
have been shown to break down the plant defense compound
hydrogen cyanide into formamide (32). The list of fungal-derived
EVOLUTION
nals (Table 1). This is particularly striking in P. ramorum and P.
sojae, where 71% and 76% of the HGT-derived genes putatively
possess N-terminal signal peptides, respectively. The fungal-derived HGTs therefore account for between 2.7% (P. infestans)
and 7.6% (P. ramorum) of the total predicted secretome of these
plant parasites (Table 1).
To investigate the putative function of all 34 HGT gene
families, we used a combination of BLAST and PFAM HMM
homology searches to annotate these genes (Table 2, SI Materials
and Methods, and Table S5). Strikingly, 13 of the 32 HGT gene
families that could be annotated are predicted to function in the
breakdown, transport, or remodeling of sugars (Fig. 2, Table 2,
and Table S5). Indeed, a total of nine fungal-derived HGT gene
families were predicted to encode extracellular polysaccharide
depolymerizing enzymes and therefore putatively to break down
rutin, hemicellulose, or pectin polysaccharides (Fig. 2, Table 2,
and Table S5) sugars, which are unique to plants. The predicted
fungi-to-oomycete HGTs also includes four esterase/lipaseencoding genes, three of which are predicted to be secreted, and
a further three enzymes that are putatively involved in the degradation of complex aromatic polymers (Fig. 2, Table 2, and
Table S5). The HGTs include examples of proteins that puta-
Pyrimidines
Phytic acid
Defense
response
Purines
Plant
cytosol
Quercetin
Carotenoids
Rutin
Suberin
Plasma membrane
Plant primary cell wall
25
Middle lamella
Cuticle
Cellulose
Hemi-cellulose
Pectin
Isothiocyanates
+ nitriles
(hydrogen cyanide)
Lignin
Cutin
24
30
30
28
26
17
7
22
Quercetin
Rhamnose
10
7
Sorbitol
6
2
9
14
Infiltration into plant
tissue results in transcript
accumulation of
pathogenesis-related
genes, production of
ROS and ethylene,
callose apposition, and
HR-like cell death
Complex
aromatic
compounds
19
Lipid
23
20
31
LysM domain proteins
implicated in prevention
of chitin-triggered
plant immunity and
progression of disease
symptoms
Xylose
9
Arabinose
Galacturonic
acid
18
Cell wall
1
Plasma membrane
29
8
Galactose
?
Effectors
Xanthine
Pyridoxine?
Lipid
pool
Fructose
3
15
13
Polyols
Glucose
3
4
TCA
cycle
Vitamins
Nitrogen
pool
16
Oomycete
parasite
cytosol
12
33
Nucleotide
pool
Glycolysis
11
Ubiquinone
biosynthesis
Fig. 2. Schematic diagram demonstrating the oomycete functional proteome derived from fungi by HGT and its putative function regarding host attack. The
majority of functions are related to attacking and/or feeding on plant cell tissue. HGTs were represented on the figure when it was possible to identify
a putative function (these are illustrated in numbered gray oblongs, with the numbers referring to the 34 HGTs identified; Table 2 and Table S5), with strongly
supported HGTs confirmed by alternative topology tests) enclosed within a black line (Figs. S1.1–S1.21). Oblongs with additional red borders represent genes
shown to be up-regulated in P. infestans microarray data (22) after 5 d infection of plant tissue (Table S5).
Richards et al.
PNAS Early Edition | 5 of 6
HGTs also encompasses a putative histidine phosphatase domain protein, which putatively functions in breakdown of phytic
acid and other organophosphate substrates (33). Phytic acid is
the primary storage form of phosphate and inositol in plants
(34). Consequently, this acquisition might provide an adaptation
for uptake of phosphates from plant tissue.
Finally, the list of HGTs includes two proteins that in fungi
have been directly implicated in plant parasitism. The LysM
domain-containing gene family acquired by HGT from fungi has,
for instance, been shown in fungal plant parasites to be linked
with suppression of plant defenses. In Cladosporium fulvum, the
causal agent of leaf mold of tomato, implicated in suppression of
chitin-triggered plant immunity (35). Second, there is an example
of a necrosis-inducing protein or (Nep1)-like protein (NLP) that
is a candidate fungi-to-oomycete HGT (36). Infiltration of NPP1
protein into leaves of Arabidopsis thaliana results in transcript
accumulation of plant defense-related genes, production of reactive oxygen species and ethylene, callose apposition, and localized cell death (36).
Conclusion
When considered together, our analysis demonstrates a pattern of
at least 21 HGTs, and probably more than 34, between fungi and
oomycetes, with the vast majority of predicted HGTs (33 in total)
transferring gene functions from fungi to oomycetes. This equates
to a small proportion of the total genome for which phylogenetic
analysis was possible (0.5–1% of the genome analyzed; Table 1), but
in many cases these gene transfers have subsequently undergone
numerous gene duplications. A large fraction of the HGT-derived
proteins are predicted to be secreted (Table 1), strongly suggesting
that HGT from fungi has played a significant role in the evolution of
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6 of 6 | www.pnas.org/cgi/doi/10.1073/pnas.1105100108
the oomycete secretome. The observed pattern of transfer may
have facilitated, or aided, the spread of oomycetes to plant hosts
and their evolution into successful plant parasites. Comparative
genomics demonstrates that these transfers do not seem to date
back to the initial transition to an osmotrophic lifestyle (19) because
they are, in the majority, absent in the animal parasitic oomycete
Saprolegnia and the free-living filamentous osmotrophic Hyphochytrium. This suggests that osmotrophy, and the capacity to grow as
strand-like hyphal cells, probably arose before diversification of
these lineages and before the acquisition of fungal genes by HGT.
Interestingly, fungal-derived HGTs may, however, represent specific acquisitions to life as a plant parasite. Our conclusion is consistent with the predicted functions of the HGT candidates aiding
entry to plant cells, allowing efficient nutrient acquisition and
leading to microbial proliferation in plant tissue.
Materials and Methods
Detailed descriptions of whole-genome gene-by-gene phylogenetic analysis,
alternative topology tests, H. catenoides DNA and RNA preparation and
sequencing, gene annotation, and identification of secreted proteins are
provided in SI Materials and Methods. All potential HGTs found in a single
oomycete genome were treated as possible cases of contamination. To test
these, we conducted phylogeny of linked genes on DNA contigs. In all cases,
we could confirm that the HGT was present within the oomycete genome
(Table S6). An example of each HGT oomycete gene family is included as
a combined FASTA file in Dataset S1.
ACKNOWLEDGMENTS. T.A.R. received fellowship support from the Leverhulme Trust and funding from the Natural Environment Research Council
(NERC) and the Biotechnology and Biological Sciences Research Council
(BBSRC). M.D.M.J. is supported by NERC Grant NE/F011709/1. G.L. is supported by BBSRC Grant BB/G00885X/1.
19. Richards TA, Dacks JB, Jenkinson JM, Thornton CR, Talbot NJ (2006) Evolution of filamentous plant pathogens: Gene exchange across eukaryotic kingdoms. Curr Biol 16:
1857e1864.
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the white rust pathogen of Arabidopsis thaliana. PLoS Biol 9:e1001094.
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fungal kingdom: Molybdenum cofactor-independent hydroxylation of xanthine via
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35. de Jonge R, et al. (2010) Conserved fungal LysM effector Ecp6 prevents chitin-triggered immunity in plants. Science 329:953e955.
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Richards et al.
Supporting Information
Richards et al. 10.1073/pnas.1105100108
SI Materials and Methods
Gene-by-Gene Phylogenetic Analysis of Four Oomycete Genomes to
Identify Cases of Horizontal Gene Transfer (HGT). The predicted
proteome of four oomycetes genomes, Phytophthora ramorum,
Phytophthora sojae, Phytophthora infestans, and Hyaloperonospora
parasitica (also named Hyaloperonospora arabidopsidis) (1–3),
were used for gene-by-gene phylogenetic analysis using a bioinformatic protocol described previously (4). The protocol followed a multistep process. Each oomycete genome was treated
separately. First, for each genome we identified and removed all
candidate transposable elements by comparison with Repbase
(5), a database of eukaryotic repetitive elements using tBLASTn
with e-value cutoff 10−20. Second, we selected the remaining
protein sequences and clustered them into genes of closely related groups across the genome of origin (i.e., identifying recent
gene duplications) using OrthoMCL (6) with an e-value cutoff
10−20 and an inflation value 1.5. Next, we identified and removed
all oomycete cluster groups that were only found in oomycete
genomes by performing BLASTp (7) searches of a representative
sequence from each cluster group against the genomes in our
local database (Table S1); proteins that had no hits other than
oomycetes were removed. This left 11,434 cluster groups ready
for phylogenetic analysis identifying 3,014, 3,018, 3,233, and
2,169 cluster groups from P. ramorum, P.sojae, P. infestans, and
H. parasitica, respectively. Because the 11,434 gene sets were
identified using a parallel process for all four genomes, this
generated some four-way redundancy within the 11,434 gene
sets. We did not attempt to remove this redundancy and instead
analyzed all 11,434 gene sets. We took this approach to use
multiple starting seeds for each gene dataset (where possible)
and to control for human error in the manual tree selection
stages (described below).
We next generated a fast-ML phylogeny (8) for all 11,434
cluster groups using a bespoke gene-by-gene phylogeny pipeline
(4). Briefly, this process consists of a series of PERL scripts,
which automatically constructed phylogenetic trees for each sequence cluster group identified. The phylogenies were calculated
from taxon sampling using a custom-built MySQL database
(www.mysql.com) containing the complete genome project-derived, predicted proteome sequence from 795 species, representing a wide diversity of eukaryotes and prokaryote taxa (Table
S1). Each candidate sequence was compared against sequences
in the database using BLASTp (7) and the best-similarity hits
from each species extracted (using the e-value 10−20 gathering
threshold). These sequences were aligned using Muscle (9),
conserved regions from this alignment were sampled using
GBlocks (10), and phylogenetic trees constructed using PhyML
(8) with a WAG (11) + Γ + I substitution model (Γ + I parameters estimated by PhyML).
This process generated many phylogenies that were unresolved,
either because taxon/sequence sampling was too narrow or because highly divergent sequences and paralogues were sampled,
limiting resolution of the tree topology. In cases in which highly
divergent sequences or too many paralogues limited tree resolution, we adjusted the sampling threshold using 10−30 and 10−40
to exclude divergent branches or to minimize paralogue sampling. In cases in which the taxon/sequence sampling was too
narrow, we increased the threshold to 10−10 and 10−5 to sample
additional members of the gene family. We then repeated the
phylogenetic analyses pipeline for these data sets.
All 11,434 phylogenies were manually inspected for tree topologies that suggested fungi–oomycete gene transfer in either
Richards et al. www.pnas.org/cgi/content/short/1105100108
direction. An HGT topology is defined as an oomycete sequence
branching within a clade of fungal sequences, or vice versa.
Phylogenetic Analysis of Putative HGT Gene Families. Candidate
HGT phylogenies totalling 51 separate cluster groups were recovered demonstrating either oomycetes branching within the
fungi or vice versa. For each candidate HGT we checked, the
genome sampling encompassed all available data by comparison
with the GenBank nr database, GenBank EST database, and the
Taxonomically Broad EST database (12). Specific attention was
made to check for additional sequence data from the Ectocarpus
and Blastocystis sequence data available in GenBank, the genome project of the Diatom Fragilariopsis cylindrus available at
the Department of Energy genome portal, the genome of the
oomycete fish parasite Saprolegnia parasitica available at the
Broad Institute’s genome portal, and the de novo-generated
genome sequence of the sister group to the oomycetes, the freeliving osmotrophic protist Hyphochytrium catenoides (description
of sequencing protocol is outlined below). Additional sequences
were added to the alignments as required. This process was facilitated using the sequence management for phylogeny programs Refgen and Treenamer (13). In many cases there were
several representatives of the gene family in a single fungal or
oomycete genome, with some of these genes often having large
sections of the amino acid sequence missing relative to the gene
family alignment. This is most likely the product of incomplete
assembly and poor gene prediction, specifically intron/exon
boundaries during automatic annotation of the genomes—
meaning that some predicted protein sequences from the genomes are incomplete. Where the presence of these putatively
incomplete sequences did not significantly alter the taxonomic
representation of the gene, incomplete sequences were excluded
from the alignment. Where the taxon sampling was vital for the
phylogenetic analysis, the genome sequence data were manually
edited and the ORF repredicted.
Each alignment was manually edited and masked to remove gaps
and ambiguous alignment positions using the alignment program
Seaview (14). All gene alignments are available at http://cogeme.
ex.ac.uk/hgt/Oomycete_fungi_HGT_alignment_files.zip.
For each candidate HGT alignment, we identified the optimal
model for phylogenetic analysis using Modelgenerator (15).
RAxML v 7.2.6 (16) analysis was then used to assess topology
and bootstrap support via our easyRAx script (http://projects.
exeter.ac.uk/ceem/easyRAx.html). RAxML- and Modelgenerator-predicted models were generally the same, but where they
were not, Modelgenerator analyses were used (Table S2). The
best-scoring RAxML tree was determined with the PROTMIX
method, starting with 10 randomized maximum parsimony trees.
Statistical support was evaluated with 100 bootstrap replicates.
The manual alignment checks combined with the second round
of phylogenetic analysis demonstrated that 10 of the alignments
did not provide strong evidence for HGT, either because the
amended taxon sampling demonstrated an alternative tree topology that did not support the HGT hypothesis or because the
bootstrap support and tree resolution was too weak to infer HGT.
Four of the HGT gene families were found only in fungi and
oomycetes, and therefore HGT is inferred on the basis of taxon
sampling only. This process left 37 datasets with phylogenetic
support for HGT ready for alternative topology comparison tests
(see below).
1 of 5
Testing Phylogenetic Support for Each HGT Using Alternative Tree
Topology Tests. For the 37 gene families with phylogenetic trees
suggesting HGT we identified and labeled the major fungal and
oomycetes taxonomic groups relative to the HGT with a taxon
code [i.e., Pezizomycotina labeled 1, Saccharomycotina 2,
Taphrinomycotina 3, Basidiomycota 4, “other fungi (including
paralogs with or without resolution)” 5, and Oomycetes 6] (Figs.
S1.1–S1.30). We then systematically calculated phylogenetic
trees with constrained monophyly of these groups and collective
groupings (i.e., 1, 2, 3, 4, 1–2, 1–3, 1–4, 1–5, and 6). This process
identified 88 constraint groups for the 37 alignments. Searches
for the maximum likelihood (ML) trees, constrained or unconstrained, were performed using RAxML v 7.2.6. It was found
that a bootstrap analysis gave better trees in most cases, and so
100 boostraps were used. Searches were carried out using the
PROT-CAT-WAG-F model, as a two-step process (default in
RAxML 7.2.6.). All of the trees, unconstrained and constrained,
from a given alignment were grouped into a single file and the
site log likelihoods calculated using RAxML. The output from
this analysis was used as input to Consel version 0.1k (17) and
the trees from each alignment compared using the approximately
unbiased (AU) test (18).
The process identified 21 gene families for which the phylogenetic data suggest horizontal gene transfer between fungi and
the oomycetes (Table S3; 20 from fungi to oomycetes and 1 from
oomycetes to fungi) and where topology comparison test could
reject the monophyly of the donor group [AU test: 1 phylogeny
at <0.1 (borderline), 5 at <0.05, 3 at <0.01, 12 at <0.001; Table
S3], demonstrating a complex pattern of transfer between these
distantly related eukaryotic microbes.
In a further nine cases the AU test could not reject monophyly
of the fungi. However, these putative HGTs are included here
because in each case the HGT hypothesis was supported by
moderate to strong bootstrap support, and/or the taxon sampling
of the gene family was restricted to fungi, oomycetes, and a few
prokaryote groups, suggesting HGT on of the basis of taxon
distribution. The evidence for HGT is noted on a case-by-case
basis in Table S3.
Analysis to Determine Whether Any Putative HGT Candidates Are the
Product of DNA Contamination. Four of the identified HGTs were
only present in a single oomycete genome. It is therefore possible
that these genes may be annotated as oomycete genes but may
be the product of DNA contamination, potentially from fungi,
during a genome-sequencing project. To investigate the four
single species HGTs, we identified genes adjacent to the putative
HGT on genome contigs and generated phylogenies using the
pipeline described above. In all four cases we could provide
evidence that the gene of putative HGT ancestry was surrounded
by oomycete genes of vertical inheritance, suggesting that the
HGT derived gene was located on the genome of the oomycete
and physically linked to native oomycete genes (Table S6).
Genome Sequencing of Hyphochytrium. An H. catenoides isolate
(ATCC 18719) was inoculated onto Emerson YpSs agar (4 g
yeast extract, 15 g soluble starch, 1 g dipotassium phosphate, 0.5
g magnesium sulfate, and 20 g agar dissolved in 1 L deionized
water; medium was boiled for 1 min with agitation to dissolve the
powder and sterilized by autoclaving at 121 °C for 15 min) and
incubated at 25 °C for 2 wk. Colonies were removed, transferred
to YpSs medium (made to the YpSs agar recipe but with the agar
omitted) and incubated at 25 °C, with agitation, for 3 wk. Biomass was harvested by filtration through micracloth. It was then
washed with ultrapure water, frozen in liquid nitrogen, and
ground to a powder using a pestle and mortar previously sterilized with 0.1 M NaOH to render them DNA and RNase free.
The resulting powder was split into two aliquots, half for DNA
and half for RNA extraction. RNA was extracted using a LiCl
Richards et al. www.pnas.org/cgi/content/short/1105100108
RNA extraction protocol. Ground mycelium was added to equal
volumes of extraction buffer [0.1 M LiCl, 0.1 M Tris (pH 8) with
HCl, 10 mM EDTA, and 1% SDS, made up to volume with
ddH2O] and phenol and mixed by inverting for 1 min. To this,
0.5 volumes of CIA (24:1 chloroform/iso-amyl alcohol) was
added and mixed by inversion for 30 s. The sample was centrifuged at 4 °C, 9,500 × g for 30 min and the upper phase transferred to a sterile tube. To this, 1 volume of 4 M LiCl was added
and the tube left on ice overnight. Centrifugation was then
carried out at 4 °C, 9,500 × g for 20 min, the supernatant removed, and the pellet washed in 70% ethanol and resuspended
in Diethylpyrocarbonate water. An equal volume of phenol: CIA
was added and the tube vortexed and centrifuged at 4 °C, 16,000 × g
for 10 min. The aqueous phase was carefully recovered and 2
volumes of 100% ethanol and 0.1 volumes of 3M sodium acetate
added. The RNA was left to precipitate overnight at −20 °C.
RNA was recovered by centrifugation at 4 °C, 10,000 × g for 20
min, the supernatant removed, and the pellet washed with 70%
ethanol. Finally, RNA was resupended in 300 μL ultrapure water. Total RNA was quantified and the purity checked using an
ND-1000 spectrophotometer (Thermo Fisher Scientific).
DNA was extracted using the Cambio UltraCleansoil DNA kit
according to the manufacturer’s alternative protocol for maximum
yields and quantified in an ND-1000 spectrophotometer. DNA
was checked for both eukaryotic and prokaryotic contamination
using SSU rDNA PCR in an MJ mini personal thermal cycler.
Each 50-μL reaction contained 2 μL of each primer (10 pMμL−1),
25 μL of Master Mix (Promega, containing 3 mM MgCl2, 400 μM
of each dNTP, and 50 U/mL of Taq DNA polymerase), 19 μL
of PCR water, and 2 μL of a 1/1,000 dilution of template DNA.
For universal eukaryotic SSU rRNA amplification primers 1F
(59CTGGTTGATCCTGCCAG-39) and 1520R (59-CTGCAGGTTCACCTA-39) and the following cycling conditions were used:
initial denatration at 95 °C for 5 min, followed by 30 identical
cycles of denaturation at 95 °C for 1 min, annealing at 57 °C for
1 min, and extension at 72 °C for 1.5 min, with a final extension at
72 °C for 10 min (19). For universal prokaryotic SSU rRNA amplification primers PA (59-AGAGTTTGATCCTGGCTCAG-39)
and PH (59-AAGGAGGTCATCCAGCCGCA-39) (20) and the
following cycling conditions were used, with Escherichia coli DNA
acting as a positive control: initial denaturation of 94 °C for 5 min,
followed by 30 cycles of denaturation at 94 °C for 1 min, annealing
at 55 °C for 1 min, and extension at 72 °C for 2 min, with a final
extension step of 72 °C for 10 min. Successful amplification was
checked by agarose gel electrophoresis on a 0.8% agarose gel, run
at 110 V for 45 min. The prokaryotic PCR was negative, whereas
the eukaryotic SSU PCR resulted in a clean band of appropriate
size. The 1F-1520R PCR product was purified using the Wizard
SV gel and PCR clean-up system (Promega) and sequenced externally on both strands by Cogenics (Essex). Chromatograms
were checked by eye for inconsistencies, which could be the result
of a multitemplate amplification before the derived sequence was
used as the seed in a BLASTn search on the National Center for
Biotechnology Information BLAST server, suggesting that the
DNA was derived from a pure culture of the target microbe.
We sequenced the Hyphochytrium genome using two approaches: (i) 454 FLX Titanium (Roche) and (ii) Illumina GA2
paired-end 76-bp sequencing. The DNA was prepared for both
sequencing platforms using the standard protocols. Five micrograms of DNA was fragmented by nebulization. Fragmented
DNA was analyzed using a Bioanalyzer (Agilent Technologies) to
ensure that the majority of the fragments were between 350 and
1,000 bp. The purified fragmented DNA was processed according
to the 454 FLX Titanium Library construction kit and protocol
(Roche Applied Science) to ligate adaptors specific to the Titanium sequencing chemistry. The resulting single-stranded DNA
library was assessed for size distribution using a Bioanalyzer
(Agilent Technologies). Library fragments were added to emul2 of 5
sion PCR beads at a ratio of 1:1 to emPCR at the optimal ratio of
1.5 DNA copy per beads and amplified according to the manufacturer’s instructions (Roche Applied Science), and a full picotitre plate was sequenced. This generated 1,219,849 sequence
reads resulting in 416,601,381 bp of sequence.
For Illumina GA2 sequencing we used a Bioruptor shearing
device to obtain 500-bp fragments (this figure is inclusive of the
adaptor sequences). V2 Cluster generation kits were used along
with v4 SBS sequencing kits. Two lanes of Illumina GA2 pairedend 76-bp sequencing was performed, yielding a total of
63,082,628 reads. Reads with adaptor present were removed.
Additionally, any reads without Q > 20 across >90% of bases
were removed. After this filtering process, 45,453,312 reads were
left in total.
The Hyphochytrium genome sequence was assembled using the
Velvet assembler (0.7.63) (reference http://genome.cshlp.org/
content/18/5/821) and resulted in 311,983 contigs spanning
85,813,724 bp at a mean coverage of 22×. Kmer size of 41 was
used along with expected kmer coverage of 8 and coverage cutoff
of 3 as determined by the Velvet Optimizer 2.1.7 script bundled
with Velvet. At this sampling level the Lander-Waterman model
(21) predicts the chance of a given base being absent from the
sequence reads as less than 1 in 1 billion. However, this is in the
ideal case of even coverage, which is never achieved in practice.
In addition, the N50 contig length of the assembly was 611 bp. It
was therefore possibile that genes would be missed in homology
searches owing to the short contig sizes.
To check genome coverage further we sequenced Hyphochytrium cDNA using 454 FLX Titanium (Roche) chemistry. The
resulting sequence reads were assembled using the Newbler assembler (Roche) on default settings and yielded 31,368 contigs.
These contigs were compared with the Hyphochytrium assembly
using BLASTn. In this simple analysis more than 99% of all
cDNAs matched the assembly with >99% identity and e-value
<1xe-10. The remaining contigs were either rich in simple sequence repeats or were very short (<100 bp) or of relatively low
raw sequence quality. This strongly indicates that there are very
few genic sequences missing from the draft assembly. We then
used the CEGMA (22) (Core Eukaryotic Genes Mapping Approach) core conserved gene dataset to investigte recovery of
core eukaryotic genes from the draft Hyphochytrium assembly.
Using CEGMA 248 and the 458 genes only 17 and 28 genes,
respectively, appear absent from the Hyphochytrium assembly
using an e-value cutoff of 1e-04 and a sequence identity
threshold of 90%. A more stringent cutoff of 1e-10 yielded 51
and 88 missing genes, respectively. The CEGMA core dataset is
based on comparison of a range of different eukaryotic organisms (e.g., animals, plants, alveolates) but does not include any
close relatives of Hyphochytrium. Nevertheless, depending upon
the stringency used the gene recovery rate for the CEGMA
dataset was between 80% and 94%.
Hyphochytrium genome sequence data have been submitted to
Sequence Read Archive for the raw data (SRP004821), and the
assembled genome has been archived at the European Bioinformatics Institute (Genome Project: 61035).
We then searched the assembly for candidate homologs of
the 34 oomycete HGTs in the Hyphochytrium genome using a
tBLASTn approach. Of the 34 oomycete HGTs, in seven cases
candidate homolog sequences were identified in Hyphochytrium.
In five cases the multiple alignment analyses demonstrated that
the Hyphochytrium sequences were distant relatives, or too divergent to be true homologs, and were therefore not relevant to
the putative HGT and excluded from further analysis. In the
remaining two cases we added the Hyphochytrium genes to the
alignments and recalculated the phylogenetic analysis. In both
cases the Hyphochytrium genes were distantly related paralogues
to the oomycetes HGTs branching separately from the fungal/
Richards et al. www.pnas.org/cgi/content/short/1105100108
oomycetes HGT branches (Figs. S1.5 and S1.16), demonstrating
that the Hyphochytrium genes have a different evolutionary
derivation and that all 34 fungal-derived HGTs are absent from
Hyphochytrium genome assembly.
Putative Functional Annotations of the HGT Gene Families and
Comparison with Phytophthora Metabolic Network Analysis. To an-
notate putative functions for all 34 HGT gene families, a representative of each HGT gene was used for BLAST (7) and PFAM
HMM homology searches (23). This process was used to assign
a putative function to each HGT gene family. Each putative
annotation was checked to exclude false annotations present in
GenBank. To investigate putative cellular locations of each
HGT-encoded protein, the complete HGT gene families, including all duplicate forms from all four oomycete genomes,
were recovered and subject to WoLFPSORT (24), SignalP (25),
and TMHMM (26) analysis for evidence of N-terminal secretion
motifs and/or transmembrane domains. The results of these
annotations are listed in Table S5. Evidence for an N-terminal
secretion motif is only listed in Table S5 when both WoLFPSORT (24) and SignalP (25) methods suggest that the protein
character is present.
To investigate where the oomycete HGT proteins putatively
function within the metabolic network of the Phytophthora species, we sought to reconstruct the oomycete metabolic network.
Complete proteome sequence files of P. ramorum, P. sojae, and
P. infestans (proteins. fasta files) were recovered from the Broad
Institute Phytophthora database. We used Kaas (Kegg automated
annotation server) to project the downloaded proteome sequences onto Kegg’s collection of metabolic pathways (27), using
BDH (bidirectional hit) orthology search (similarity index
threshold: 60) to explore the Kaas reference genome set (enriched with available fungi and protozoa genomes). Initially this
analysis was performed to check and correct the annotations for
the 34 HGT gene families (discussed above). Then we used this
process to investigate where the HGT candidates fitted into the
oomycete metabolic network map. This network analysis often
demonstrated partial or missing pathways. In these cases we
exploited a minimal threshold (28) in a combination with an
SDH (single-direction hit) method to recheck specific components of pathways putatively connected to the HGT functions.
The BDH and SDH methods were completed for all three
Phytophthora predicted proteomes. We also used BLASTn and
tBLASTn additionally to query the Broad Institute Phytophthora
databases for the missing functions by known protein and gene
sequences to reconfirm incomplete pathways. Finally, we used
the SEED database (29) “Compare regions” tool to investigate
synteny of each HGT gene family across distantly related taxa to
help define evidence of potential functional linkage of putative
homologs of the HGT genes.
Using microarray data for the P. infestans transcriptome, we
identified evidence of altered transcript abundance both before
and after infection. To do this we used publicly available data sets
(2) recording the expression of genes in P. infestans over a 5-d time
course of a potato infection to identify genes previously classified
as “genes induced or repressed during infection.” These candidate genes were identified by comparing expression intensities
derived from samples of infected potato tissue to baseline expression intensities provided by samples derived from mycelium
growing in axenic culture (Pea, V8, or RS agar). The data were
published as part of the P. infestans genome project (2). Normalized transcript abundance values between the two samples
were compared using the Student t test. Of the 18 HGT gene
families present in the P. infestans genome, 6 HGT gene families
showed evidence of up-regulation in planta [2 gene families at
<0.1 (borderline), 2 at <0.05, and 2 at <0.01; Table S5].
3 of 5
1. Tyler BM, et al. (2006) Phytophthora genome sequences uncover evolutionary origins
and mechanisms of pathogenesis. Science 313:1261e1266.
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3. Baxter L, et al. (2010) Signatures of adaptation to obligate biotrophy in the
Hyaloperonospora arabidopsidis genome. Science 330:1549e1551.
4. Richards TA, et al. (2009) Phylogenomic analysis demonstrates a pattern of rare and
ancient horizontal gene transfer between plants and fungi. Plant Cell 21:1897e1911.
5. Jurka J, et al. (2005) Repbase Update, a database of eukaryotic repetitive elements.
Cytogenet Genome Res 110:462e467.
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use in phylogenetic analysis. Mol Biol Evol 17:540e552.
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from multiple protein families using a maximum-likelihood approach. Mol Biol Evol
18:691e699.
12. O’Brien EA, et al. (2007) TBestDB: A taxonomically broad database of expressed
sequence tags (ESTs). Nucleic Acids Res 35(Database issue):D445eD451.
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analyses with thousands of taxa and mixed models. Bioinformatics 22:2688e2690.
17. Shimodaira H, Hasegawa M (2001) CONSEL: For assessing the confidence of
phylogenetic tree selection. Bioinformatics 17:1246e1247.
18. Shimodaira H (2002) An approximately unbiased test of phylogenetic tree selection.
Syst Biol 51:492e508.
19. Lefèvre E, et al. (2007) Unveiling fungal zooflagellates as members of freshwater
picoeukaryotes: evidence from a molecular diversity study in a deep meromictic lake.
Environ Microbiol 9:61e71.
20. Edwards U, Rogall T, Blöcker H, Emde M, Böttger EC (1989) Isolation and direct
complete nucleotide determination of entire genes. Characterization of a gene
coding for 16S ribosomal RNA. Nucleic Acids Res 17:7843e7853.
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a mathematical analysis. Genomics 2:231e239.
22. Parra G, Bradnam K, Korf I (2007) CEGMA: A pipeline to accurately annotate core
genes in eukaryotic genomes. Bioinformatics 23:1061e1067.
23. Marchler-Bauer A, et al. (2005) CDD: A Conserved Domain Database for protein
classification. Nucleic Acids Res 33(Database issue):D192eD196.
24. Horton P, et al. (2007) WoLF PSORT: Protein localization predictor. Nucleic Acids Res
35(Web Server issue):W585eW587.
25. Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal
peptides: SignalP 3.0. J Mol Biol 340:783e795.
26. Sonnhammer EL, von Heijne G, Krogh A (1998) A hidden Markov model for predicting
transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol 6:
175e182.
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genome annotation and pathway reconstruction server. Nucleic Acids Res 35(Web
Server issue):W182eW185.
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(Database issue):D138eD141.
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in the project to annotate 1000 genomes. Nucleic Acids Res 33:5691e5702.
Figs. S1.1–S1.30. Phylogenetic evidence for fungi–oomycete HGTs. Phylogenies are calculated as described in SI Materials and Methods. Each figure contains
a key describing the figure notations. Note that Figs. S1.5 and S1.16 are the datasets with representation from Hyphochytrium
Figs. S1.1–S1.30
Table S1.
List of genomes included in the phylogenetic pipeline database used in this study
Table S1
Table S2. Model parameters used for phylogenetic analysis estimated by Modelgenerator (RaxML has a preset α parameter for the Γ
distribution, so no α value is given, etc.)
Table S2
Table S3.
Phylogeny topology comparison tests to confirm branching position of HGT within donor group
Table S3
HGT in red demonstrate transfer in opposite direction. Transfers in gray are not supported by alternative topology comparison test, or alternatively the HGT
hypothesis is based on taxon distribution data only, suggesting a weaker standard of support for the HGT. Sequences for P. ramorum and P. sojae are available
from the Department of Energy, Joint Genome Institute website. Protein sequences can be obtained using the protein ID and searching at http://genome.jgi-psf.
org/pages/search-for-genes.jsf?organism=Phyra1_1 for P. ramorum and http://genome.jgi-psf.org/pages/search-for-genes.jsf?organism=Physo1_1 for P. sojae.
Richards et al. www.pnas.org/cgi/content/short/1105100108
4 of 5
Table S4.
Evidence of conserved introns across donor and recipient groups in eight HGT gene families
Table S4
Of the 30 HGTs supported by phylogenetic data, we searched for conserved introns in the HGT gene families of the recipient taxa. We found 15 cases in
which the transferred gene family had one or more conserved intron. Of these 15 HGT families, 8 conserved introns were also present in the donor groups,
suggesting that the pattern of HGT is from eukaryote-to-eukaryote and not as a eukaryotic-to-prokaryotic-to-eukaryotic transfer.
Table S5.
Annotation of putative HGT candidates from fungi to oomycetes
Table S5
The HGT shaded in red demonstrates a putative transfer in opposite direction (oomycete to fungi). Transfers in gray are not supported by AU alternative
topology comparison test (1), or alternatively the HGT hypothesis is based on taxon distribution data only, suggesting a weaker standard of support for the
HGT. Evidence for secretion was identified using both the SignalP and WolfP-Sort methods, as described in SI Materials and Methods. Presence of a putative Nterminal secretion motif is only suggested when both methods agree. Sequences for P. ramorum and P. sojae are available from the Department of Energy,
Joint Genome Institute website. Protein sequences can be obtained using the protein ID and searching at the Department of Energy Joint Genome Institute
website: http://genome.jgi-psf.org/pages/search-for-genes.jsf?organism=Phyra1_1 for P. ramorum and http://genome.jgi-psf.org/pages/search-for-genes.jsf?
organism=Physo1_1 for P. sojae. Overlap between this analysis and the results reported by Richards et al. (2) is also listed in column 3. In this previous study
we identified an additional three tentative HGTs [one Aconitase genes family and two divergent paralogues of the Esterase/Lipase gene family; Fig. S3 of the
2006 paper (2)]. In the 2006 study we could not provide strong evidence either to support or refute the HGT hypothesis. These three HGTs were not recovered
in this analysis.
1. Shimodaira H (2002) An approximately unbiased test of phylogenetic tree selection. Syst Biol 51:492e508.
2. Richards TA, Dacks JB, Jenkinson JM, Thornton CR, Talbot NJ (2006) Evolution of filamentous plant pathogens: gene exchange across eukaryotic kingdoms. Curr Biol 16:1857e1864.
Table S6.
Check for contaminant sequences by phylogeny of genes adjacent to HGT
Table S6
Other Supporting Information Files
Dataset S1
Richards et al. www.pnas.org/cgi/content/short/1105100108
5 of 5
21
21
37
66
24
Support for within Fungi
Support for with Fungi
Oomycetes
Fungi
Fig. 1.1
65
0.5
58040064_Gluconobacter_oxydans_621H
123441532_Yersinia_enterocolitica_subsp_enterocolitica_8081
170082756_Escherichia_coli_str_K−12_substr_DH10B
69
100
156935741_Enterobacter_sakazakii_ATCC_BAA−894
43
88
157148795_Citrobacter_koseri_ATCC_BAA−895
57 161506099_Salmonella_enterica_subsp_arizonae_serovar_62
161486122_Escherichia_coli_CFT073
35
56421968_Geobacillus_kaustophilus_HTA426
100
138897006_Geobacillus_thermodenitrificans_NG80−2
169796348_Acinetobacter_baumannii
100
148558485_Brucella_ovis_ATCC_25840
77
67
169796361_Acinetobacter_baumannii
21219914_Streptomyces_coelicolor_A3
100 29833483_Streptomyces_avermitilis_MA−4680
64
97
108805211_Rubrobacter_xylanophilus_DSM_9941
73541195_Ralstonia_eutropha_JMP134
96
121611649_Verminephrobacter_eiseniae_EF01−2
97
100
53
94 120612165_Acidovorax_avenae_subsp_citrulli_AAC00−1
73542134_Ralstonia_eutropha_JMP134
170740206_Methylobacterium_sp_4−46
36
79
116252197_Rhizobium_leguminosarum_bv_viciae_3841
36
161521659_Burkholderia_multivorans_ATCC_17616
100
148546553_Pseudomonas_putida_F1
100 77457631_Pseudomonas_fluorescens_PfO−1
21
161524867_Burkholderia_multivorans_ATCC_17616
27
172064804_Burkholderia_ambifaria_MC40−6
31
163857512_Bordetella_petrii_DSM_12804
98
45441488_Yersinia_pestis_biovar_Microtus_str_91001
43
70730918_Pseudomonas_fluorescens_Pf−5
70607845_Sulfolobus_acidocaldarius_DSM_639
100
16081303_Thermoplasma_acidophilum_DSM_1728
100 13540901_Thermoplasma_volcanium_GSS1
100 16081684_Thermoplasma_acidophilum_DSM_1728
13541425_Thermoplasma_volcanium_GSS1
116252685_Rhizobium_leguminosarum_bv_viciae_3841
91783038_Burkholderia_xenovorans_LB400
85
170732862_Burkholderia_cenocepacia_MC0−3
92 76809112_Burkholderia_pseudomallei_1710b
79
34497871_Chromobacterium_violaceum_ATCC_12472
162145876_Gluconacetobacter_diazotrophicus_PAl_5
69
99
161504453_Salmonella_enterica_subsp_arizonae_serovar_62
152970307_Klebsiella_pneumoniae_subsp_pneumoniae_MGH_78578
157372993_Serratia_proteamaculans_568
99
116621822_Solibacter_usitatus_Ellin6076
118618356_Mycobacterium_ulcerans_Agy99
31793095_Mycobacterium_bovis_AF2122_97
100 38
118465387_Mycobacterium_avium_104
.5._Phybl66009_Phycomyces_blakesleeanus
.5._Muci91638_Mucor_circinelloides
98
97
99.5._RO3G_01230_Rhizopus_oryzae
61
.5._RO3G_16963_Rhizopus_oryzae
.5._Phybl78354_Phycomyces_blakesleeanus
.5._Mela73670_Melampsora_laricis−populina
.5._CNAG_04704_Cryptococcus_neoformans
74
.5._UM05122_Ustilago_maydis
24
.5._Spro11334_Sporobolomyces_roseus
24
.5._Scco75764_Schizophyllum_commune
37
45
.5._Scco64395_Schizophyllum_commune
65
.5._CC1G_10170_Coprinus_cinereus
44
97
.5._Labi143634_Laccaria_bicolor
.5._Popl54179_Postia_placenta
.5._UM00529_Ustilago_maydis
89
.5._AB00066_Alternaria_brassicicola
.5._Cohe80973_Cochliobolus_heterostrophus
100
.5._PTRG_10296_Pyrenophora_tritici−repentis
73
77
.5._Myfi55853_Mycosphaerella_fijiensis
49
88 58 .5._MGG_03360_Magnaporthe_grisea
.5._NCU01231_Neurospora_crassa
.5._CHG07662_Chaetomium_globosum
.5._Pa_2_6980_Podospora_anserina
32
30
.5._FGSG_05882_Fusarium_graminearum
97.5._FVEG04557_Fusarium_verticillioides
57
91
.5._Neha48646_Nectria_haematococca
93
.5._Trat29031_Trichoderma_atoviride
11
.5._Trre121441_Trichoderma_reesei
44
.5._Trvi89880_Trichoderma_virens
66
.5._NFIA084940_Neosartorya_fischeri
41
.5._AN6095_Aspergillus_nidulans
40
21 35.5._A011000744_Aspergillus_oryzae
18
.5._Asni45610_Aspergillus_niger
.5._ACLA081240_Aspergillus_clavatus
23 32 .5._ATEG_09833_Aspergillus_terreus
45
21
.5._PABG08813_Paracoccidioides_brasiliensis
90
.5._MGYG_00617_Microsporum_gypseum
82
79
.5._MCYG_03451_Microsporum_canis
.5._UREG_01993_Uncinocarpus_reesii
48 81
.5._CIMG_03956_Coccidioides_immitis
.5._BDBG_02496_Blastomyces_dermatitidis
.5._VDBG_06218_Verticillium_albo−atrum
.5._Asni41415_Aspergillus_niger
99 Phra38546_Phytophthora_ramorum
PITG_00329_Phytophthora_infestans
61 Phca115830_Phytophthora_capsici
95
supercont1_3_Saprolegnia_parasitica
Phso127933_Phytophthora_sojae
53
90
Phra71620_Phytophthora_ramorum
98
PITG_05902_Phytophthora_infestans
60
.1._PTRG_05045_Pyrenophora_tritici−repentis
98
.1._AB05583_Alternaria_brassicicola
.1._Cohe10578_Cochliobolus_heterostrophus
79
.1._Asni180069_Aspergillus_niger
.1._AN6703_Aspergillus_nidulans
35 100
100
99
.1._Afu7g05550_Aspergillus_fumigatus
46
.1._NFIA026760_Neosartorya_fischeri
75
.1._ACLA007250_Aspergillus_clavatus
24
.1._ATEG_06379_Aspergillus_terreus
84
.1._AFL00410_Aspergillus_flavus
31
.1._VDAG_08124_Verticillium_dahliae
57
98.1._Trvi54396_Trichoderma_virens
.1._Trre44175_Trichoderma_reesei
70
.1._FGSG_04204_Fusarium_graminearum
100.1._FVEG10394_Fusarium_verticillioides
61
33
43
.1._Crpa39004_Cryphonectria_parasitica
.1._Pa_3_2490_Podospora_anserina
30
31
94
.1._NCU07607_Neurospora_crassa
52
.1._MGG_09827_Magnaporthe_grisea
.1._SS1G_08467_Sclerotinia_sclerotiorum
94
.1._BC1G_03160_Botrytis_cinerea
a
99 .1._Mygr76200_Mycosphaerella_graminicol
.1._Myfi53445_Mycosphaerella_fijiensis
.2._Pist85334_Pichia_stipitis
100
.2._C19_5307_Candida_albicans_SC5314
73
.2._6322632_Saccharomyces_cerevisiae
.2._C19_7447_Candida_albicans_SC5314
99
100
.2._Pist30177_Pichia_stipitis
100
.2._50425053_Debaryomyces_hansenii
99
89
75
.2._50425843_Debaryomyces_hansenii
.2._50421515_Debaryomyces_hansenii
.2._45198851_Ashbya_gossypii
86
100 .2._45185017_Ashbya_gossypi
i
63
100
.2._45185020_Ashbya_gossypii
99
.2._50554595_Yarrowia_lipolytica
.2._50551169_Yarrowia_lipolytica
.2._50548803_Yarrowia_lipolytica
66
.5._Mygr32600_Mycosphaerella_graminicola
100
.5._Mygr38280_Mycosphaerella_graminicola
100
.5._ATEG_06465_Aspergillus_terreus
100
94
.5._Afu8g00770_Aspergillus_fumigatus
.5._NFIA094200_Neosartorya_fischeri
63
.5._CPSG05438_Coccidioides_posadasii
97
.5._MGYG_06624_Microsporum_gypseum
100 .5._MCYG_06188_Microsporum_canis
21
34
34
.1._Neha90706_Nectria_haematococca
86 .1._FGSG_09181_Fusarium_graminearum
100
.1._FVEG03675_Fusarium_verticillioides
99
.1._FOXG_05802_Fusarium_oxysporum
27
.1._ATEG_02475_Aspergillus_terreus
91
.1._AFL04966_Aspergillus_flavus
100
.1._Asni185927_Aspergillus_niger
31
.1._MGG_02130_Magnaporthe_grisea
10
.1._FOXG_09686_Fusarium_oxysporum
78
.1._Neha90554_Nectria_haematococca
100
.1._VDAG_05545_Verticillium_dahliae
64
.1._FOXG_17501_Fusarium_oxysporum
100
.1._Neha56618_Nectria_haematococca
Phca71207_Phytophthora_capsici
76
19
100 Phra82761_Phytophthora_ramorum
Phso135217_Phytophthora_sojae
86
Phca36461_Phytophthora_capsici
85 Phso135222_Phytophthora_sojae
84
95
Phra72046_Phytophthora_ramorum
13
62
69Phra82759_Phytophthora_ramorum
Phso135221_Phytophthora_sojae
88
Phra82760_Phytophthora_ramorum
.1._Crpa61678_Cryphonectria_parasitica
.1._Myfi59107_Mycosphaerella_fijiensis
5
.1._SS1G_01472_Sclerotinia_sclerotiorum
89
.1._CHG03999_Chaetomium_globosum
13
91
.1._CHG04046_Chaetomium_globosum
48
.1._Crpa75777_Cryphonectria_parasitica
.1._ATEG_04042_Aspergillus_terreus
.1._Asni173684_Aspergillus_niger
100 26
.1._AFL03632_Aspergillus_flavus
29 38
.1._Afu3g13880_Aspergillus_fumigatus
.1._AN5321_Aspergillus_nidulans
12
43
.1._AN5016_Aspergillus_nidulans
85
.1._SNU14174_Stagonospora_nodorum
73
.1._Cohe116876_Cochliobolus_heterostrophus
70
95
.1._AB01943_Alternaria_brassicicola
7
.1._Mygr108908_Mycosphaerella_graminicola
.5._FGSG_03243_Fusarium_graminearum
100
.5._A113000074_Aspergillus_oryzae
.5._Spro2111_Sporobolomyces_roseus
10
.5._Myfi33466_Mycosphaerella_fijiensis
100
.5._Cohe101276_Cochliobolus_heterostrophus
13
.5._Afu4g04010_Aspergillus_fumigatus
100
.5._AB01390_Alternaria_brassicicola
100
26
.5._PTRG_09754_Pyrenophora_tritici−repentis
6
.5._VDBG_02767_Verticillium_albo−atrum
.5._NFIA033190_Neosartorya_fischeri
68
.5._Trvi49586_Trichoderma_virens
96
100
.5._Trre70631_Trichoderma_reesei
100
17
.5._Trvi69271_Trichoderma_virens
.5._Trvi32558_Trichoderma_virens
69
.5._AB00367_Alternaria_brassicicola
72
.5._50422039_Debaryomyces_hansenii
.5._Pa_5_510_Podospora_anserina
100
34
.5._CHG10112_Chaetomium_globosum
47
.5._UM04638_Ustilago_maydis
.5._UM00182_Ustilago_maydis
.5._Scco104285_Schizophyllum_commune
47
.5._Labi303983_Laccaria_bicolor
66
100
.5._CC1G_03614_Coprinus_cinereus
59
.5._CNAG_04869_Cryptococcus_neoformans
.5._Popl43588_Postia_placenta
100
.5._Popl115141_Postia_placenta
41
90
.5._CC1G_07672_Coprinus_cinereus
94
.5._CC1G_03408_Coprinus_cinereus
93
.5._Labi187526_Laccaria_bicolor
.5._Mela110127_Melampsora_laricis−populina
82
100
.5._Mela37873_Melampsora_laricis−populina
.5._Myfi57762_Mycosphaerella_fijiensis
88
.5._Mygr72632_Mycosphaerella_graminicola
53
.5._PTRG_10004_Pyrenophora_tritici−repentis
87
.5._TEQG_07096_Trichophyton_equinum
52
100
.5._MCYG_07502_Microsporum_canis
100
73 .5._MGYG_05274_Microsporum_gypseum
73
86 .5._ACLA043190_Aspergillus_clavatus
.5._Afu8g02530_Aspergillus_fumigatus
100
.5._ATEG_10345_Aspergillus_terreus
95
.5._Trre59723_Trichoderma_reesei
26
.5._Trre78828_Trichoderma_reesei
100
.5._Trat43822_Trichoderma_atoviride
74
59
.5._MGG_00314_Magnaporthe_grisea
40
.5._VDAG_05410_Verticillium_dahliae
36
.5._NCU09575_Neurospora_crassa
81
.5._Pa_5_2830_Podospora_anserina
.5._CPSG03971_Coccidioides_posadasii
96
99 .5._TEQG_00322_Trichophyton_equinum
.5._MCYG_07850_Microsporum_canis
100
30
.5._Mygr50790_Mycosphaerella_graminicola
73
.5._SS1G_13982_Sclerotinia_sclerotiorum
.5._MCYG_04986_Microsporum_canis
Acetylcholinesterase
1
precursor_[EER07696.1]
93
Acetylcholinesterase 1 precursor_[EEQ98534.1]
100
Acetylcholinesterase precursor_[EEQ98535.1]
45
37
Acetylcholinesterase precursor_[EER16155.1]
Mobr38638_Monosiga_brevicollis
Nematostella
vectensis_[XP_001627490.1]
47
neuroligin 4_[ABM84537.1]
Branchiostoma floridae_[XP_002593421.1]
89 4557351_Homo_sapiens
60
Rattus norvegicus_[NP_075231.1]
100
Gallus gallus_[NP_989977.1]
79
Ornithorhynchus anatinus_[XP_001505841.1]
53
27
51
sapiens_[NP_000656.1]
100Homo
Mus musculus_[ACF22905.1]
Dermacentor variabilis_[AAP49303.1]
95
87
Aedes aegypti_[XP_001656977.1]
Branchiostoma floridae_[XP_002588674.1]
41
Branchiostoma
floridae_[XP_002590081.1]
11
99
Branchiostoma floridae_[XP_002599125.1]
Trad61104_Trichoplax_adhaerens
carboxylesterase_[XP_641615.1]
20
57
Polysphondylium pallidum PN500_[EFA84953.1]
100
Polysphondylium pallidum PN500_[EFA75216.1]
100 Polysphondylium
pallidum PN500_[EFA85623.1]
Robiginitalea biformata HTCC2501_[YP_003196436.1]
Asticcacaulis excentricus CB 48_[ZP_04771813.1]
26
carboxylesterase_[YP_780006.1]
100
15
Rhizobium etli Kim 5_[ZP_03502106.1]
100 Rhizobium
leguminosarum bv viciae 3841_[YP_766735.1]
44
Burkholderia
multivorans CGD1_[ZP_03582487.1]
100 Burkholderia phytofirmans
PsJN_[YP_001890332.1]
Asticcacaulis
excentricus
CB
48_[ZP_04771594.1]
40
46
49
Acidobacterium capsulatumA
carboxylesterase_[YP_497004.1]
27
42
Caulobacter segnis ATCC 21756_[ZP_06120188.1]
13
Pectobacterium carotovorum subsp brasiliensis PBR1692_[ZP_03828690.1]
46
Tolumonas auensis DSM 9187_[YP_002894281.1]
30
Bradyrhizobium japonicum USDA 110_[NP_773103.1]
56
Phenylobacterium zucineum HLK1_[YP_002132098.1]
carboxylesterase_[YP_001155227.1]
Acidobacterium capsulatumB
92
Pseudoalteromonas atlantica T6c_[YP_660093.1]
99
Spirosoma linguale DSM 74_[ZP_04490313.1]
13
37
carboxylesterase_[YP_827738.1]
66
24
carboxylesterase_[YP_824312.1]
Acidobacterium capsulatumC
22
32
100
Verrucomicrobiae bacterium DG1235_[ZP_05058482.1]
100
Opitutus terrae PB90−1_[YP_001820106.1]
marine gamma proteobacterium HTCC2143_[ZP_01616133.1]
Haliangium ochraceum DSM 14365_[YP_003266314.1]
Streptomyces sp ACT−1_[ZP_06283266.1]
43
Streptomyces sp AA4_[ZP_05480974.1
]
Bacillus niacini_[AAQ03995.1]
28
89
Bacillus coagulans 36D1_[ZP_04430857.1]
45
Geobacillus sp Y412MC10_[YP_003240902.1]
62
Bacillus licheniformis_[CAC51386.1]
61
Bacillus licheniformis ATCC 14580_[YP_077866.1]
75
95
Bacillus amyloliquefaciens FZB42_[YP_001422731.1]
56
Bacillus
subtilis_[ABB54394.1]
54
97 Bacillus sp BP−7_[CAB93516.1]
78
Bacillus sp NRRL B−14911_[ZP_01172823.1]
Rhodococcus opacus B4_[YP_002778491.1]
83
Rhodococcus jostii RHA1_[YP_701270.1]
15
90
Gordonia bronchialis DSM 43247_[YP_003272019.1]
92
Mycobacterium marinum M_[YP_001852625.1]
77
carboxylesterase_[YP_001134683.1]
72
Mycobacterium abscessus_[YP_001704066.1]
59
Tsukamurella paurometabola DSM 20162_[ZP_04026339.1]
81
Rhodococcus jostii RHA1_[YP_705499.1]
86
Sanguibacter keddieii DSM 10542_[YP_003313052.1]
Xanthomonas campestris pv vesicatoria str 85−10_[YP_362973.1]
96
Parvularcula bermudensis HTCC2503_[ZP_01018403.1]
12
Thermomonospora curvata DSM 43183_[YP_003297898.1]
35
carboxylesterase_[YP_779190.1]
39
Streptomyces sviceus ATCC 29083_[ZP_05016198.1]
22
49
Stackebrandtia nassauensis DSM 44728_[ZP_04482057.1]
40
20
Actinosynnema mirum DSM 43827_[YP_003102285.1]
Mycobacterium abscessus_[YP_001704532.1]
88
carboxylesterase_[YP_638181.1]
95
Mycobacterium smegmatis str MC2 155_[YP_885815.1]
46
9
46
carboxylesterase_[YP_001136305.1]
carboxylesterase_[NP_296345.1]
Fungi
Tolumonas auensis DSM 9187_[YP_002892699.1]
74
Methylocella silvestris BL2_[YP_002361017.1]
86
Tolumonas auensis DSM 9187_[YP_002892531.1]
Oomycetes
carboxylesterase_[YP_001403939.1]
100
Candidatus Methanosphaerula palustris E1−9c_[YP_002466477.1]
94
Candidatus Methanosphaerula palustris E1−9c_[YP_002466932.1]
18
Support for with Fungi
Sorangium cellulosum So ce 56 _[YP_001615352.1]
32
Carboxylesterase_[ZP_01385717.1]
Polysphondylium pallidum PN500_[EFA76380.1]
Support for within Fungi
Dictyostelium discoideum AX4_[XP_639223.1]
98
Polysphondylium pallidum PN500_[EFA77234.1]
95
81
Polysphondylium pallidum PN500_[EFA75987.1]
80
Dictyostelium discoideum AX4_[XP_635153.1]
47
Dictyostelium discoideum AX4_[XP_638123.1]
18
65
Dictyostelium discoideum AX4_[XP_638122.1]
100
Dictyostelium discoideum AX4_[XP_642939.1]
Phaeodactylum tricornutum CCAP 1055/1_[XP_002186227.1]
Fig. 1.2
0.4
2
0
109898993_Pseudoalteromonas_atlantica_T6c
78358694_Desulfovibrio_desulfuricans_G20
116687117_Burkholderia_cenocepacia_HI2424
12
4
29
6
25
11
1
4
0
0
1
0
0
43
5
Eubacteria
91778350_Burkholderia_xenovorans_LB400
34496850_Chromobacterium_violaceum_ATCC_12472
152964252_Kineococcus_radiotolerans_SRS30216
182440400_Streptomyces_griseus_subsp_griseus_NBRC_13350
152967583_Kineococcus_radiotolerans_SRS30216
162456496_Sorangium_cellulosum_So_ce_56
Eubacteria
146298876_Flavobacterium_johnsoniae_UW101
71425900_Trypanosoma_cruzi
38
100
Lm23_0430_Leishmania_major
34
120436496_Gramella_forsetii_KT0803
17557428_Caenorhabditis_elegans
23
Fungi
100
.2._6319493_Saccharomyces_cerevisiae
100
.2._6324399_Saccharomyces_cerevisiae
100
.2._6322004_Saccharomyces_cerevisiae
90
.2._Pist76750_Pichia_stipitis
61
.2._C19_3672_Candida_albicans_SC5314
89
.3._19113650_Schizosaccharomyces_pombe
97
.2._50418541_Debaryomyces_hansenii
PITG_16865_Phytophthora_infestans
100
Phra71309_Phytophthora_ramorum
58 Phca103231_Phytophthora_capsici
.1._Asni56084_Aspergillus_niger
97
99
.1._AN3432_Aspergillus_nidulans
47
.1._ATEG_08962_Aspergillus_terreus
89
.1._AFL11228_Aspergillus_flavus
69
.1._NFIA071470_Neosartorya_fischeri
91
.1._ACLA033730_Aspergillus_clavatus
.1._UREG_06952_Uncinocarpus_reesi
i
86
97
.1._CPSG03919_Coccidioides_posadasi
i
98
.1._TEQG_01598_Trichophyton_equinum
100
96
.1._MGYG_05653_Microsporum_gypseum
35
15
.1._BDBG_08970_Blastomyces_dermatitidis
.1._Crpa49385_Cryphonectria_parasitica
19
.1._NCU09705_Neurospora_crassa
32
10
.1._CHG09949_Chaetomium_globosum
23
.1._Pa_5_890_Podospora_anserina
.1._Neha38340_Nectria_haematococca
13
61
96
.1._FVEG04693_Fusarium_verticillioides
11
.1._Trat131335_Trichoderma_atoviride
100
10
.1._Trre121661_Trichoderma_reesei
.1._MGG_03853_Magnaporthe_grisea
31
.1._SNU12085_Stagonospora_nodorum
83
.1._AB02230_Alternaria_brassicicola
95
.1._Cohe25662_Cochliobolus_heterostrophus
51
.1._PTRG_06392_Pyrenophora_tritici−repentis
.1._Mygr111250_Mycosphaerella_graminicola
100
.1._Myfi87208_Mycosphaerella_fijiensis
.5._BDEG04283_Batrachochytrium_dendrobatidis
32
.5._Phybl30377_Phycomyces_blakesleeanus
89
.5._Muci92859_Mucor_circinelloides
77
.5._RO3G_02920_Rhizopus_oryzae
71
.5._Rhizopus stolonifer_[AAQ24378.1]
91788960_Polaromonas_sp_JS666
29
42526865_Treponema_denticola_ATCC_35405
32471300_Rhodopirellula_baltica_SH_1
Planctomyces limnophilus DSM 3776_[ZP_04427264.1]
160902642_Petrotoga_mobilis_SJ95
Rhodothermus marinus DSM 4252_[YP_003289764.1]
Emhu454011_Emiliania_huxleyi
182679980_Beijerinckia_indica_subsp_indica_ATCC_9039
94
154244970_Xanthobacter_autotrophicus_Py2
82
27378317_Bradyrhizobium_japonicum_USDA_110
91
146338876_Bradyrhizobium_sp_ORS278
170747746_Methylobacterium_radiotolerans_JCM_2831
87
170742750_Methylobacterium_sp_4−46
24
87198841_Novosphingobium_aromaticivorans_DSM_12444
18
103486230_Sphingopyxis_alaskensis_RB2256
49
167647580_Caulobacter_sp_K31
97
16125667_Caulobacter_crescentus_CB15
Phtr56439_Phaeodactylum_tricornutum
100
Thps15858_Thalassiosira_pseudonana
Oslu51907_Ostreococcus_lucimarinus
15
100
OsRC31531_Ostreococcus_RCC809
58
Mipu18425_Micromonas_pusilla
9
68
Micromonas sp RCC299_[XP_002505458.1]
Viridaeplantae
10
Mobr8499_Monosiga_brevicollis
24668282_Drosophila_melanogaster
100
24583720_Drosophila_melanogaster
94
24668278_Drosophila_melanogaster
42
Dapu99401_Daphnia_pulex
99
Dapu60468_Daphnia_pulex
Strongylocentrotus purpuratus_[XP_794587.2]
20
Trad28936_Trichoplax_adhaerens
Neve229971_Nematostella_vectensi
s
Danio rerio_[CAX14763.1]
21
51
0
Xetr451378_Xenopus_tropicalis
90
28892785_Mus_musculus
4
97
20270355_Homo_sapiens
Ciona intestinalis_[XP_002125905.1]
0
Branchiostoma floridae_[XP_002596830.1]
CapI221220_Capitella_sp_I
0
ChNC9386_Chlorella_NC64A
0
27
CapI223938_Capitella_sp_I
1
Logi236572_Lottia_gigantea
Teth9006_Tetrahymena_thermophila
162449238_Sorangium_cellulosum_So_ce_56
65
Gemmata obscuriglobus UQM 2246_[ZP_02734020.1]
109899835_Pseudoalteromonas_atlantica_T6c
90020834_Saccharophagus_degradans_2−40
148269766_Thermotoga_petrophila_RKU−1
70
154249889_Fervidobacterium_nodosum_Rt17−B1
Eubacteria
21220874_Streptomyces_coelicolor_A3
100
29832309_Streptomyces_avermitilis_MA−4680
182438895_Streptomyces_griseus_subsp_griseus_NBRC_13350
96
21220860_Streptomyces_coelicolor_A
13
152964590_Kineococcus_radiotolerans_SRS30216
28869825_Pseudomonas_syringae_pv_tomato_str_DC3000
99
77459953_Pseudomonas_fluorescens_PfO−1
117928818_Acidothermus_cellulolyticus_11B
19
183982567_Mycobacterium_marinum_M
182413205_Opitutus_terrae_PB90−1
9
90020435_Saccharophagus_degradans_2−40
12
Verrucomicrobiae bacterium DG1235_[ZP_05055899.1]
94967352_Acidobacteria_bacterium_Ellin345
68
94968176_Acidobacteria_bacterium_Ellin345
17
116620579_Solibacter_usitatus_Ellin6076
150019276_Clostridium_beijerinckii_NCIMB_8052
47
160878714_Clostridium_phytofermentans_ISD
81
150391529_Alkaliphilus_metalliredigens_QYMF
1
53715665_Bacteroides_fragilis_YCH46
60679891_Bacteroides_fragilis_NCTC_9343
91
150010316_Parabacteroides_distasonis_ATCC_8503
8
Pedobacter sp BAL39_[ZP_01885546.1]
49
146299785_Flavobacterium_johnsoniae_UW101
7
39
Sphingobacterium spiritivorum ATCC 33300_[ZP_03969193.1]
22
349m00045_Entamoeba_histolytica
100
3
0
Entamoeba dispar SA760_[XP_001741629.1]
60681157_Bacteroides_fragilis_NCTC_9343
25
123433719_Trichomonas_vaginalis
29
34541278_Porphyromonas_gingivalis_W83
93
150008295_Parabacteroides_distasonis_ATCC_8503
32474327_Rhodopirellula_baltica_SH_1
10
92112927_Chromohalobacter_salexigens_DSM_3043
5
Leeuwenhoekiella blandensis MED217_[ZP_01060789.1]
63
120435058_Gramella_forsetii_KT0803
46
146298883_Flavobacterium_johnsoniae_UW101
170750507_Methylobacterium_radiotolerans_JCM_2831
163852291_Methylobacterium_extorquens_PA1
148260041_Acidiphilium_cryptum_JF−5
114327460_Granulibacter_bethesdensis_CGDNIH1
Eubacteria
100
11
2
11
16
0
Fungi
Oomycetes
Support for with Fungi
0
0
Support for within Fungi
Fig. 1.3
0
2
0
0
9
11
1
50
0
8
0
0
9
0
0
0
98
7
4
0
10
0.3
100
100
38
11
69
0.3
Fig. 1.4
Support for within Fungi
Support for with Fungi
Oomycetes
Fungi
XanA
.5._Talaromyces stipitatus ATCC 10500_[XP_002478372.1]
.5._Cohe28674_Cochliobolus_heterostrophus
.5._Penicillium marneffei ATCC 18224_[XP_002152193.1]
100
.5._Talaromyces stipitatus ATCC 10500_[XP_002478374.1]
.4._UM03386_Ustilago_maydis
100
.1._Talaromyces stipitatus ATCC 10500_[XP_002487810.1]
33
.1._Penicillium marneffei ATCC 18224_[XP_002153618.1]
Phra71178_Phytophthora_ramorum
89
99
.1._BC1G_00077_Botrytis_cinerea
23
.1._SS1G_04722_Sclerotinia_sclerotioru
m
30
.1._Penicillium chrysogenum isconsin 54−1255_[XP_002568417.1]
.1._Asni35399_Aspergillus_niger
45
62
100 .1._AFL07390_Aspergillus_flavus
87
.1._A001000152_Aspergillus_oryzae
42
.1._ATEG_04979_Aspergillus_terreus
16
.1._Emericella nidulans_[CAI47587.1]
.5._Crpa97903_Cryphonectria_parasitica
17
.5._NCU09738_Neurospora_crassa
45
.5._Pa_6_2860_Podospora_anserina
26
82
.5._Trat34916_Trichoderma_atoviride
.5._Trre77767_Trichoderma_reesei
19
99
.5._Trat147509_Trichoderma_atoviride
13
.5._VDAG_04163_Verticillium_dahliae
.5._Muci28299_Mucor_circinelloides
100
.5._RO3G_16101_Rhizopus_oryzae
58
.5._Spro9935_Sporobolomyces_roseus
53
89
.5._CNAG_01542_Cryptococcus_neoformans
56
.5._CC1G_00658_Coprinus_cinereus
52
.5._Labi181264_Laccaria_bicolor
39
.5._Scco68337_Schizophyllum_commune
34
.5._Phch140431_Phanerochaete_chrysosporium
34
.5._Popl120022_Postia_placenta
.5._63054461_Schizosaccharomyces_pombe
.5._Myfi58865_Mycosphaerella_fijiensis
.5._50543326_Yarrowia_lipolytic
a
59
.5._Kluyveromyces lactis_[XP_454141.1]
83
79
.5._Lachancea thermotolerans_[XP_002551618.1]
60
.5._Zygosaccharomyces rouxii_[XP_002497140.1]
.5._C19_1461_Candida_albicans_SC5314
100
83
.5._Candida tropicalis MYA−3404_[XP_002546939.1]
51
.5._Pist34838_Pichia_stipitis
39
.5._Lodderomyces elongisporus NRRL YB−4239_[XP_001528608.1]
21
.5._Pichia guilliermondii ATCC 6260_[EDK40841.2]
91
26
.5._50405537_Debaryomyces_hanseni
i
.5._Clavispora lusitaniae ATCC 42720_[XP_002616029.1]
Diaphorobacter sp TPSY_[YP_002551991.1]
Ralstonia eutropha JMP134_[YP_293521.1]
100
21
Ralstonia eutropha H16_[YP_725771.1]
putative taurine dioxygenase_[YP_001237505.1]
73
66
Acinetobacter junii SH205_[ZP_06066452.1]
61
dioxygenase_[YP_103265.1]
57
Gordonia bronchialis DSM 43247_[YP_003272551.1]
98
2
Streptomyces sp ACTE_[ZP_06271905.1]
Photorhabdus luminescens subsp laumondii TTO1_[NP_928338.1]
36
Erythrobacter litoralis HTCC2594_[YP_458158.1]
5
Nostoc
punctiforme
PCC
73102_[YP_001869111.1]
2
alpha−ketoglutarate−dependent 2_[ZP_05068539.1]
27
2
Streptomyces avermitilis MA−4680_[NP_824171.1]
Micromonas sp RCC299_[XP_002502918.1]
33
Bordetella bronchiseptica RB50_[NP_887599.1]
Silicibacter sp TM1040_[YP_611286.1]
24
putative alpha KG dependent 2_[YP_553181.1]
69
alpha−ketoglutarate−dependent 2_[NP_880388.1]
20
dioxygenase_[NP_792423.1]
Frankia sp EuI1c_[ZP_06239536.1]
96
100
Frankia sp EAN1pec_[YP_001508006.1]
40
Frankia sp EAN1pec_[YP_001504833.1]
97
Frankia sp EAN1pec_[YP_001504880.1]
54
158318648_Frankia_sp_EAN1pec
Taurine catabolism dioxygenase TauD_[XP_001031478.1]
100
Taurine catabolism dioxygenase TauD_[XP_001031478.1]
25
Pseudoalteromonas haloplanktis TAC125_[YP_340645.1]
100
TauD
0
Outgroup
13471828_Mesorhizobium_loti_MAFF303099
170736361_Burkholderia_cenocepacia_MC0−3
3
86157172_Anaeromyxobacter_dehalogenans_2CP−C
38
162451522_Sorangium_cellulosum_So_ce_56
Myfi31107_Mycosphaerella_fijiensis
148262103_Geobacter_uraniireducens_Rf4
1 8
163852562_Methylobacterium_extorquens_PA1
26
108759002_Myxococcus_xanthus_DK_1622
4
114326762_Granulibacter_bethesdensis_CGDNIH
27
83814602_Salinibacter_ruber_DSM_13855
Trat34322_Trichoderma_atovirid
e
Myfi57868_Mycosphaerella_fijiensi
s
Neha52268_Nectria_haematococca
MGG_00270_Magnaporthe_grisea
AFL04557_Aspergillus_flavus
90
11
93
Asni190222_Aspergillus_niger
58
96 NFIA107930_Neosartorya_fischeri
94
Afu4g08240_Aspergillus_fumigatus
8
ACLA047590_Aspergillus_clavatus
33
12
AFL08559_Aspergillus_flavus
33
46
Pa_5_10420_Podospora_anserin
a
90
NCU09285_Neurospora_crassa
Crpa103641_Cryphonectria_parasitic
a
FGSG_00236_Fusarium_graminearum
SS1G_08348_Sclerotinia_sclerotiorum
45
7
97
BC1G_03072_Botrytis_cinerea
35
12
BC1G_15502_Botrytis_cinerea
SNU08513_Stagonospora_nodorum
11
20
79
AB00496_Alternaria_brassicicola
100 PTRG_09024_Pyrenophora_tritici−repentis
22
61
Cohe116137_Cochliobolus_heterostrophus
Mygr105735_Mycosphaerella_graminicola
FOXG_02354_Fusarium_oxysporum
30
Trvi56510_Trichoderma_virens
98
100
Trre22271_Trichoderma_reesei
58
HCAG_02952_Histoplasma_capsulatum
100
2
BDBG_08446_Blastomyces_dermatitidis
BDBG_01442_Blastomyces_dermatitidis
95
Trre23292_Trichoderma_reesei
87199881_Novosphingobium_aromaticivorans_DSM_12444
13
0
19111913_Schizosaccharomyces_pombe
UM01885_Ustilago_maydis
Scco16740_Schizophyllum_commune
Labi318806_Laccaria_bicolor
89
59
15
CC1G_01609_Coprinus_cinereus
100
CC1G_01618_Coprinus_cinereus
51
Phch5793_Phanerochaete_chrysosporium
32
22
Popl107382_Postia_placenta
35
Popl105379_Postia_placenta
Nagr73866_Naegleria_gruber
i
99
Nagr51101_Naegleria_gruber
i
91
Nagr56126_Naegleria_gruber
i
.5._FOXG_01243_Fusarium_oxysporum
100
.5._Neha36808_Nectria_haematococca
2
.5._ATEG_08132_Aspergillus_terreus
80
.5._ACLA094300_Aspergillus_clavatus
100
.5._Afu2g00970_Aspergillus_fumigatus
53
60
91 .5._NFIA033280_Neosartorya_fischeri
93
.5._A701000350_Aspergillus_oryzae
.5._AN7636_Aspergillus_nidulans
.5._FGSG_01630_Fusarium_graminearum
72
.5._Mygr65978_Mycosphaerella_graminicola
100
87
.5._Myfi55784_Mycosphaerella_fijiensis
15
.5._SS1G_08952_Sclerotinia_sclerotiorum
9
.5._Pa_5_120_Podospora_anserina
66
17
.5._NCU06303_Neurospora_crassa
.5._Crpa99156_Cryphonectria_parasitica
.5._MGG_07773_Magnaporthe_grisea
21
.5._Cohe108192_Cochliobolus_heterostrophus
30
100
.5._AB04779_Alternaria_brassicicola
38
.5._PTRG_01705_Pyrenophora_tritici−repentis
24
.5._SNU14424_Stagonospora_nodorum
18
Phra71649_Phytophthora_ramorum
Phca123395_Phytophthora_capsici
96
94
Phra80182_Phytophthora_ramorum
0
48
Phso143999_Phytophthora_sojae
100
Phca30421_Phytophthora_capsici
52
.5._FOXG_07385_Fusarium_oxysporum
79
.5._Neha37345_Nectria_haematococca
.5._Asni205355_Aspergillus_niger
42
53
.5._XP_002569137_Penicillium_chrysogenum
32
60
.5._Asni142020_Aspergillus_niger
30
44
.5._Trat50730_Trichoderma_atoviride
100
.5._Trvi52718_Trichoderma_virens
98
.5._50405399_Debaryomyces_hansenii
.5._Trat34965_Trichoderma_atoviride
.5._Muci33912_Mucor_circinelloides
100
.5._Muci74131_Mucor_circinelloides
76
.5._CHG04995_Chaetomium_globosum
100
.5._Pa_5_1120_Podospora_anserina
99
.5._VDAG_07197_Verticillium_dahliae
100
.5._MGYG_07943_Microsporum_gypseum
100
.5._TEQG_02791_Trichophyton_equinum
Spro4429_Sporobolomyces_roseus
39
NODE_77366_Hyphochytrium
A001000566_Aspergillus_oryzae
0
100
NFIA040500_Neosartorya_fischera
11
91778675_Burkholderia_xenovorans_LB400
41
86159945_Anaeromyxobacter_dehalogenans_2CP−C
26
13476772_Mesorhizobium_loti_MAFF303099
0
30
0.3
Fungi
Oomycetes
Support for with Fungi
Support for within Fungi
Fig. 1.5
100
100
60
96
54
90
100
100
0.4
45
Spirosoma linguale DSM 74_[ZP_04489919.1]
Spirosoma linguale DSM 74_[ZP_04487898.1]
100
100
.1._Trvi31141_Trichoderma_virens
.1._Trre54761_Trichoderma_reesei
.1._A003001534_Aspergillus_oryzae
.1._Myfi65382_Mycosphaerella_fijiensis
.1._SS1G_11412_Sclerotinia_sclerotiorum
100
.1._BC1G_08856_Botrytis_cinerea
.1._Cohe104702_Cochliobolus_heterostrophus
Fig. 1.6
Support for within Fungi
Support for with Fungi
Oomycetes
Fungi
.1._AN6772_Aspergillus_nidulans
95 .1._AFL08107_Aspergillus_flavus
45
.1._Asni36394_Aspergillus_niger
55
.1._ quercetin 2_[ABV24349.1]
99
.1._Penicillium chrysogenum isconsin 54−1255_[XP_002561483.1]
Phso139597_Phytophthora_sojae
Phca18391_Phytophthora_capsici
Phra72257_Phytophthora_ramorum
53 48
44
70
100
.1._Asni191468_Aspergillus_niger
.1._Crpa38102_Cryphonectria_parasitica
.1._BC1G_01481_Botrytis_cinerea
100
Rhodococcus jostii RHA1_[YP_703864.1]
Corynebacterium glutamicum ATCC 13032_[NP_600123.1]
Arthrobacter chlorophenolicus A6_[YP_002486542.1]
89 Rhodococcus opacus B4_[YP_002780965.1]
16081050_Bacillus_subtilis_subsp_subtilis_str_168
.1._Myfi89095_Mycosphaerella_fijiensis
100
100
94972247_Deinococcus_geothermalis_DSM_11300
96
96
44
73
55
53
72
25
100
42
54
34
39
0.4
Fig. 1.7
FGSG_12585_Fusarium_graminearum
VDBG_03500_Verticillium_albo−atrum m
Fungi
.1._Myfi40788_Mycosphaerella_fijiensis
.1._BC1G_13407_Botrytis_cinerea
91
100
.1._MGG_12880_Magnaporthe_grisea
Oomycetes
47
.1._AFL03939_Aspergillus_flavus
95
PITG_19561_Phytophthora_infestans
34
Support for with Fungi
100
Phso127729_Phytophthora_sojae
Phso144622_Phytophthora_sojae
99
Phra73895_Phytophthora_ramorum
Support for within Fungi
Philodina roseola_[ACD54790.1]
100
Nagr73456_Naegleria_gruberi
CHG06672_Chaetomium_globosum
Trvi68030_Trichoderma_virens
52
Neha106099_Nectria_haematococca
53
100
FOXG_10159_Fusarium_oxysporum
100
FVEG08355_Fusarium_verticillioides
100
81
FGSG_04743_Fusarium_graminearum
BC1G_07101_Botrytis_cinerea
Asni176718_Aspergillus_niger
69
100
AFL07340_Aspergillus_flavus
70
NFIA004560_Neosartorya_fischer
i
56
Afu3g02880_Aspergillus_fumigatus
100
ATEG_05089_Aspergillus_terreus
Trre58887_Trichoderma_reesei
100
Trat43821_Trichoderma_atoviride
Trat11817_Trichoderma_atoviride
Cohe45960_Cochliobolus_heterostrophus
74
62
VDAG_07955_Verticillium_dahliae
99
AN10277_Aspergillus_nidulans
55
SS1G_13501_Sclerotinia_sclerotiorum
89
Afu1g06130_Aspergillus_fumigatus
93
ATEG_03018_Aspergillus_terreus
58
Asni170172_Aspergillus_niger
100
A003001291_Aspergillus_oryza
e
57
82
NFIA022970_Neosartorya_fischer
i
100
Afu1g01660_Aspergillus_fumigatus
99
Crpa90219_Cryphonectria_parasitica
60
Crpa64851_Cryphonectria_parasitica
Myfi43770_Mycosphaerella_fijiensis
42
Cohe110857_Cochliobolus_heterostrophus
100
97
PTRG_05955_Pyrenophora_tritici−repentis
69
76
100
38
SNU10370_Stagonospora_nodorum
Crpa52455_Cryphonectria_parasitica
Popl51992_Postia_placenta
100
Popl52078_Postia_placenta
93
Scco59132_Schizophyllum_commune
100
Scco41341_Schizophyllum_commune
Stigmatella aurantiaca D4/3−1_[ZP_01461681.1]
100
Catenulispora acidiphila
Burkholderia ambifaria MC40−6_[YP_001807923.1]
46
116688192_Burkholderia_cenocepacia_HI2424
Catenulispora acidiphila DSM 44928
Thalassiosira pseudonana CCMP1335_[XP_002297169.1]
Pediococcus acidilactici 7_4_[ZP_06196645.1]
99
Ruminococcus obeum ATCC 29174_[ZP_01964696.1]
44
conserved hypothetical protein [Enterococcus faecium 1_[ZP_05660616.1]
98
Paenibacillus sp JDR−2_[YP_003012390.1]
62
Pedobacter heparinus DSM 2366_[YP_003093034.1]
85
Chitinophaga pinensis DSM 2588_[YP_003122417.1]
34
Flavobacterium johnsoniae U101_[YP_001196432.1]
24
Bacteroides coprocola DSM 17136_[ZP_03011443.1]
98
Bacteroides eggerthii DSM 20697_[ZP_03457857.1]
78 Bacteroides thetaiotaomicron VPI−5482_[NP_809914.1]
42
Bacteroides dorei DSM 17855_[ZP_03302772.1]
Clostridium methylpentosum DSM 5476_[ZP_03708185.1]
Victivallis vadensis ATCC BAA−548_[ZP_06243072.1]
Rhodopirellula baltica SH 1_[NP_864051.1]
100
99
Opitutaceae bacterium TAV2_[ZP_03727960.1]
87
Pedobacter heparinus DSM 2366_[YP_003094227.1]
100
Pedobacter sp BAL39_[ZP_01881837.1]
Bacteroides eggerthii DSM 20697_[ZP_03457854.1]
69
Opitutaceae bacterium TAV2_[ZP_03724287.1]
Bacteroides capillosus ATCC 29799_[ZP_02034625.1]
100
100
Ruminococcus gnavus ATCC 29149_[ZP_02041040.1]
Streptomyces scabiei 8722_[CBG75597.1]
99
Kineococcus radiotolerans SRS30216_[YP_001359873.1
]
69
73
Beutenbergia cavernae DSM 12333_[YP_002883624.1]
40
Frankia sp EAN1pec_[YP_001504801.1]
91
55
Kribbella flavida DSM 17836_[ZP_03862616.1]
Arthrobacter chlorophenolicus A6_[YP_002486523.1]
100
Rhodococcus jostii RHA1_[YP_703860.1]
Bacteroides intestinalis DSM 17393_[ZP_03012486.1]
100
Bacteroides sp D1_[ZP_04546142.1]
Opitutaceae bacterium TAV2_[ZP_03725725.1]
66
Chloroflexus aggregans DSM 9485_[YP_002461907.1]
100
163849101_Chloroflexus_aurantiacus_J−10−f
Algoriphagus sp PR1_[ZP_01717450.1]
100
Roseiflexus castenholzii DSM 13941_[YP_001431054.1]
54
Opitutus terrae PB90−1_[YP_001820591.1]
42
Chitinophaga pinensis DSM 2588_[YP_003125641.1]
100
Robiginitalea biformata HTCC2501_[YP_003196403.1]
100
43
43
15
57
56
74
45
93
93
18
96
80
23
5
22
2
3
47
5
13
32
24
14
17
40
Outgroup
Fig. 1.8
Support for within Fungi
Support for with Fungi
Oomycetes
Fungi
0.4
90
55
88
89
152965459_Kineococcus_radiotolerans_SRS30216
119962729_Arthrobacter_aurescens_TC1
113868966_Ralstonia_eutropha_H16
157372166_Serratia_proteamaculans_568
15603113_Pasteurella_multocida_subsp_multocida_str_Pm70
15805308_Deinococcus_radiodurans_R
1
28868553_Pseudomonas_syringae_pv_tomato_str_DC3000
97
66044019_Pseudomonas_syringae_pv_syringae_B728a
99
170729823_Xylella_fastidiosa_M12
84625690_Xanthomonas_oryzae_pv_oryzae_MAFF_311018
170745490_Methylobacterium_radiotolerans_JCM_283
1
163850054_Methylobacterium_extorquens_PA1
32472391_Rhodopirellula_baltica_SH_1
119898632_Azoarcus_sp_BH72
61
32477681_Rhodopirellula_baltica_SH_1
56552545_Zymomonas_mobilis_subsp_mobilis_ZM4
167644593_Caulobacter_sp_K31
16125474_Caulobacter_crescentus_CB15
42
78049909_Xanthomonas_campestris_pv_vesicatoria_str_85−10
100 66770501_Xanthomonas_campestris_pv_campestris_str_8004
182415988_Opitutus_terrae_PB90−1
110639927_Cytophaga_hutchinsonii_ATCC_33406
148656620_Roseiflexus_sp_RS−1
99
156742808_Roseiflexus_castenholzii_DSM_13941
148243021_Synechococcus_sp_RCC307
100
113955561_Synechococcus_sp_CC9311
100
148256148_Bradyrhizobium_sp_BTAi1
56697404_Silicibacter_pomeroyi_DSS−3
76
.5._Crpa15980_Cryphonectria_parasitica
.5._Myfi45825_Mycosphaerella_fijiensis
.5._Mygr40839_Mycosphaerella_graminicola
.5._ACLA077800_Aspergillus_clavatus
100
.5._NFIA014250_Neosartorya_fischer
i
.5._Afu1g11330_Aspergillus_fumigatus
80
.1._PABG06527_Paracoccidioides_brasiliensis
.1._MCYG_06774_Microsporum_canis
100
.1._MGYG_03858_Microsporum_gypseum
49
58 .1._BDBG_08531_Blastomyces_dermatitidis
.1._HCAG_03025_Histoplasma_capsulatum
.1._SNU09892_Stagonospora_nodorum
73
.1._PTRG_10696_Pyrenophora_tritici−repentis
56
.1._Cohe113940_Cochliobolus_heterostrophus
53
.1._AB00890_Alternaria_brassicicola
100
53 Phra74844_Phytophthora_ramorum
Phra74887_Phytophthora_ramorum
Phca69598_Phytophthora_capsic
i
100
100
PITG_04624_Phytophthora_infestans
47
100 PITG_21468_Phytophthora_infestans
Phra74867_Phytophthora_ramorum
.5._AFL01512_Aspergillus_flavu
s
90
.5._Asni177169_Aspergillus_niger
98
.5._NFIA016650_Neosartorya_fischer
i
92
.5._ACLA026480_Aspergillus_clavatus
100
.5._Pa_1_22160_Podospora_anserina
.5._VDAG_08282_Verticillium_dahlia
e
.5._FOXG_16906_Fusarium_oxysporum
45
.5._AB09852_Alternaria_brassicicola
99
94
.5._PTRG_11454_Pyrenophora_tritici−repentis
93
80
.5._Cohe113010_Cochliobolus_heterostrophus
.5._FGSG_03393_Fusarium_graminearum
52 .5._FVEG10940_Fusarium_verticillioides
99
89
79
.5._FOXG_12377_Fusarium_oxysporum
.5._Neha97553_Nectria_haematococca
.5._Crpa78912_Cryphonectria_parasitica
46
88
.5._CNAG_04753_Cryptococcus_neoformans
47
.5._Trat153146_Trichoderma_atovirida
100
.5._Trvi72259_Trichoderma_virens
60
.5._Trre62581_Trichoderma_reesei
.5._Labi248522_Laccaria_bicolor
52
.5._Phch7809_Phanerochaete_chrysosporium
40
.5._Scco61623_Schizophyllum_commune
89
99
.5._Popl62164_Postia_placenta
100
.5._Popl59363_Postia_placenta
.5._Scco61940_Schizophyllum_commune
.5._AN8977_Aspergillus_nidulans
.5._MGG_09681_Magnaporthe_grisea
35
.5._Asni212961_Aspergillus_niger
.5._Mygr43806_Mycosphaerella_graminicola
4
68
.5._Myfi58890_Mycosphaerella_fijiensis
24
.5._SNU12135_Stagonospora_nodorum
18
19
.5._SS1G_13841_Sclerotinia_sclerotiorum
.5._A701000487_Aspergillus_oryza
e
97
.5._Asni45025_Aspergillus_niger
100 .5._FVEG03063_Fusarium_verticillioides
18
.5._FOXG_05070_Fusarium_oxysporum
Emhu446776_Emiliania_huxleyi
Phpa94545_Physcomitrella_patens
100
Phpa63780_Physcomitrella_patens
63
77
100
74
18
66825459_Dictyostelium_discoideum
66826055_Dictyostelium_discoideum
Outgroup
17
Outgroup
8
115468464_Oryza_sativa
Sbi4897598_Sorghum_bicolor
Potr785160_Populus_trichocarpa
100
42
Potr772216_Populus_trichocarpa
46
15221497_Arabidopsis_thaliana
100
15233416_Arabidopsis_thaliana
22
15241474_Arabidopsis_thaliana
ChNC135038_Chlorella_NC64A
Phso143536_Phytophthora_sojae
100
Phso143531_Phytophthora_sojae
55 Phca83968_Phytophthora_capsici
71
Hyp709062_Hyaloperonospora_parasitica
64
Phra81161_Phytophthora_ramorum
.4._Mela58493_Melampsora_laricis−populina
.1._AB07340_Alternaria_brassicicola
100
.1._VDAG_02827_Verticillium_dahliae
100
100
.1._Neha82632_Nectria_haematococca
.1._FOXG_03535_Fusarium_oxysporum
57
.1._FGSG_08824_Fusarium_graminearum
74
81
Hyp701243_Hyaloperonospora_parasitica
Phra80501_Phytophthora_ramorum
96 PITG_02935_Phytophthora_infestans
100
PITG_02930_Phytophthora_infestans
29
PITG_02928_Phytophthora_infestans
54 Phso145088_Phytophthora_sojae
8 68
3 25
Phso136232_Phytophthora_sojae
100 Phso136233_Phytophthora_sojae
Phca120413_Phytophthora_capsici
Phso127171_Phytophthora_sojae
85
15
Phso132682_Phytophthora_sojae
43
23
PITG_06591_Phytophthora_infestans
80
18
Phca67592_Phytophthora_capsici
Phra83272_Phytophthora_ramorum
.5._UM05945_Ustilago_maydis
98
.5._Myfi43519_Mycosphaerella_fijiensis
99
.5._A026000115_Aspergillus_oryzae
.5._VDAG_06138_Verticillium_dahliae
.5._MGG_05337_Magnaporthe_grisea
37
99
.5._Pa_2_4280_Podospora_anserina
94
.5._CHG07389_Chaetomium_globosum
71
.5._CHG02330_Chaetomium_globosum
100
34
.5._Pa_7_11630_Podospora_anserina
.5._FGSG_10998_Fusarium_graminearum
100
.5._FVEG11731_Fusarium_verticillioides
89
58
.5._Neha47477_Nectria_haematococca
26
100
.5._FVEG11198_Fusarium_verticillioides
97
.5._Crpa74675_Cryphonectria_parasitica
.5._PTRG_08332_Pyrenophora_tritici−repentis
50
.5._Cohe28883_Cochliobolus_heterostrophus
99
26
.5._SNU08044_Stagonospora_nodorum
.5._MGG_09717_Magnaporthe_grisea
.5._PTRG_04015_Pyrenophora_tritici−repentis
100
100
.5._AB05507_Alternaria_brassicicola
66
.5._Cohe114221_Cochliobolus_heterostrophus
72
.5._SNU14007_Stagonospora_nodorum
.5._BC1G_01791_Botrytis_cinerea
100
26
97
.5._SS1G_12200_Sclerotinia_sclerotiorum
.5._Labi314722_Laccaria_bicolor
58
.5._CC1G_09292_Coprinus_cinereus
96
.5._Scco83274_Schizophyllum_commune
91
.5._PGTG_14143_Puccinia_graminis
100
.5._Mela89999_Melampsora_laricis−populina
19
.5._Neha79719_Nectria_haematococca
.5._CHG07649_Chaetomium_globosum
98
.5._AN10388_Aspergillus_nidulans
92
.5._Myfi56747_Mycosphaerella_fijiensis
.5._AFL07475_Aspergillus_flavus
84
.5._A026000299_Aspergillus_oryzae
36
66
100
.5._Asni44512_Aspergillus_niger
68
41
.5._ATEG_01295_Aspergillus_terreus
.5._ACLA047620_Aspergillus_clavatus
68
.5._Cohe102963_Cochliobolus_heterostrophus
.5._AB07593_Alternaria_brassicicola
79
56
63
.5._PTRG_00812_Pyrenophora_tritici−repentis
.5._Crpa45425_Cryphonectria_parasitica
99
.5._Pa_7_4440_Podospora_anserina
96
.5._NCU08199_Neurospora_crassa
183983447_Mycobacterium_marinum_M
52
183980145_Mycobacterium_marinum_M
100
Fungi
183981201_Mycobacterium_marinum_M
Emhu217799_Emiliania_huxleyi
Oomycetes
97
27
16
25
18
7
6
0.5
Support for with Fungi
Support for within Fungi
Fig. 1.9
Fig. 1.10
0.3
146295421_Caldicellulosiruptor_saccharolyticus_DSM_8903
52081512_Bacillus_licheniformis_ATCC_14580
98
157693415_Bacillus_pumilus_SAFR−032
99
16080064_Bacillus_subtilis_subsp_subtilis_str_168
100
13
23099541_Oceanobacillus_iheyensis_HTE831
57
56962921_Bacillus_clausii_KSM−K16
56
15613048_Bacillus_halodurans_C−12
5
150004351_Bacteroides_vulgatus_ATCC_8482
23
100
29349516_Bacteroides_thetaiotaomicron_VPI−5482
15
29346421_Bacteroides_thetaiotaomicron_VPI−5482
100
150005173_Bacteroides_vulgatus_ATCC_8482
57
78
36
150004425_Bacteroides_vulgatus_ATCC_8482
182416077_Opitutus_terrae_PB90−1
19
146301986_Flavobacterium_johnsoniae_UW101
100
146301987_Flavobacterium_johnsoniae_UW101
48
146301988_Flavobacterium_johnsoniae_UW101
159185616_Agrobacterium_tumefaciens_str_C58
81
150388727_Alkaliphilus_metalliredigens_QYMF
65
41
160878361_Clostridium_phytofermentans_ISDg
15893650_Clostridium_acetobutylicum_ATCC_824
Phpa127007_Physcomitrella_patens
100
Phpa118261_Physcomitrella_patens
100
Phpa123152_Physcomitrella_patens
.1._FGSG_03143_Fusarium_graminearum
100
.1._FOXG_10183_Fusarium_oxysporum
19
.1._Crpa62995_Cryphonectria_parasitica
.1._Neha52013_Nectria_haematococca
28
.1._MGG_02340_Magnaporthe_grisea
59
.1._VDAG_05036_Verticillium_dahliae
88
.1._Neha106608_Nectria_haematococca
74
61
100
.1._FGSG_02866_Fusarium_graminearum
100
64
.1._FVEG13183_Fusarium_verticillioides
78
.1._AN7828_Aspergillus_nidulans
.1._Myfi46172_Mycosphaerella_fijiensis
25
58
.1._MGG_04305_Magnaporthe_grisea
.1._Cohe84827_Cochliobolus_heterostrophus
100
.1._AB07530_Alternaria_brassicicola
.1._AFL07308_Aspergillus_flavus
21
49
69
.1._AN9383_Aspergillus_nidulans
100
.1._NFIA089840_Neosartorya_fischeri
42
.1._BC1G_13690_Botrytis_cinerea
.1._VDAG_08105_Verticillium_dahliae
78
.1._AB02305_Alternaria_brassicicola
100
100
.1._Neha46339_Nectria_haematococca
.1._SNU02220_Stagonospora_nodorum
.1._A113000146_Aspergillus_oryzae
98
100
.1._Asni41877_Aspergillus_niger
Phca21050_Phytophthora_capsici
100
Phso127158_Phytophthora_sojae
60
31
Phra83050_Phytophthora_ramorum
Fungi
35
PITG_19782_Phytophthora_infestans
100
Oomycetes
99 PITG_11632_Phytophthora_infestans
82
.1._Crpa75138_Cryphonectria_parasitica
Support for with Fungi
.1._ACLA077810_Aspergillus_clavatus
99
.1._Myfi41491_Mycosphaerella_fijiensis
Support for within Fungi
100
.1._Mygr57259_Mycosphaerella_graminicola
15
15
0
4
28
24
28
0.3
Fig. 1.11
10−20 kb_[EC724147.1]
126176444_Shewanella_baltica_OS155
114562031_Shewanella_frigidimarina_NCIMB_400
FE249396 CAPH2253rev CAPH Naegleria gruberi amoeba stage Naegleria gruberi cDNA clone CAPH2253 3’ _[FE249396.1]
19
Ferroplasma acidarmanus fer1_[ZP_05571183.1]
56420249_Geobacillus_kaustophilus_HTA426
47
49186316_Bacillus_anthracis_str_Sterne
73
183219788_Leptospira_biflexa_serovar_Patoc_strain_Patoc_1
43
Nematostella vectensis_[XP_001617689.1]
99
110639878_Cytophaga_hutchinsonii_ATCC_33406
33595131_Bordetella_parapertussis_12822
162453820_Sorangium_cellulosum_So_ce_56
94970668_Acidobacteria_bacterium_Ellin345
83649542_Hahella_chejuensis_KCTC_2396
13470340_Mesorhizobium_loti_MAFF303099
94
157369709_Serratia_proteamaculans_568
73
170747096_Methylobacterium_radiotolerans_JCM_2831
65
170744631_Methylobacterium_sp_4−46
23
.5._50405503_Debaryomyces_hansenii
100
.5._Pist50195_Pichia_stipitis
100
.5._C19_7098_Candida_albicans_SC5314
57
.5._UM00224_Ustilago_maydis
.5._50556894_Yarrowia_lipolytica
.5._CNAG_04964_Cryptococcus_neoformans
70
.5._Neha43139_Nectria_haematococca
94
.5._FGSG_04209_Fusarium_graminearum
44
.5._Trvi47715_Trichoderma_virens
13
12
.5._Trvi47554_Trichoderma_virens
.5._FVEG01722_Fusarium_verticillioides
46
.5._Trre112330_Trichoderma_reesei
75
5
.5._Trvi51254_Trichoderma_virens
99
.5._Trat7364_Trichoderma_atoviride
9
.5._AFL03755_Aspergillus_flavus
.5._BC1G_00739_Botrytis_cinerea
23
16
.5._A011000567_Aspergillus_oryzae
100
.5._Asni42622_Aspergillus_niger
5
.5._NFIA073130_Neosartorya_fischeri
.5._Asni43980_Aspergillus_niger
22
0
64
.5._AN10108_Aspergillus_nidulans
62
14
.5._ATEG_10059_Aspergillus_terreus
13
34
.5._CPSG03843_Coccidioides_posadasii
1
.5._ACLA016780_Aspergillus_clavatus
1
.5._MGG_09031_Magnaporthe_grisea
0
.5._Cohe106436_Cochliobolus_heterostrophus
4
36
.5._Phch139578_Phanerochaete_chrysosporium
18
Phra83543_Phytophthora_ramorum
.5._Asni187015_Aspergillus_nige
r
80
.5._A003001422_Aspergillus_oryzae
15
.5._CHG07501_Chaetomium_globosum
.5._Neha95966_Nectria_haematococca
94
.5._FGSG_07583_Fusarium_graminearum
89
.5._FVEG12686_Fusarium_verticillioides
26
.5._VDAG_02531_Verticillium_dahliae
96
.5._VDAG_04838_Verticillium_dahliae
94967306_Acidobacteria_bacterium_Ellin345
13475160_Mesorhizobium_loti_MAFF303099
21
100
126464903_Rhodobacter_sphaeroides_ATCC_17029
29
28
71735349_Pseudomonas_syringae_pv_phaseolicola_1448A
99
Fungi
25
148550452_Pseudomonas_putida_F
1
148260466_Acidiphilium_cryptum_JF−5
Oomycetes
118473404_Mycobacterium_smegmatis_str_MC2_155
35
100
169631865_Mycobacterium_abscessus
56
Support for with Fungi
158316551_Frankia_sp_EAN1pec
90
111223158_Frankia_alni_ACN14a
2
77
116671001_Arthrobacter_sp_FB24
Support for within Fungi
100
119960565_Arthrobacter_aurescens_TC1
171061004_Leptothrix_cholodnii_SP−6
79
89902156_Rhodoferax_ferrireducens_T118
85
171056719_Leptothrix_cholodnii_SP−6
7
119898744_Azoarcus_sp_BH72
16
92113282_Chromohalobacter_salexigens_DSM_3043
34
15838632_Xylella_fastidiosa_9a5c
79
89056159_Jannaschia_sp_CCS1
3
Eubacteria
99
100
100
89
83
27
66
45
25
34
52
82
93
30
56
148264565_Geobacter_uraniireducens_Rf4
100
0.3
116254192_Rhizobium_leguminosarum_bv_viciae_3841
87
100
82
Prokaryotes
52
Prokaryotes
16263884_Sinorhizobium_meliloti_1021
73542755_Ralstonia_eutropha_JMP134
77459652_Pseudomonas_fluorescens_PfO−1
100
78061486_Burkholderia_sp_383
16081338_Thermoplasma_acidophilum_DSM_1728
16263649_Sinorhizobium_meliloti_1021
Prokaryotes
Fig. 1.12
Support for within Fungi
Support for with Fungi
Oomycetes
Fungi
16077432_Bacillus_subtilis_subsp_subtilis_str_168
15803255_Escherichia_coli_O157_H7_EDL933
100
134098658_Saccharopolyspora_erythraea_NRRL_2338
100
146275487_Novosphingobium_aromaticivorans_DSM_12444
54
83589249_Moorella_thermoacetica_ATCC_39073
159036708_Salinispora_arenicola_CNS−205
100
123443235_Yersinia_enterocolitica_subsp_enterocolitica_8081
.5._A003000424_Aspergillus_oryzae
100
.5._Asni141117_Aspergillus_niger
.5._FOXG_02622_Fusarium_oxysporum
71
.5._AB10285_Alternaria_brassicicola
68
100
.5._FGSG_04669_Fusarium_graminearum
56
.5._Cohe76450_Cochliobolus_heterostrophus
.5._FVEG03405_Fusarium_verticillioides
99
.5._FOXG_13395_Fusarium_oxysporum
77
.5._CNAG_03519_Cryptococcus_neoformans
27 100
.5._A001000093_Aspergillus_oryzae
.5._NFIA026010_Neosartorya_fischeri
19
100 Phra85044_Phytophthora_ramorum
55
55 45
Phso117491_Phytophthora_sojae
.5._ATEG_10347_Aspergillus_terreus
60
90
.5._Asni44615_Aspergillus_niger
.5._Trat53567_Trichoderma_atoviride
96
45
.5._Trvi69398_Trichoderma_virens
62
63
82
.5._Trat35115_Trichoderma_atoviride
100
.5._Trvi53354_Trichoderma_virens
61
.5._Neha55997_Nectria_haematococca
.5._BC1G_15775_Botrytis_cinerea
.5._6320748_Saccharomyces_cerevisiae
100
.5._50425933_Debaryomyces_hanseni
i
Asni42056_Aspergillus_niger
76
152987714_Pseudomonas_aeruginosa_PA7
56477195_Azoarcus_sp_EbN1
Natrialba magadii ATCC 43099_[ZP_03692419.1]
88
55380295_Haloarcula_marismortui_ATCC_43049
76802345_Natronomonas_pharaonis_DSM_2160
78223309_Geobacter_metallireducens_GS−15
58616487_Azoarcus_sp_EbN1
56478650_Azoarcus_sp_EbN1
40
32
41407735_Mycobacterium_avium_subsp_paratuberculosis_K−10
60
110635255_Mesorhizobium_sp_BNC1
14
15920229_Sulfolobus_tokodaii_str_7
100
70607772_Sulfolobus_acidocaldarius_DSM_639
148553827_Sphingomonas_wittichii_RW1
100
50
50
47
35
58
24
99
Trichoplax adhaerens_[XP_002110338.1]
Mus musculus_[NP_653103.1]
Homo sapiens_[NP_203740.1]
97
Bos taurus_[NP_001095445.1]
100
80
99
0.4
Fig. 1.13
Support for within Fungi
Support for with Fungi
Oomycetes
Sbi5060329_Sorghum_bicolor
115463311_Oryza_sativa
Potr808742_Populus_trichocarpa
90
15230555_Arabidopsis_thaliana
Semo90159_Selaginella_moellendorffii
100
81
Semo91570_Selaginella_moellendorffii
Potr177316_Populus_trichocarpa
75
77
79318998_Arabidopsis_thaliana
87
100
115469468_Oryza_sativa
73
Sbi146894_Sorghum_bicolor
Sbi128220_Sorghum_bicolor
88
Potr269235_Populus_trichocarpa
Physarum polycephalum TBestDB_PPL00000684_Patellin
Polysphondylium pallidum PN500_[EFA84049.1]
99
66826247_Dictyostelium_discoideum
100
Dipu152120_Dictyostelium_purpureum
Voca60677_Volvox_carteri
100
Chre111979_Chlamydomonas_reinhardtii
.5._Muci71097_Mucor_circinelloides
99
.5._RO3G_05646_Rhizopus_oryzae
.5._Phybl77187_Phycomyces_blakesleeanus
.5._Scco53657_Schizophyllum_commune
87
.5._Labi305410_Laccaria_bicolor
99
.5._CC1G_05714_Coprinus_cinereus
100
.5._Popl121949_Postia_placenta
59
.5._Phch2149_Phanerochaete_chrysosporium
.2._50550241_Yarrowia_lipolytica
.2._50415512_Debaryomyces_hansenii
100
43
.2._Pist30049_Pichia_stipitis
92
.2._C19_4897_Candida_albicans_SC5314
93
.2._6322316_Saccharomyces_cerevisiae
99
.2._50290153_Candida_glabrata
100
.2._45185933_Ashbya_gossypii
99
.1._BC1G_07204_Botrytis_cinerea
.1._SS1G_10044_Sclerotinia_sclerotiorum
97 .1._BDBG_01342_Blastomyces_dermatitidis
.1._HCAG_00557_Histoplasma_capsulatum
.1._MCYG_01818_Microsporum_canis
98
34
.1._MGYG_04250_Microsporum_gypseum
55
.1._TEQG_03525_Trichophyton_equinum
79
93
.1._UREG_03863_Uncinocarpus_reesii
50
92
.1._CIMG_06582_Coccidioides_immitis
.1._AN8233_Aspergillus_nidulans
53
100
.1._ATEG_08041_Aspergillus_terreus
59
.1._A102000579_Aspergillus_oryzae
79
.1._ACLA001490_Aspergillus_clavatus
47
73
.1._Afu5g03690_Aspergillus_fumigatus
.1._Neha16399_Nectria_haematococca
85
.1._FVEG02522_Fusarium_verticillioides
88
.1._FGSG_08917_Fusarium_graminearum
95
.1._Trat149651_Trichoderma_atoviride
88
60
.1._Trvi4652_Trichoderma_virens
34
.1._MGG_09991_Magnaporthe_grisea
.1._NCU02200_Neurospora_crassa
100
.1._Crpa107405_Cryphonectria_parasitica
26
40
.1._VDBG_10048_Verticillium_albo−atrum
23
.1._Pa_5_9800_Podospora_anserina
38
.1._CHG11078_Chaetomium_globosum
73
Phra96851_Phytophthora_ramorum
97
Phca112296_Phytophthora_capsici
Phso158206_Phytophthora_sojae
72
83
.1._Myfi58084_Mycosphaerella_fijiensis
.1._AB01938_Alternaria_brassicicola
78
94
.1._PTRG_08463_Pyrenophora_tritici−repentis
64
90
.1._Cohe39574_Cochliobolus_heterostrophus
Fungi
.1._SNU02554_Stagonospora_nodorum
.4._CNAG_02104_Cryptococcus_neoformans
99
7
7
34
23
20
41
70
70
98
95
44
47
33
93
99
56
99
97
100
53
39
38
0. 3
Fig. 1.14
Support for within Fungi
Support for with Fungi
Oomycetes
Fungi
Stenotrophomonas maltophilia K279a_[YP_001973448.1]
54027206_Nocardia_farcinica_IFM_10152
Gordonia bronchialis DSM 43247_[YP_003271501.1]
172041531_Corynebacterium_urealyticum_DSM_7109
99
65
68537051_Corynebacterium_jeikeium_K411
145224503_Mycobacterium_gilvum_PYR−GCK
38
73
126434485_Mycobacterium_sp_JLS
87
118472890_Mycobacterium_smegmatis_str_MC2_155
37
Tsukamurella paurometabola DSM 20162_[ZP_04027842.1]
111021270_Rhodococcus_sp_RHA1
126442405_Burkholderia_pseudomallei_668
100
71737174_Pseudomonas_syringae_pv_phaseolicola_1448A
100 78063461_Burkholderia_sp_383
116691623_Burkholderia_cenocepacia_HI2424
58038990_Gluconobacter_oxydans_621H
169633155_Acinetobacter_baumannii
100
50085360_Acinetobacter_sp_ADP1
Streptomyces sp SPB78_[ZP_05489172.1]
Streptomyces sp SPB74_[ZP_04993103.1]
54025105_Nocardia_farcinica_IFM_10152
110633778_Mesorhizobium_sp_BNC1
Conexibacter woesei DSM 14684_[ADB52238.1]
145589616_Polynucleobacter_sp_QLW−P1DMWA−1
100
145588737_Polynucleobacter_sp_QLW−P1DMWA− 1
Micrococcus luteus NCTC 2665_[YP_002956320.1]
32
Saccharomonospora viridis DSM 43017_[YP_003135592.1]
34
118462549_Mycobacterium_avium_104
45
Rhodococcus jostii RHA1_[YP_702626.1]
113866902_Ralstonia_eutropha_H16
27
111224342_Frankia_alni_ACN14a
158422570_Azorhizobium_caulinodans_ORS_571
145222588_Mycobacterium_gilvum_PYR−GCK
111022005_Rhodococcus_sp_RHA1
.1._MGG_01882_Magnaporthe_grise a
.1._MGG_14628_Magnaporthe_grise a
100
37
.1._AFL00519_Aspergillus_flavus
46
.1._FVEG12539_Fusarium_verticillioide s
54
55
.1._FGSG_07671_Fusarium_graminearum
.1._Neha92081_Nectria_haematococca
.1._SNU10223_Stagonospora_nodorum
.1._FOXG_17164_Fusarium_oxysporum
99
.1._FVEG13050_Fusarium_verticillioide s
98
89
.1._Neha86384_Nectria_haematococca
94
.1._Afu3g03890_Aspergillus_fumigatus
100
.1._NFIA006160_Neosartorya_fischeri
71
.1._Trat92447_Trichoderma_atoviride
86
.1._Neha84257_Nectria_haematococca
98
.1._FOXG_10357_Fusarium_oxysporum
.1._Trvi53621_Trichoderma_virens
100
.1._Trat4807_Trichoderma_atoviride
100
Phso133521_Phytophthora_sojae
79
.1._FOXG_02481_Fusarium_oxysporum
46
.1._NFIA100340_Neosartorya_fischeri
100
.1._AFL00476_Aspergillus_flavus
68
.1._BC1G_09791_Botrytis_cinerea
100
.1._SS1G_05612_Sclerotinia_sclerotiorum
134101315_Saccharopolyspora_erythraea_NRRL_2338
119715217_Nocardioides_sp_JS614
100
35
Streptomyces roseosporus NRRL 15998_[ZP_04697640.1]
Streptomyces albus J1074_[ZP_04704394.1]
Outgroup
33
81
32
35
7
71
111024052_Rhodococcus_sp_RHA1
118468410_Mycobacterium_smegmatis_str_MC2_155
Streptomyces scabiei 8722_[CBG67513.1]
100
Streptomyces sviceus ATCC 29083_[ZP_05018032.1]
162448444_Sorangium_cellulosum_So_ce_56
.1._Trvi40028_Trichoderma_virens
.1._SNU16360_Stagonospora_nodorum
.1._Trvi29562_Trichoderma_virens
48
.1._Trvi25763_Trichoderma_virens
60
100
.1._Trat33769_Trichoderma_atoviride
.1._MCYG_02756_Microsporum_canis
29
100
.1._TEQG_04124_Trichophyton_equinum
45
.1._PABG03456_Paracoccidioides_brasiliensis
29
.1._ACLA062740_Aspergillus_clavatus
100
.1._NFIA061970_Neosartorya_fischeri
.1._BC1G_02285_Botrytis_cinerea
26
.1._SNU11286_Stagonospora_nodorum
.1._Pa_6_670_Podospora_anserina
.1._Crpa62371_Cryphonectria_parasitica
.1._Trre69742_Trichoderma_reesei
63
9
100
.1._Trat82720_Trichoderma_atoviride
0
61
.1._BC1G_07453_Botrytis_cinerea
100
100
.1._SS1G_08558_Sclerotinia_sclerotiorum
83
.1._NFIA055750_Neosartorya_fischeri
.1._Afu4g08715_Aspergillus_fumigatus
99
4
.1._NFIA007730_Neosartorya_fischeri
.1._Trat89998_Trichoderma_atoviride
0
50
75
.1._MCYG_07748_Microsporum_canis
81
.1._TEQG_00225_Trichophyton_equinum
4
98
.1._MGYG_05011_Microsporum_gypseum
.1._SS1G_11027_Sclerotinia_sclerotiorum
.1._Cohe33422_Cochliobolus_heterostrophus
2
.1._PGTG_04947_Puccinia_graminis
.1._CPSG04973_Coccidioides_posadasii
26
20
0
.1._AN7130_Aspergillus_nidulans
100
.1._AFL11331_Aspergillus_flavus
64
.1._ATEG_10124_Aspergillus_terreus
.1._Pa_1_17940_Podospora_anserina
100
.1._PTRG_09106_Pyrenophora_tritici−repentis
40
.1._MCYG_00162_Microsporum_canis
100
.1._TEQG_02557_Trichophyton_equinum
1
.1._HCAG_05093_Histoplasma_capsulatum
1
0
.1._SS1G_07096_Sclerotinia_sclerotiorum
.1._ATEG_06645_Aspergillus_terreus
23
.1._FGSG_03116_Fusarium_graminearum
100
.1._FVEG10840_Fusarium_verticillioides
.1._Asni142878_Aspergillus_niger
.1._AN10320_Aspergillus_nidulans
Phso142730_Phytophthora_sojae
0
100
.1._Crpa98228_Cryphonectria_parasitica
14
74
.1._FGSG_03658_Fusarium_graminearum
26
97
.1._FVEG08764_Fusarium_verticillioides
31
76
.1._FVEG03542_Fusarium_verticillioides
100
90
.1._FGSG_10086_Fusarium_graminearum
45
.1._Neha56035_Nectria_haematococca
.1._Cohe97364_Cochliobolus_heterostrophus
.1._Crpa93693_Cryphonectria_parasitica
12
45
.1._MGG_13101_Magnaporthe_grisea
75
.1._NCU09845_Neurospora_crassa
96
47
.1._CHG04367_Chaetomium_globosum
59
.1._MGG_07850_Magnaporthe_grisea
58
.1._Asni191756_Aspergillus_niger
62
.1._AN2942_Aspergillus_nidulans
34
24
.1._Cohe58680_Cochliobolus_heterostrophus
3
.1._A102000287_Aspergillus_oryzae
56
.1._CPSG00642_Coccidioides_posadasii
.1._MGG_09610_Magnaporthe_grisea
.1._Asni42613_Aspergillus_niger
99
.1._Myfi30650_Mycosphaerella_fijiensis
.1._Mygr70724_Mycosphaerella_graminicola
32
.1._Mygr17842_Mycosphaerella_graminicola
95
.1._Mygr32167_Mycosphaerella_graminicola
4
.1._Neha43023_Nectria_haematococca
42
Fungi
.1._VDBG_09093_Verticillium_albo−atrum
54
.1._Neha85253_Nectria_haematococca
Oomycetes
0.3
Support for with Fungi
Support for within Fungi
Fig. 1.15
11
65
147678016_Pelotomaculum_thermopropionicum_SI
116624463_Solibacter_usitatus_Ellin6076
148260656_Acidiphilium_cryptum_JF−5
119714375_Nocardioides_sp_JS614
94
NODE_7678_Hyphochytrium
126699894_Clostridium_difficile_630
46
100
150015434_Clostridium_beijerinckii_NCIMB_8052
99
126698067_Clostridium_difficile_630
16799581_Listeria_innocua_Clip11262
65
15612750_Bacillus_halodurans_C−125
97
78
56965104_Bacillus_clausii_KSM−K16
64
82749956_Staphylococcus_aureus_RF122
159046682_Dinoroseobacter_shibae_DFL_12
100
30018850_Bacillus_cereus_ATCC_14579
96
23100808_Oceanobacillus_iheyensis_HTE831
53
116052136_Pseudomonas_aeruginosa_UCBPP−PA14
100
115359746_Burkholderia_ambifaria_AMMD
159040760_Caldivirga_maquilingensis_IC−167
43
32473990_Rhodopirellula_baltica_SH_1
100
116626572_Solibacter_usitatus_Ellin6076
0
5
2
4
Outgroup
5
12
14
78043661_Carboxydothermus_hydrogenoformans_Z−2901
16272027_Haemophilus_influenzae_Rd_KW20
125972909_Clostridium_thermocellum_ATCC_27405
23100713_Oceanobacillus_iheyensis_HTE831
47
99
5
2
Outgroups
100
89
15
50
14
29
44
.5._Phybl35906_Phycomyces_blakesleeanus
.5._Trvi64876_Trichoderma_virens
88
.5._Asni37988_Aspergillus_niger
100
.5._Mygr31918_Mycosphaerella_graminicola
85
.5._Myfi85679_Mycosphaerella_fijiensis
86
.5._Neha81006_Nectria_haematococca
.5._19111912_Schizosaccharomyces_pombe
12 30
.5._UM02150_Ustilago_maydis
.5._Pist86924_Pichia_stipitis
99
.5._50410146_Debaryomyces_hansenii
22
69
57
.5._C19_7676_Candida_albicans_SC5314
55
.5._45185461_Ashbya_gossypii
61
.5._6319955_Saccharomyces_cerevisiae
87
50
.5._6323099_Saccharomyces_cerevisiae
.5._50552908_Yarrowia_lipolytica
.4._Scco64180_Schizophyllum_commune
.4._CC1G_00399_Coprinus_cinereus
79
.4._Labi188827_Laccaria_bicolor
94
29
.4._Phch1675_Phanerochaete_chrysosporium
79
.4._Popl110360_Postia_placenta
66
83
.4._CNAG_00269_Cryptococcus_neoformans
65
.4._CNAG_00115_Cryptococcus_neoformans
76
.4._Spro15345_Sporobolomyces_roseus
.1._Mygr70997_Mycosphaerella_graminicola
65
.1._Myfi89205_Mycosphaerella_fijiensis
48
Phca114955_Phytophthora_capsici
100
94 PITG_04121_Phytophthora_infestans
PITG_04989_Phytophthora_infestans
67
.1._SNU11390_Stagonospora_nodorum
.1._Cohe114076_Cochliobolus_heterostrophus
100
78 .1._PTRG_04783_Pyrenophora_tritici−repentis
.1._A020000647_Aspergillus_oryzae
38 .1._Afu7g02550_Aspergillus_fumigatus
57
.1._Asni203198_Aspergillus_niger
68
31
7
.1._A038000631_Aspergillus_oryzae
72
46 25 .1._AN9064_Aspergillus_nidulans
.1._ATEG_01882_Aspergillus_terreus
.1._ACLA065000_Aspergillus_clavatus
.1._MCYG_06103_Microsporum_canis
29 100 .1._TEQG_07046_Trichophyton_equinum
50 .1._MGYG_05846_Microsporum_gypseum
.1._CPSG05546_Coccidioides_posadasii
77
33
97 .1._UREG_07581_Uncinocarpus_reesii
.1._BDBG_02009_Blastomyces_dermatitidis
43 98
37
.1._PABG01429_Paracoccidioides_brasiliensis
100 .1._BC1G_09425_Botrytis_cinerea
.1._SS1G_05978_Sclerotinia_sclerotiorum
.1._NCU00891_Neurospora_crassa
100
.1._MGG_01176_Magnaporthe_grisea
22
35
.1._CHG01963_Chaetomium_globosum
.1._VDAG_06181_Verticillium_dahliae
50 57
43 .1._Pa_1_1490_Podospora_anserina
.1._Trat129143_Trichoderma_atoviride
25
89.1._Trre81271_Trichoderma_reesei
93 .1._FGSG_04922_Fusarium_graminearum
37
.1._FVEG03564_Fusarium_verticillioides
.1._Neha99030_Nectria_haematococca
49 74
.1._Crpa107356_Cryphonectria_parasitica
100
.1._Cohe110673_Cochliobolus_heterostrophus
54
.1._SNU14172_Stagonospora_nodorum
100
.1._NFIA098450_Neosartorya_fischeri
.1._Neha96600_Nectria_haematococca
100
.1._FGSG_04247_Fusarium_graminearum
.1._FVEG10437_Fusarium_verticillioides
98
44
.1._Afu1g11030_Aspergillus_fumigatus
74 79
.1._NFIA095670_Neosartorya_fischeri
.1._Asni53356_Aspergillus_niger
50
.1._AN2666_Aspergillus_nidulans
59
98
.1._AFL10710_Aspergillus_flavus
.1._SNU15160_Stagonospora_nodorum
.5._Muci78258_Mucor_circinelloides
.5._ACLA021030_Aspergillus_clavatus
.5._CPSG06884_Coccidioides_posadasii
100 100
.5._UREG_07050_Uncinocarpus_reesii
74
.5._BDBG_06386_Blastomyces_dermatitidis
53
.5._HCAG_02323_Histoplasma_capsulatum
100
.5._MGG_13917_Magnaporthe_grisea
100 .5._BC1G_12937_Botrytis_cinerea
83 70
.5._SS1G_12678_Sclerotinia_sclerotiorum
44
.5._Trre76784_Trichoderma_reesei
58
.5._VDAG_04952_Verticillium_dahliae
32
.5._Crpa100120_Cryphonectria_parasitica
28
62
.5._Pa_1_21070_Podospora_anserina
66
.5._CHG06639_Chaetomium_globosum
.5._Mygr98589_Mycosphaerella_graminicola
92
79
.5._AB07198_Alternaria_brassicicola
100 .5._Cohe80562_Cochliobolus_heterostrophus
.5._Scco86257_Schizophyllum_commune
98
.5._Phch136745_Phanerochaete_chrysosporium
44
.5._Popl60468_Postia_placenta
48
.5._CC1G_07722_Coprinus_cinereus
73
64
.5._Labi174052_Laccaria_bicolor
.5._CNAG_04677_Cryptococcus_neoformans
55
.5._Mela39449_Melampsora_laricis−populina
CMA009C_Cyanidioschyzon_merolae
ChNC30796_Chlorella_NC64A
88
Semo271876_Selaginella_moellendorffii
80
115477633_Oryza_sativa
77
Sbi4891452_Sorghum_bicolor
27
97
15242240_Arabidopsis_thaliana
81
6229Potr823499_Populus_trichocarpa
Potr422575_Populus_trichocarpa
97
Phpa150811_Physcomitrella_patens
96
Phpa179590_Physcomitrella_patens
Sorbitol dehydrogenase_[EER19926.1]
17562878_Caenorhabditis_elegans
100
17562876_Caenorhabditis_elegans
20
Ciin387979_Ciona_intestinalis
Taru578893_Takifugu_rubripes
100
41 924507155_Homo_sapiens
22128627_Mus_musculus
50752703_Gallus_gallus
73
29
77 Xetr456369_Xenopus_tropicalis
Logi208637_Lottia_gigantea
41
17137530_Drosophila_melanogaster
69 40
100
17737897_Drosophila_melanogaster
64
Dapu303131_Daphnia_pulex
Logi205809_Lottia_gigantea
53
CapI149787_Capitella_sp_I
Phybl36787_Phycomyces_blakesleeanus
100
Muci95700_Mucor_circinelloides
Pist40172_Pichia_stipitis
24
100
50415925_Debaryomyces_hansenii
96
VDAG_05086_Verticillium_dahliae
99
AB00332_Alternaria_brassicicola
54
Myfi39289_Mycosphaerella_fijiensis
PGTG_16500_Puccinia_graminis
30
97
PGTG_16501_Puccinia_graminis
100
Mela74240_Melampsora_laricis−populina
96
55
PGTG_15701_Puccinia_graminis
71
50417778_Debaryomyces_hansenii
AB03193_Alternaria_brassicicola
99
89
PTRG_04786_Pyrenophora_tritici−repentis
ACLA019290_Aspergillus_clavatus
97
80
BDBG_07601_Blastomyces_dermatitidis
SS1G_05959_Sclerotinia_sclerotiorum
100
38 BC1G_15180_Botrytis_cinerea
96
VDBG_07375_Verticillium_albo−atrum
Crpa91631_Cryphonectria_parasitica
26 52
Trat153403_Trichoderma_atoviride
27 95
Trre49753_Trichoderma_reesei
36
FGSG_00655_Fusarium_graminearum
51
99
FVEG00541_Fusarium_verticillioides
Pa_1_2490_Podospora_anserina
6265 MGG_01231_Magnaporthe_grisea
34CHG01694_Chaetomium_globosum
NCU00643_Neurospora_crassa
UM00418_Ustilago_maydis
0.3
Fungi
Oomycetes
Support for with Fungi
Support for within Fungi
Fig. 1.16
32
32
8
28
62
21
91
8
24
30
22
98
92
0.2
Fig. 1.17
Reinekea sp MED297_[ZP_01114943.1]
Cellulomonas flavigena DSM 20109_[ZP_04367696.1]
Sanguibacter keddieii DSM 10542_[YP_003313251.1]
Arabinan endo−1_[YP_003160483.1]
arabinan endo−1_[YP_526488.1]
99
154687015_Bacillus_amyloliquefaciens_FZB42
79
46
52081383_Bacillus_licheniformis_ATCC_14580
Geobacillus stearothermophilus_[ACE73676.1]
arabinan endo−1_[YP_526260.1]
endo−1_[YP_734125.1]
96
100 arabinanarabinan
endo−1_[YP_963350.1]
61
71
arabinanase and alpha−L−arabinofuranosidase_[YP_001981313.1]
Leeuwenhoekiella
blandensis MED217_[ZP_01060796.1]
86
76
arabinan endo−1_[YP_860738.1]
Arabinan endo−1_[YP_003088651.1]
42
arabinan endo−1_[ZP_06252944.1]
162449756_Sorangium_cellulosum_So_ce_56
43
Clostridium cellulovorans 743B_[ZP_04806637.1]
18
100
Thermoanaerobacterium thermosaccharolyticum DSM 571_[ZP_05336780.1]
Bacillus cellulosilyticus DSM 2522_[ZP_06361511.1]
arabinan endo−1_[ZP_05282180.1]
100
cellulosilyticus DSM 14838_[ZP_03677432.1]
54
98 Bacteroides
23
Bacteroides uniformis ATCC 8492_[ZP_02069669.1]
100
Prevotella oris F0302_[ZP_06256859.1]
100 Prevotella
94
76
sp oral taxon 472 str F0295_[ZP_05917953.1]
arabinan endo−1_[ZP_01718643.1]
100
Halorhabdus utahensis DSM 12940_[YP_003131348.1]
21
arabinan endo−1_[YP_705329.1]
Solibacter usitatus Ellin6076_[YP_825687.1]
Arabinan endo−1_[YP_003323923.1]
Fibrobacter succinogenes subsp succinogenes S85_[YP_003250688.1]
100
Fibrobacter succinogenes subsp succinogenes S85_[YP_003250689.1]
38
152964049_Kineococcus_radiotolerans_SRS30216
Streptomyces sviceus ATCC 29083_[ZP_05018517.1]
100
21220892_Streptomyces_coelicolor_A3
Thermomonospora curvata DSM 43183_[YP_003300396.1]
.5._Scco233313_Schizophyllum_commune
.5._Crpa39058_Cryphonectria_parasitica
.5._A138000055_Aspergillus_oryzae
36
.5._AN8007_Aspergillus_nidulans
46
30
.5._ATEG_03688_Aspergillus_terreus
65
89
.5._NFIA047920_Neosartorya_fischeri
100
.5._Afu6g00770_Aspergillus_fumigatus
95
.5._ACLA098980_Aspergillus_clavatus
29
.5._Asni197735_Aspergillus_niger
.5._MGG_02373_Magnaporthe_grisea
32
74
.5._Crpa68782_Cryphonectria_parasitica
.5._Crpa43708_Cryphonectria_parasitica
31
.5._Mela33109_Melampsora_laricis−populina
98
.5._Mela53635_Melampsora_laricis−populina
100
96
.5._Mela36943_Melampsora_laricis−populina
.5._BC1G_10322_Botrytis_cinerea
99
43
.5._SS1G_11922_Sclerotinia_sclerotiorum
.5._Asni203143_Aspergillus_niger
89 .5._NFIA062660_Neosartorya_fischeri
26
.5._ACLA042100_Aspergillus_clavatus
.5._AN2534_Aspergillus_nidulans
18
.5._A701000481_Aspergillus_oryzae
7
.5._HCAG_04127_Histoplasma_capsulatum
14
100
.5._BDBG_01737_Blastomyces_dermatitidis
11
12
.5._ATEG_03520_Aspergillus_terreus
Hyp702714_Hyaloperonospora_parasitica
100
Phca20921_Phytophthora_capsici
93
Phso108739_Phytophthora_sojae
63 Phra71648_Phytophthora_ramorum
.5._Myfi35447_Mycosphaerella_fijiensis
12
53
.5._SNU06043_Stagonospora_nodorum
100
.5._Cohe75928_Cochliobolus_heterostrophus
.5._PTRG_09645_Pyrenophora_tritici−repentis
100
10
.5._AB06680_Alternaria_brassicicola
.5._SNU13084_Stagonospora_nodorum
37
.5._Neha53602_Nectria_haematococca
89
34
.5._CHG02150_Chaetomium_globosum
100 Phso144175_Phytophthora_sojae
37
Phso145393_Phytophthora_sojae
44
100
Phca68901_Phytophthora_capsici
87 Phra75229_Phytophthora_ramorum
Phca21206_Phytophthora_capsici
37
83 100 Phso109739_Phytophthora_sojae
Phso109619_Phytophthora_sojae
71 100 Phra75232_Phytophthora_ramorum
57
Phra75228_Phytophthora_ramorum
Phca21135_Phytophthora_capsici
76 Phca35864_Phytophthora_capsici
Fungi
Phra75237_Phytophthora_ramorum
98
Phca26385_Phytophthora_capsici
78
Phra75238_Phytophthora_ramorum
90
Oomycetes
Phso144182_Phytophthora_sojae
74
98 Phso144181_Phytophthora_sojae
.5._Scco232783_Schizophyllum_commune
Support for with Fungi
.5._ATEG_01407_Aspergillus_terreus
74
29
.5._Asni134398_Aspergillus_niger
.5._NFIA008030_Neosartorya_fischeri
100
Support for within Fungi
85
.5._ACLA037080_Aspergillus_clavatus
72
95
.5._A005001320_Aspergillus_oryzae
.5._CPSG04136_Coccidioides_posadasii
.5._RO3G_16784_Rhizopus_oryzae
Arabinan endo−1_[YP_003101479.1]
Arabinan endo−1_[ZP_06217088.1]
53
Nocardiopsis dassonvillei subsp dassonvillei DSM 43111_[ZP_04335564.1]
FGSG_03002_Fusarium_graminearum
85
Neha93138_Nectria_haematococca
94
CHG10959_Chaetomium_globosum
68
VDAG_03708_Verticillium_dahliae
77
100
100
25
55
100
21
44
0.5
100
Fig. 1.18
Support for within Fungi
Support for with Fungi
Oomycetes
Fungi
.1._MGG_00158_Magnaporthe_grisea
.1._SS1G_06006_Sclerotinia_sclerotiorum
.1._BC1G_01533_Botrytis_cinerea
.1._HCAG_04493_Histoplasma_capsulatum
.1._SNU09751_Stagonospora_nodorum
.1._NFIA085310_Neosartorya_fischeri
48
.1._Asni200921_Aspergillus_niger
53
71
54
.1._AFL05396_Aspergillus_flavus
100 13
.1._ACLA068940_Aspergillus_clavatus
43
.1._AN10767_Aspergillus_nidulans
75
86
.1._Myfi46231_Mycosphaerella_fijiensis
88 Phso108212_Phytophthora_sojae
Phra85201_Phytophthora_ramorum
100 Phca119127_Phytophthora_capsici
.2._Pist75870_Pichia_stipitis
100
.2._C19_333_Candida_albicans_SC5314
.2._Pist72073_Pichia_stipitis
100
100
.2._50423539_Debaryomyces_hansenii
.2._45187799_Ashbya_gossypii
63
.2._6320902_Saccharomyces_cerevisiae
58
.2._50290799_Candida_glabrata
100
52
.2._6320903_Saccharomyces_cerevisiae
98 .2._6320897_Saccharomyces_cerevisiae
20
97
.2._50285525_Candida_glabrata
66
.2._50292741_Candida_glabrata
.4._Spro14515_Sporobolomyces_roseus
100
.4._Popl119532_Postia_placenta
100
.4._Scco57332_Schizophyllum_commune
.5._Spro11294_Sporobolomyces_roseus
.5._CNAG_04276_Cryptococcus_neoformans
.5._Scco76987_Schizophyllum_commune
89
.5._Phch138287_Phanerochaete_chrysosporium
80
.5._Labi185256_Laccaria_bicolor
96
92
.5._CC1G_05220_Coprinus_cinereus
100
.5._CC1G_03606_Coprinus_cinereus
18
100
.5._CC1G_05218_Coprinus_cinereus
59
.5._FVEG08316_Fusarium_verticillioides
86
100
.5._CPSG04795_Coccidioides_posadasii
.5._UREG_06450_Uncinocarpus_reesii
100
.5._MCYG_04344_Microsporum_canis
100
.5._TEQG_01848_Trichophyton_equinum
100
.5._NCU04195_Neurospora_crassa
96
.5._Pa_2_8780_Podospora_anserina
70
28
72
.5._MGG_04868_Magnaporthe_grisea
98
82
.5._VDBG_09834_Verticillium_albo−atrum
94
100 .5._Neha88224_Nectria_haematococca
.5._FGSG_07858_Fusarium_graminearum
57
84
.5._Trre62198_Trichoderma_reesei
100
.5._Trat42174_Trichoderma_atoviride
.5._SNU05591_Stagonospora_nodorum
100
.5._PTRG_03796_Pyrenophora_tritici−repentis
100 .5._Cohe76988_Cochliobolus_heterostrophus
.5._UM04197_Ustilago_maydis
.5._CNAG_01681_Cryptococcus_neoformans
.5._Popl125785_Postia_placenta
.5._A010000345_Aspergillus_oryzae
91
.5._MCYG_02096_Microsporum_canis
100
.5._SS1G_01111_Sclerotinia_sclerotiorum
.5._Trvi3262_Trichoderma_virens
88
.5._Myfi33001_Mycosphaerella_fijiensis
.5._Mygr50627_Mycosphaerella_graminicola
76
97
.5._PTRG_08244_Pyrenophora_tritici−repentis
.5._AB01739_Alternaria_brassicicola
46
100
47
87
.5._Trre52489_Trichoderma_reesei
.5._Cohe29185_Cochliobolus_heterostrophus
96
100
57
100
.5._FGSG_13426_Fusarium_graminearum
.5._FVEG04323_Fusarium_verticillioides
.5._Crpa93902_Cryphonectria_parasitica
44
.5._Asni208782_Aspergillus_niger
100
.5._Afu2g04690_Aspergillus_fumigatus
.5._BC1G_03380_Botrytis_cinerea
82
100 .5._Trat86592_Trichoderma_atoviride
.5._Trvi52981_Trichoderma_virens
.5._Mygr98150_Mycosphaerella_graminicola
76
87
.5._SNU00497_Stagonospora_nodorum
100
.5._Cohe76653_Cochliobolus_heterostrophus
100
.5._PTRG_10627_Pyrenophora_tritici−repentis
99
72
.5._SS1G_06212_Sclerotinia_sclerotiorum
61
.5._NFIA035350_Neosartorya_fischeri
59
38
100
.5._AN4526_Aspergillus_nidulans
.5._ATEG_09594_Aspergillus_terreus
.5._FGSG_03477_Fusarium_graminearum
53
70
68
.5._FVEG13611_Fusarium_verticillioides
100
.5._Neha51571_Nectria_haematococca
.5._ACLA024620_Aspergillus_clavatus
100
.5._NFIA014750_Neosartorya_fischeri
.5._50550113_Yarrowia_lipolytica
.5._50418635_Debaryomyces_hansenii
100
.5._C19_7331_Candida_albicans_SC5314
83
68
.5._Pist30904_Pichia_stipitis
100
.5._50425821_Debaryomyces_hansenii
.5._A010000529_Aspergillus_oryzae
116672239_Arthrobacter_sp_FB24
118472142_Mycobacterium_smegmatis_str_MC2_155
Eubacteria
100
111022116_Rhodococcus_sp_RHA1
100
152966032_Kineococcus_radiotolerans_SRS30216
148260153_Acidiphilium_cryptum_JF−5
94
25
25
13
38
29
33
16
15
22
38
18
29
67
47
0.4
Outgroup
Fig. 1.19
Support for within Fungi
Support for with Fungi
Oomycetes
Fungi
uncultured bacterium_[ADB22436.1]
Haliangium ochraceum DSM 14365_[YP_003269160.1]
Enterobacter cloacae_[AAL82802.1]
Tolumonas auensis DSM 9187_[YP_002892531.1]
Thermomonospora curvata DSM 43183_[YP_003297898.1]
Stackebrandtia nassauensis DSM 44728_[ZP_04482057.1]
carboxylesterase_[YP_779190.1]
31
Mycobacterium smegmatis str MC2 155_[YP_885815.1]
Acanthamoeba polyphaga mimivirus_[YP_143260.1]
Naegleria gruberi_[EFC40261.1]
96
Naegleria gruberi_[EFC39235.1]
95
Naegleria gruberi_[EFC43050.1]
96
Naegleria gruberi_[EFC40283.1]
100
Naegleria gruberi_[EFC47534.1]
Dictyostelium discoideum AX4_[XP_639223.1]
100
Polysphondylium pallidum PN500_[EFA77234.1]
87
Dictyostelium discoideum AX4_[XP_635153.1]
100
Polysphondylium pallidum PN500_[EFA75987.1]
82
Polysphondylium pallidum PN500_[EFA76380.1]
73
Dictyostelium discoideum AX4_[XP_638123.1]
100
Dictyostelium discoideum AX4_[XP_642939.1]
Acetylcholinesterase 1 precursor_[EEQ98534.1]
100
Acetylcholinesterase precursor_[EER16155.1]
Dictyostelium discoideum_[XP_641615.1]
100
Polysphondylium pallidum PN500_[EFA85623.1]
Aspergillus niger_[XP_001396760.1]
27
Botryotinia fuckeliana B0510_[XP_001554081.1]
13
Ustilago maydis 521_[XP_756329.1]
67
Aspergillus niger_[XP_001390531.1]
100
Hypocrea lixii_[CAJ55827.1]
49
Microsporum canis CBS 113480_[EEQ34683.1]
Nectria haematococca mpVI 77−13−4_[EEU37588.1]
Verticillium albo−atrum VaMs102_[EEY23880.1]
Magnaporthe grisea 70−15_[XP_366195.1]
78
73
Nectria haematococca mpVI 77−13−4_[EEU41280.1]
100
Gibberella zeae PH−1_[XP_383777.1]
Pyrenophora tritici−repentis Pt−1C−BFP_[XP_001931605.1]
Microsporum canis CBS 113480_[EEQ35031.1]
100
Trichophyton equinum_[ACJ04072.1]
31
49
Uncinocarpus reesii 1704_[XP_002541973.1]
100
22
Coccidioides immitis RS_[XP_001248461.1]
64
75
Ajellomyces dermatitidis ER−3_[EEQ88894.1]
35
85
Ajellomyces capsulatus G186AR_[EEH06590.1]
100
33
Paracoccidioides brasiliensis Pb01_[EEH33629.1]
Penicillium marneffei_[XP_002150847.1]
100
Talaromyces stipitatus_[XP_002483257.1]
Aspergillus niger_[XP_001398185.1]
73
31
Aspergillus oryzae RIB40_[XP_001826653.1]
42
11
98
Aspergillus nidulans FGSC A4_[XP_659037.1]
9
Aspergillus clavatus_[XP_001276526.1]
91
Aspergillus fumigatus Af293_[XP_747228.1]
15
Penicillium chrysogenum isconsin 54−1255_[XP_002568149.1]
31
triacylglycerol lipase_[XP_001276526.1]
Botryotinia fuckeliana B0510_[XP_001552464.1]
Aspergillus niger_[XP_001396326.1]
64
80
Penicillium chrysogenum isconsin 54−1255_[XP_002558148.1]
45
78
Aspergillus terreus NIH2624_[XP_001211057.1]
Aspergillus flavus_[XP_002378758.1]
Penicillium marneffei_[XP_002146826.1]
100
Ajellomyces dermatitidis SLH14081_[XP_002628097.1]
.5._CNAG_02638_Cryptococcus_neoformans
.5._BC1G_02016_Botrytis_cinerea
100
Phra78870_Phytophthora_ramorum
100
64
Phra84465_Phytophthora_ramorum
31
76
Phca18274_Phytophthora_capsici
62
22
Phso141185_Phytophthora_sojae
98
Phra84466_Phytophthora_ramorum
.5._Microsporum canis CBS 113480_[EEQ34281.1]
89
.5._Nectria haematococca mpVI 77−13−4_[EEU44553.1]
47
.5._Microsporum canis CBS 113480_[EEQ28242.1]
100
.5._Microsporum canis CBS 113480_[EEQ33159.1]
85
.5._Trichophyton rubrum_[ABG67898.1]
.5._Aspergillus clavatus NRRL 1_[XP_001273084.1]
36
100
.5._Penicillium griseofulvum_[ACR02671.1]
.5._Pyrenophora tritici−repentis
100
13
.5._Pyrenophora tritici−repentis
22
.5._Penicillium chrysogenum isconsin 54−1255_[XP_002564102.1]
87
38
.5._Neosartorya fischeri NRRL 181_[XP_001262314.1]
.5._Sclerotinia sclerotiorum 1980_[XP_001586824.1]
100
.5._Botryotinia fuckeliana B0510_[XP_001547629.1]
Drosophila erecta_[XP_001979190.1]
100
Tribolium castaneum_[XP_972277.1]
Rattus norvegicus_[NP_001099645.1]
78
Mus musculus_[NP_932116.2]
100 87
Rattus norvegicus_[NP_001094469.1]
mCG142671_[EDL11234.1]
100 Mus musculus_[NP_937814.1]
EST1_MESAU RecName Full=Liver carboxylesterase Flags Precursor_[Q64419.1]
51
69
Mus musculus_[NP_598721.1]
95
Rattus norvegicus_[EDL87214.1]
95
Rattus norvegicus_[XP_212849.3]
100
.5._Nectria_haematococca_Neha92582
.5._Fusarium_graminearum_FGSG_06017
.5._PTRG_10591_Pyrenophora_tritici-repentis
73
.5._Cochliobolus_heterostrophus_Cohe15415
.5._AN3211_Aspergillus_nidulans
28
.5._GW099189_Glomus_intraradices
91
68
100 .5._Aspergillus flavus NRRL3357_[EED54123.1]
.5._AFL03025_Aspergillus_flavus
83 41
20
.5._AFL10616_Aspergillus_flavus
.5._Talaromyces stipitatus ATCC 10500_[EED23782.1]
.5._Mycgr43961_Mycosphaerella_graminicola
.5._MGG_08454_Magnaporthe grisea
100 .5._Moniliophthora perniciosa_[EF114673.1]
.5._Moniliophthora perniciosa_[XM_002388242.1]
36
.5._Moniliophthora perniciosa necrosis− and ethylene−inducing protein 1 gene _[EF109894.1]
.5._Magnaporthe grisea MGG_10532
35
100 .5._A113000178_Aspergillus_oryzae
27
66 .5._AFL08649_Aspergillus_flavus
.5._Neha53292_Nectria_haematococca
89
.5._BC1G_06310_Botrytis_cinerea
42
79
.5._Botryotinia draytonii_[CAJ31828.1]
100 57
.5._Botryotinia squamosa_[CAJ31840.1]
.5._Botrytis galanthina_[CAJ31845.1]
30
77
78
.5._SS1G_03080_Sclerotinia_sclerotiorum
.5._Neha79720_Nectria_haematococca
46
.5._FOXG_15072_Fusarium_oxysporum
100
.5._FOXG_17014_Fusarium_oxysporum
100 Pythium aphanidermatum_[AAD53944.1]
Pythium monospermum_[AAQ89593.1]
Phytophthora parasitica_[AAK19753.1]
Phso108607 Phytophthora_sojae
35
53
Phra71477 Phytophthora_ramorum
14
92 Phra76249 Phytophthora_ramorum
51
Phra42876 Phytophthora_ramorum
80
PITG_10839 Phytophthora_infestans
15
34
Phso127887 Phytophthora_sojae
PITG_00759 Phytophthora_infestans
Phso138853 Phytophthora_sojae
31
73
Hyp708904 Hyaloperonospora_parasitica
Hyp709154 Hyaloperonospora_parasitica
Hyp700841 Hyaloperonospora_parasitica
42
7
100
Hyp706365 Hyaloperonospora_parasitica
68
35
Hyp700860 Hyaloperonospora_parasitica
Hyp710771 Hyaloperonospora_parasitica
20
PITG_00957 Phytophthora_infestans
59
Phso140225 Phytophthora_sojae
54
Phra72475 Phytophthora_ramorum
100
Phra71618 Phytophthora_ramorum
44
63
Phra72165 Phytophthora_ramorum
PITG_04248 Phytophthora_infestans
99
PITG_19936 Phytophthora_infestans
Bacillus subtilis subsp spizizenii ATCC 6633_[ZP_06873106.1]
50
Bacillus halodurans C−125_[NP_241261.1]
99
Bacillus licheniformis ATCC 14580_[YP_078774.1]
71
Sinorhizobium medicae WSM419_[YP_001327306.1]
94
Sinorhizobium medicae SM419_[YP_001327532.1]
97
46
71
Fungi
0.3
Oomycetes
Support for with Fungi
Support for within Fungi
Fig. 1.20
97
97
64
0.4
36
Fig. 1.21
Burkholderia multivorans CGD2M_[ZP_03575028.1]
Cyanothece sp PCC 7822_[ZP_03155100.1]
Parachlamydia acanthamoebae str Hall’s coccus_[ZP_06299161.1]
53
Halorhabdus utahensis DSM 12940_[YP_003130165.1]
72
Rhodococcus erythropolis SK121_[ZP_04385553.1]
100
Rhodococcus erythropolis PR4_[YP_002768942.1]
Thermomicrobium roseum DSM 5159_[YP_002523353.1]
72
Streptomyces scabiei 8722_[CBG67736.1]
100
Streptomyces hygroscopicus ATCC 53653_[ZP_05515385.1]
64
Streptomyces viridochromogenes DSM 40736_[ZP_05532166.1]
99 .6._Phra79223_Phytophthora_ramorum
62
.6._Phra79224_Phytophthora_ramorum
.6._Phca39518_Phytophthora_capsici
25
.6._Phso139112_Phytophthora_sojae
87
.6._Phra80592_Phytophthora_ramorum
100 .6._Phra80591_Phytophthora_ramorum
.6._Phra86219_Phytophthora_ramorum
.6._Phso139106_Phytophthora_sojae
82
.6._PITG_02685_Phytophthora_infestans
60
.6._Phca18502_Phytophthora_capsici
66
.6._Phra79219_Phytophthora_ramorum
54
100 .6._Phca96147_Phytophthora_capsici
.6._Phca44084_Phytophthora_capsici
89
.6._PITG_02688_Phytophthora_infestans
.6._Phso139107_Phytophthora_sojae
52
68
.6._Phra79222_Phytophthora_ramorum
39
100 .6._Phso139127_Phytophthora_sojae
.6._Phso139122_Phytophthora_sojae
Myfi51336_Mycosphaerella_fijiensis
87
Mygr70873_Mycosphaerella_graminicola
SNU02817_Stagonospora_nodorum
32
AB08301_Alternaria_brassicicola
AN3616_Aspergillus_nidulans
26
89 AFL11767_Aspergillus_flavus
81
NFIA000880_Neosartorya_fischeri
48
ATEG_02895_Aspergillus_terreus
9
Afu3g00350_Aspergillus_fumigatus
Asni44778_Aspergillus_niger
51
Cohe93912_Cochliobolus_heterostrophus
71
PTRG_01914_Pyrenophora_tritici−repentis
93 FGSG_13560_Fusarium_graminearum
FOXG_05897_Fusarium_oxysporum
86 FVEG03768_Fusarium_verticillioides
83
5
Scco232589_Schizophyllum_commune
22
CNAG_04237_Cryptococcus_neoformans
14
Crpa36895_Cryphonectria_parasitica
76
BC1G_14770_Botrytis_cinerea
34
SS1G_01648_Sclerotinia_sclerotiorum
99
VDAG_03949_Verticillium_dahliae
97 VDBG_03038_Verticillium_albo−atrum
.6._PITG_02687_Phytophthora_infestans
Fungi
.6._PITG_21033_Phytophthora_infestans
56 .6._Phca96152_Phytophthora_capsici
Oomycetes
.6._Phso139108_Phytophthora_sojae
Support for with Oomycetes
.6._Hyp703537_Hyaloperonospora_parasitica
48
57 .6._Phra79221_Phytophthora_ramorum
Support for within Oomycetes
.6._Phra79220_Phytophthora_ramorum
30
51
51
Fig. 1.22
100
59
87
85
39
81
35
27
98
100
Erwinia chrysanthemi [P0C1A4.1]
Bacillus halodurans [Bacillus halodurans]
Bacillus subtilis [NP_389746.1]
Rhodopirellula baltica [NP_866630.1]
Dictyoglomus
p thermophilum [YP_002250198.1]
Dictyoglomus turgidum [YP_002352346.1]
Bacillus sp. [ACY38198.1]
uncultured bacterium [AAP70368.1]
74
Saccharophagus degradans [YP_526417.1]
98
97
Saccharophagus degradans [YP_526417.1]
88
Pseudoalteromonas haloplanktis [AAF86343.2]
64
Streptomyces flavogriseus [ZP_05803310.1]
92
Alteromonas macleodii [ZP_04713986.1]
Dictyoglomus turgidum [YP_002352347.1]
Fibrobacter succinogenes [YP_003250061.1]
162453184_Sorangium_cellulosum_So_ce_56
83645917_Hahella_chejuensis_KCTC_2396
Teredinibacter turnerae [YP_003071817.1]
0.3
Pseudomonas
f fluorescens [YP_002871877.1]
28871420_Pseudomonas_syringae_pv_tomato_str_DC3000
84
71736163_Pseudomonas_syringae_pv_phaseolicola_1448A
79
66047212_Pseudomonas_syringae_pv_syringae_B728a
.5._Mela44084_Melampsora_laricis−populina
94
.5._Mela72436_Melampsora_laricis−populina
90
.5._Mela93893_Melampsora_laricis−populina
.5._VDBG_08488_Verticillium_albo−atrum
84
.5._Neha122319_Nectria_haematococca
63
.5._NFIA077100_Neosartorya_fischeri
.5._VDBG_05494_Verticillium_albo−atrum
12
99
.5._AB06199_Alternaria_brassicicola
22
.5._VDAG_03656_Verticillium_dahliae
2
.5._BC1G_11690_Botrytis_cinerea
100
.5._SS1G_00040_Sclerotinia_sclerotiorum
.5._Asni210387_Aspergillus_niger
.5._A003001295_Aspergillus_oryzae
77
32
.5._ATEG_00950_Aspergillus_terreus
33
.5._AN4882_Aspergillus_nidulans
.5._Cohe64232_Cochliobolus_heterostrophus
71
100 .5._PTRG_00517_Pyrenophora_tritici−repentis
.5._AB07436_Alternaria_brassicicola
11
.5._UM04708_Ustilago_maydis
.5._VDAG_07238_Verticillium_dahliae
.5._Cohe117798_Cochliobolus_heterostrophus
73
32
.5._PTRG_03919_Pyrenophora_tritici−repentis
99 55
.5._AB03768_Alternaria_brassicicola
.5._SNU05296_Stagonospora_nodorum
14
.5._Crpa69046_Cryphonectria_parasitica
.5._Afu5g10380_Aspergillus_fumigatus
3
.5._BC1G_12517_Botrytis_cinerea
99
12
.5._SS1G_10071_Sclerotinia_sclerotiorum
10
25
.5._ATEG_01216_Aspergillus_terreus
16
41
.5._ACLA094210_Aspergillus_clavatus
17
62
24
.5._A010000087_Aspergillus_oryzae
54
10
.5._AN9439_Aspergillus_nidulans
.5._ACLA013470_Aspergillus_clavatus
53
.5._A010000504_Aspergillus_oryzae
.5._AN2331_Aspergillus_nidulans
4
.5._Crpa98319_Cryphonectria_parasitica
6
.5._Afu7g05030_Aspergillus_fumigatus
14
74
.5._Asni55212_Aspergillus_niger
36
5
.5._Asni41815_Aspergillus_niger
.5._CHG02337_Chaetomium_globosum
.5._Neha30203_Nectria_haematococca
98
.5._FGSG_01607_Fusarium_graminearum
4
96
.5._FVEG09702_Fusarium_verticillioides
.5._FGSG_03483_Fusarium_graminearum
1
100
.5._FOXG_16516_Fusarium_oxysporum
16
.5._FVEG03470_Fusarium_verticillioides
99
.5._Neha44358_Nectria_haematococca
0
7
.5._FGSG_03121_Fusarium_graminearum
49
.5._Crpa39853_Cryphonectria_parasitica
99
.5._Trat53176_Trichoderma_atoviride
.5._BC1G_12017_Botrytis_cinerea
100
.5._SS1G_07942_Sclerotinia_sclerotiorum
Phso132227_Phytophthora_sojae
Phso145391_Phytophthora_sojae
28
97 Phso140272_Phytophthora_sojae
Phso132225_Phytophthora_sojae
23
29
Phra85623_Phytophthora_ramorum
51
6
Phca84769_Phytophthora_capsici
29
Phca1119_Phytophthora_capsici
40
13
Phra86921_Phytophthora_ramorum
40
Hyp710387_Hyaloperonospora_parasitica
Phca25655_Phytophthora_capsici
97
Phra85622_Phytophthora_ramorum
Hyp710383_Hyaloperonospora_parasitica
100 Phso140270_Phytophthora_sojae
46
Phso140268_Phytophthora_sojae
82
94
Phso141647_Phytophthora_sojae
Phra77010_Phytophthora_ramorum
100
Phca115597_Phytophthora_capsici
Phso128355_Phytophthora_sojae
53
Phso133199_Phytophthora_sojae
86
Phso132218_Phytophthora_sojae
100
27
Phca25476_Phytophthora_capsici
PITG_00872_Phytophthora_infestans
87
Phra77715_Phytophthora_ramorum
25
26
supercont1_15_Saprolegnia_parasitica
99
supercont1_11_Saprolegnia_parasitica
Fungi
Phca79318_Phytophthora_capsici
79
Phca21313_Phytophthora_capsici
78
48
Phra75231_Phytophthora_ramorum
21
Oomycetes
Phca38885_Phytophthora_capsici
100
Phso143943_Phytophthora_sojae
100 PITG_21462_Phytophthora_infestans
Support for with Fungi
54
PITG_09465_Phytophthora_infestans
42
Phra75227_Phytophthora_ramorum
4
Support for within Fungi
Hyp709214_Hyaloperonospora_parasitica
40
Phca21323_Phytophthora_capsici
52
92
Phso145395_Phytophthora_sojae
PITG_21463_Phytophthora_infestans
100 Phso144197_Phytophthora_sojae
56
Phso144196_Phytophthora_sojae
73
Phso144191_Phytophthora_sojae
91
Phra75225_Phytophthora_ramorum
62
Phra75226_Phytophthora_ramorum
100
Phca121321_Phytophthora_capsici
95
59
86
86
71
62
87
50
17
59
52
40
0.3
Fig. 1.23
Support for within Fungi
Support for with Fungi
Oomycetes
Fungi
37528247_Photorhabdus_luminescens_subsp._laumondii_TTO1
Pectobacterium carotovorum subsp carotovorum PC1_[YP_003019323.1]
77460581_Pseudomonas_fluorescens_PfO−1
51597563_Yersinia_pseudotuberculosis_IP_32953
22
Nagr62877_Naegleria_gruberi
29830777_Streptomyces_avermitilis_MA−4680
37
29832304_Streptomyces_avermitilis_MA−4680
29832301_Streptomyces_avermitilis_MA−4680
62
Saccharopolyspora erythraea NRRL 2338_[YP_001104202.1]
Rhodococcus erythropolis SK121_[ZP_04382846.1]
98
66
Rhodococcus opacus B4_[YP_002782371.1]
41
111022086_Rhodococcus_sp._RHA1
86
Corynebacterium matruchotii ATCC 14266_[ZP_04835997.1]
55981480_Thermus_thermophilus_HB8
54
159900040_Herpetosiphon_aurantiacus_ATCC_23779
Methylovorus sp SIP3−4_[YP_003051066.1]
49
156741569_Roseiflexus_castenholzii_DSM_13941
90
148655099_Roseiflexus_sp._RS−1
75
39
protocatechuate 3_[ZP_04037829.1]
82703214_Nitrosospira_multiformis_ATCC_25196
17
26
158334326_Acaryochloris_marina_MBIC11017
50
77165877_Nitrosococcus_oceani_ATCC_19707
88
13
77164637_Nitrosococcus_oceani_ATCC_19707
28
159901350_Herpetosiphon_aurantiacus_ATCC_23779
9
74317220_Thiobacillus_denitrificans_ATCC_25259
8
Deinococcus deserti VCD115_[YP_002784902.1]
26
12
Thermobaculum terrenum ATCC BAA−798_[YP_003323670.1]
Marinomonas sp MED121_[ZP_01076090.1]
76
116252761_Rhizobium_leguminosarum_bv._viciae_3841
49
41
Comamonas testosteroni CNB−2_[YP_003280206.1]
protocatechuate
3_[ZP_01459590.1]
50
73539064_Ralstonia_eutropha_JMP134
90
72
Cupriavidus taiwanensis_[YP_002007309.1]
28
39
116694741_Ralstonia_eutropha_H16
protocatechuate 3_[YP_001617686.1]
Hyphomicrobium denitrificans ATCC 51888_[ZP_05374819.1]
30
110635176_Mesorhizobium_sp._BNC1
39
36
Roseovarius sp HTCC2601_[ZP_01444072.1]
35
94314194_Ralstonia_metallidurans_CH34
7 9
Methylobacterium chloromethanicum CM4_[YP_002423474.1]
96
148258566_Bradyrhizobium_sp._BTAi1
98
146337837_Bradyrhizobium_sp._ORS278
Chitinophaga pinensis DSM 2588_[YP_003120875.1]
protocatechuate 3_[ZP_04488635.1]
61
64
Dyadobacter fermentans DSM 18053_[YP_003088138.1]
Schistosoma mansoni_[XP_002569539.1]
82
46
79
146299440_Flavobacterium_johnsoniae_UW101
Flavobacteriales bacterium ALC−1_[ZP_02181399.1]
90
50
Delftia acidovorans SPH−1_[YP_001564166.1]
94972304_Deinococcus_geothermalis_DSM_11300
100
Gemmatimonas aurantiaca T−27_[YP_002762722.1]
67
protocatechuate 3_[ZP_03864996.1]
94
52
116672671_Arthrobacter_sp._FB24
99
119962051_Arthrobacter_aurescens_TC1
Cellvibrio japonicus Ueda107_[YP_001983304.1]
.5._Neha84393_Nectria_haematococca
.5._50423557_Debaryomyces_hansenii
.5._SS1G_09100_Sclerotinia_sclerotiorum
5
10
.5._Pa_2_14180_Podospora_anserina
.5._NFIA032260_Neosartorya_fischeri
39
.5._NCU01849_Neurospora_crassa
.5._Trvi59138_Trichoderma_virens
13
.5._CHG03878_Chaetomium_globosum
.5._Trre71094_Trichoderma_reesei
.5._FGSG_08037_Fusarium_graminearum
9
2
14
.5._Pa_6_8190_Podospora_anserina
2
.5._FGSG_01982_Fusarium_graminearum
92
.5._Neha50592_Nectria_haematococca
23
.5._Crpa41869_Cryphonectria_parasitica
.5._CHG02140_Chaetomium_globosum
38
.5._VDBG_03876_Verticillium_albo−atrum
2
.5._AFL06538_Aspergillus_flavus
67
100 .5._NFIA049420_Neosartorya_fischeri
.5._Afu6g03070_Aspergillus_fumigatus
11
.5._PABG01862_Paracoccidioides_brasiliensis
.5._AN7161_Aspergillus_nidulans
20
.5._AN1301_Aspergillus_nidulans
98
.5._AFL03657_Aspergillus_flavus
6
.5._Asni49638_Aspergillus_niger
76
Phso133860_Phytophthora_sojae
100 Phso133856_Phytophthora_sojae
69
Phso145388_Phytophthora_sojae
2
Phca22106_Phytophthora_capsici
85
Phra41396_Phytophthora_ramorum
55
Phra45452_Phytophthora_ramorum
Phra44325_Phytophthora_ramorum
74 Phra72402_Phytophthora_ramorum
0
30
Phra85045_Phytophthora_ramorum
4
Phra80732_Phytophthora_ramorum
100
Phso133354_Phytophthora_sojae
Phso133391_Phytophthora_sojae
93
38
Phra80735_Phytophthora_ramorum
26
45
43
Phra81438_Phytophthora_ramorum
Phso140106_Phytophthora_sojae
Phca25055_Phytophthora_capsici
96
PITG_04071_Phytophthora_infestans
91
Phra83986_Phytophthora_ramorum
3
Phca66589_Phytophthora_capsici
99
36
2
Phca4623_Phytophthora_capsici
Phra83951_Phytophthora_ramorum
0
0
100 Phra83952_Phytophthora_ramorum
.5._Asni42189_Aspergillus_niger
.5._Myfi37681_Mycosphaerella_fijiensis
.5._AFL12172_Aspergillus_flavus
73
.5._AN4203_Aspergillus_nidulans
56
.5._Asni45961_Aspergillus_niger
43
.5._Crpa27175_Cryphonectria_parasitica
.5._Crpa51525_Cryphonectria_parasitica
18
12
16
47
.5._A026000214_Aspergillus_oryzae
.5._Afu3g14630_Aspergillus_fumigatus
.5._UM04111_Ustilago_maydis
3
.5._Neha92188_Nectria_haematococca
71
98.5._FVEG05753_Fusarium_verticillioides
.5._FGSG_04685_Fusarium_graminearum
98
.5._BC1G_10768_Botrytis_cinerea
88
.5._SS1G_14321_Sclerotinia_sclerotiorum
57
.5._ATEG_06081_Aspergillus_terreus
99
.5._Afu3g01800_Aspergillus_fumigatus
.5._Cohe25759_Cochliobolus_heterostrophus
.5._MGG_08431_Magnaporthe_grisea
100
.5._BDBG_01175_Blastomyces_dermatitidis
7 6
.5._SNU00562_Stagonospora_nodorum
99
.5._PTRG_10291_Pyrenophora_tritici−repentis
50
.5._Cohe59831_Cochliobolus_heterostrophus
.5._AB00069_Alternaria_brassicicola
65
.5._UM05988_Ustilago_maydis
100 .5._Mela70972_Melampsora_laricis−populina
100
.5._Mela70973_Melampsora_laricis−populina
76
.5._PGTG_10156_Puccinia_graminis
59
.5._CC1G_09813_Coprinus_cinereus
97
.5._Labi184112_Laccaria_bicolor
.5._CC1G_05902_Coprinus_cinereus
.5._Scco37594_Schizophyllum_commune
100
78
78
27
2
2
1
52
97
0.4
Fig. 1.24
Support for within Fungi
Support for with Fungi
Oomycetes
Fungi
Burkholderia glumae BGR1_[YP_002908805.1]
Pectobacterium carotovorum subsp carotovorum PC1_[YP_003017082.1]
Bacillus licheniformis ATCC 14580_[YP_080412.1]
secreted
endo−1_[ZP_04603971.1]
69
29829110_Streptomyces_avermitilis_MA−4680
Acidothermus cellulolyticus 11B_[YP_872378.1]
74 Acidothermus
cellulolyticus
100
Catenulispora acidiphila DSM 44928_[YP_003114348.1]
endo−1_[ZP_04994021.1]
Streptomyces sp 11AG8_[AAF91283.1]
53
Streptomyces sviceus ATCC 29083_[ZP_05016224.1]
91 100 endo−1_[NP_821730.1]
100
19
29827096_Streptomyces_avermitilis_MA−4680
Streptomyces coelicolor A3_[NP_625477.1]
33
69
Streptomyces ambofaciens ATCC 23877_[CAJ90159.1]
Streptomyces ghanaensis ATCC 14672_[ZP_04683886.1]
22
97
18
Streptomyces flavogriseus ATCC 33331_[ZP_05801764.1]
7
Streptomyces scabiei 8722_[CBG67793.1]
12
32
Streptomyces griseoflavus Tu4000_[ZP_05536909.1]
Streptomyces rochei_[CAA52139.1]
Micromonospora
aurantiaca
ATCC 27029_[ZP_06215034.1]
97
secreted endo−1_[ZP_04607827.1]
52
145596933_Salinispora_tropica_CNB−440
97
Salinispora arenicola CNS−205_[YP_001539639.1]
57
Actinosynnema mirum DSM 43827_[YP_003101698.1]
.5._ACLA007820_Aspergillus_clavatus
80
97.5._NFIA027400_Neosartorya_fischeri
.5._Afu7g06150_Aspergillus_fumigatus
50
.5._A026000102_Aspergillus_oryzae
75
100
.5._Asni211053_Aspergillus_niger
99
.5._ATEG_05519_Aspergillus_terreus
.5._ATEG_09894_Aspergillus_terreus
.5._MGG_00677_Magnaporthe_grisea
.5._CHG03786_Chaetomium_globosum
50
.5._SNU08921_Stagonospora_nodorum
95
50
37
.5._SNU13099_Stagonospora_nodorum
73
39
.5._MGG_08537_Magnaporthe_grisea
40
.5._Pa_4_6020_Podospora_anserina
24
.5._CHG04975_Chaetomium_globosum
.5._Mygr105871_Mycosphaerella_graminicola
50
.5._Cohe119592_Cochliobolus_heterostrophus
100
55
.5._PTRG_06274_Pyrenophora_tritici−repentis
.5._Trvi67800_Trichoderma_virens
.5._Trre123232_Trichoderma_reesei
100
92
.5._Trvi42536_Trichoderma_virens
62
55
.5._Trat44429_Trichoderma_atoviride
.5._FGSG_11037_Fusarium_graminearum
100
.5._FOXG_17404_Fusarium_oxysporum
93.5._FVEG12486_Fusarium_verticillioides
.1._Trat82406_Trichoderma_atoviride
.1._Neha106477_Nectria_haematococca
94
88
.1._FGSG_05851_Fusarium_graminearum
82
31
.1._Neha48733_Nectria_haematococca
89
.1._Trvi28149_Trichoderma_virens
10
.1._Crpa62910_Cryphonectria_parasitica
.1._Crpa58977_Cryphonectria_parasitica
.4._Labi308280_Laccaria_bicolor
100
6
.4._Phch7048_Phanerochaete_chrysosporium
65
.4._Popl121191_Postia_placenta
73
.4._Phch8466_Phanerochaete_chrysosporium
99
13
11
.4._Popl52805_Postia_placenta
.1._SS1G_02369_Sclerotinia_sclerotiorum
.1._BC1G_00594_Botrytis_cinerea
100
.1._SS1G_00501_Sclerotinia_sclerotiorum
.1._Myfi40655_Mycosphaerella_fijiensis
.1._SNU01962_Stagonospora_nodorum
92
.1._PTRG_10242_Pyrenophora_tritici−repentis
19
77
.1._Cohe29798_Cochliobolus_heterostrophus
29
.1._VDBG_03110_Verticillium_albo−atrum
40
63
.1._Neha29778_Nectria_haematococca
.1._VDAG_07406_Verticillium_dahliae
Phca118606_Phytophthora_capsici
100
Phso109681_Phytophthora_sojae
95
Phca27694_Phytophthora_capsici
Phca27600_Phytophthora_capsici
94
Phca21841_Phytophthora_capsici
Hyp705511_Hyaloperonospora_parasitica
46
73
PITG_06962_Phytophthora_infestans
99
Phso138787_Phytophthora_sojae
31
42
Phca69472_Phytophthora_capsici
55
Phra79939_Phytophthora_ramorum
Phca82397_Phytophthora_capsici
Phso140301_Phytophthora_sojae
78
Phca23894_Phytophthora_capsici
88
79
PITG_16992_Phytophthora_infestans
13
21
Phso140302_Phytophthora_sojae
Phra83139_Phytophthora_ramorum
Phca71077_Phytophthora_capsici
11
Phca23733_Phytophthora_capsici
80
Phra72080_Phytophthora_ramorum
32
17
Phso109281_Phytophthora_sojae
13
23
Phca85025_Phytophthora_capsici
15
Hyp703817_Hyaloperonospora_parasitica
88
10
Phca23582_Phytophthora_capsici
Phra72081_Phytophthora_ramorum
67
9
65
6
Phso109280_Phytophthora_sojae
33
PITG_08944_Phytophthora_infestans
98
Phca82399_Phytophthora_capsici
PITG_16991_Phytophthora_infestans
Phso140300_Phytophthora_sojae
Phso140303_Phytophthora_sojae
Phra83138_Phytophthora_ramorum
100
.1._Asni191511_Aspergillus_niger
42
.1._Asni52011_Aspergillus_niger
12
.1._Afu1g04730_Aspergillus_fumigatus
93
.1._ACLA029940_Aspergillus_clavatus
3
.1._AN0452_Aspergillus_nidulans
54
.1._AFL02120_Aspergillus_flavus
.1._AFL04893_Aspergillus_flavus
58
Vitis vinifera_[XP_002276870.1]
Vitis vinifera_[XP_002273619.1]
Sorghum bicolor_[XP_002466207.1]
100
Hordeum vulgare_[ABJ98329.1]
35
100
Triticum aestivum_[ABJ98332.1]
Populus trichocarpa_[XP_002315140.1]
48
Arabidopsis thaliana_[NP_563856.1]
Entamoeba histolytica HM−1IMSS_[XP_652901.2]
multiple inositol polyphosphate phosphatase 1_[EEY64239.1]
Hydra magnipapillata_[XP_002167713.1]
23
Nematostella vectensis_[XP_001640538.1]
Branchiostoma floridae_[XP_002596211.1]
51
Danio rerio_[AAH66753.1]
13
100
21
Tetraodon nigroviridis_[CAF98607.1]
Ciona intestinalis_[XP_002121164.1]
22
Dapu248902_Daphnia_pulex
Culex quinquefasciatus_[XP_001844573.1]
91
86
Dapu301637_Daphnia_pulex
52
multiple inositol polyphosphate phosphatase 1 precursor_[XP_002429332.1]
Acyrthosiphon pisum_[XP_001949247.1]
80
Nasonia vitripennis_[XP_001605328.1]
22
multiple inositol polyphosphate phosphatase 1_[NP_524109.2]
75
Drosophila persimilis_[XP_002024888.1]
100
23
Drosophila virilis_[XP_002046258.1]
98
Aedes aegypti_[XP_001650363.1]
100
72
Culex quinquefasciatus_[XP_001861930.1]
Tribolium castaneum_[XP_972932.1]
.5._19113639_Schizosaccharomyces_pombe
100
98 .5._19111973_Schizosaccharomyces_pombe
.5._19112720_Schizosaccharomyces_pombe
.5._UM06428_Ustilago_maydis
100
.5._Phch8249_Phanerochaete_chrysosporium
.5._50424211_Debaryomyces_hansenii
98
.5._Pist46121_Pichia_stipitis
.5._50419057_Debaryomyces_hansenii
.5._C19_3727_Candida_albicans_SC5314
98
100
45
.5._C19_2619_Candida_albicans_SC5314
70
.5._Pist46975_Pichia_stipitis
35
.5._50424219_Debaryomyces_hansenii
82
42
.5._Pist61096_Pichia_stipitis
94
96
.5._C19_4584_Candida_albicans_SC5314
.5._6319569_Saccharomyces_cerevisiae
100 .5._6319351_Saccharomyces_cerevisiae
.5._Asni190797_Aspergillus_niger
100
.5._Asni47229_Aspergillus_niger
46
76
.5._NFIA108020_Neosartorya_fischeri
100
.5._ACLA047520_Aspergillus_clavatus
.5._AN11111_Aspergillus_nidulans
94
.5._A120000167_Aspergillus_oryzae
100
100
.5._Cohe48077_Cochliobolus_heterostrophus
.5._PTRG_05327_Pyrenophora_tritici−repentis
52
31
.5._Mygr109391_Mycosphaerella_graminicola
100
.5._SS1G_06333_Sclerotinia_sclerotiorum
.5._BC1G_11306_Botrytis_cinerea
99
.5._Crpa35521_Cryphonectria_parasitica
.5._ATEG_05038_Aspergillus_terreus
100
.5._AN0564_Aspergillus_nidulans
100
.5._ACLA085000_Aspergillus_clavatus
56
61
.5._NFIA057030_Neosartorya_fischeri
100
.5._Afu6g11330_Aspergillus_fumigatus
71
33
.5._AFL04322_Aspergillus_flavus
53
.5._SNU12840_Stagonospora_nodorum
100
.5._PTRG_09617_Pyrenophora_tritici−repentis
62
.5._AB08706_Alternaria_brassicicola
65
37
.5._Cohe33529_Cochliobolus_heterostrophus
.5._Neha53415_Nectria_haematococca
99
.5._FGSG_03366_Fusarium_graminearum
96
66
.5._FOXG_12400_Fusarium_oxysporum
PITG_17872_Phytophthora_infestans
100
Phra73528_Phytophthora_ramorum
45 Phca4202_Phytophthora_capsici
.5._Neha45294_Nectria_haematococca
.5._SNU00343_Stagonospora_nodorum
.5._Cohe100959_Cochliobolus_heterostrophus
88
74
.5._PTRG_07362_Pyrenophora_tritici−repentis
100
80
.5._AB08920_Alternaria_brassicicola
.5._Scco57608_Schizophyllum_commune
74
.5._Mygr70454_Mycosphaerella_graminicola
41
100
.5._Myfi65734_Mycosphaerella_fijiensis
58
.5._Crpa48535_Cryphonectria_parasitica
.5._FOXG_12362_Fusarium_oxysporum
94
100 .5._FGSG_03402_Fusarium_graminearum
96
18
.5._Neha64414_Nectria_haematococca
.5._ACLA043950_Aspergillus_clavatus
52
.5._A011000174_Aspergillus_oryzae
41
.5._Asni44563_Aspergillus_niger
11
.5._SS1G_07022_Sclerotinia_sclerotiorum
100
.5._BC1G_11751_Botrytis_cinerea
.5._Popl92462_Postia_placenta
87
.5._Labi142568_Laccaria_bicolor
.5._Spro8365_Sporobolomyces_roseus
100
.5._CNAG_02944_Cryptococcus_neoformans
100
.5._Trat151059_Trichoderma_atoviride
100
100
.5._AB00986_Alternaria_brassicicola
46
75 .5._Phch121720_Phanerochaete_chrysosporium
.5._Popl110571_Postia_placenta
100
.5._CC1G_03021_Coprinus_cinereus
41
31
.5._Labi157734_Laccaria_bicolor
53
.5._Scco66724_Schizophyllum_commune
.5._Spro1872_Sporobolomyces_roseus
93
.5._PGTG_11120_Puccinia_graminis
36
99
.5._Mela84480_Melampsora_laricis−populina
13
.5._CNAG_06967_Cryptococcus_neoformans
27
.5._Mela77108_Melampsora_laricis−populina
.5._50548135_Yarrowia_lipolytica
.5._UM04282_Ustilago_maydis
43
.5._ATEG_00823_Aspergillus_terreus
45
.5._Trre73604_Trichoderma_reesei
100
100
45 .5._Trvi31340_Trichoderma_virens
.5._Trat133042_Trichoderma_atoviride
57
100
.5._FOXG_00526_Fusarium_oxysporum
98
.5._FGSG_00530_Fusarium_graminearum
.5._NCU03255_Neurospora_crassa
56
71
.5._Crpa62916_Cryphonectria_parasitica
.5._Phch121577_Phanerochaete_chrysosporium
98
.5._Scco38239_Schizophyllum_commune
54
.5._Labi239833_Laccaria_bicolor
.5._MGG_06167_Magnaporthe_grisea
100
.5._Myfi84206_Mycosphaerella_fijiensis
21
.5._SS1G_09959_Sclerotinia_sclerotiorum
100
.5._CHG03880_Chaetomium_globosum
88
.5._Pa_1_22690_Podospora_anserina
29
.5._VDAG_00574_Verticillium_dahliae
21
.5._UREG_02470_Uncinocarpus_reesii
99
.5._CIMG_08290_Coccidioides_immitis
73
99
.5._BDBG_00518_Blastomyces_dermatitidis
25
.5._HCAG_06203_Histoplasma_capsulatum
32
83
.5._MCYG_02670_Microsporum_canis
100
.5._MGYG_08398_Microsporum_gypseum
67 .5._TEQG_06967_Trichophyton_equinum
32
.5._AFL04515_Aspergillus_flavus
87
84
.5._Afu4g08630_Aspergillus_fumigatus
80
.5._AN1685_Aspergillus_nidulans
.5._Trre71566_Trichoderma_reesei
100
.5._Trvi48755_Trichoderma_virens
67
.5._Trat47748_Trichoderma_atoviride
.5._UM03382_Ustilago_maydis
100
22
100
39
42
100
77
73
Fungi
Oomycetes
0. 5
Support for with Fungi
Support for within Fungi
Fig. 1.25
74
74
2
0
7
26
1
4
65
3
40
18
50
53
2
36
8
92
5
7
72
16
Voca94058_Volvox_carteri
31
68
98
0.4
Fig. 1.26
Support for within Fungi
Support for with Fungi
Oomycetes
Fungi
90019830_Saccharophagus_degradans_2−40
182416415_Opitutus_terrae_PB90−1
58584051_Xanthomonas_oryzae_pv_oryzae_KACC10331
91
120612237_Acidovorax_avenae_subsp_citrulli_AAC00−1
91
21233540_Xanthomonas_campestris_pv_campestris_str_ATCC_33913
15004819_Clostridium_acetobutylicum_ATCC_824
22299445_Thermosynechococcus_elongatus_BP−1
CapI180458_Capitella_sp_I
94
CapI228148_Capitella_sp_I
157692340_Bacillus_pumilus_SAFR−032
60
97
125975073_Clostridium_thermocellum_ATCC_27405
44
Semo111304_Selaginella_moellendorffii
115434376_Oryza_sativa
99
Sbi4999622_Sorghum_bicolor
100 115471925_Oryza_sativa
62
15218406_Arabidopsis_thaliana
41
115454551_Oryza_sativa
83
57
Sbi5048406_Sorghum_bicolor
100
19
Potr411700_Populus_trichocarpa
37
36
15217948_Arabidopsis_thaliana
Phpa215929_Physcomitrella_patens
Potr557521_Populus_trichocarpa
100
Potr557520_Populus_trichocarpa
94
Sbi5030322_Sorghum_bicolor
100
42567513_Arabidopsis_thaliana
Eubacteria
152966503_Kineococcus_radiotolerans_SRS30216
62
AN2356_Aspergillus_nidulans
99
100
Asni50977_Aspergillus_niger
148271268_Clavibacter_michiganensis_subsp_michiganensis_NCPPB_382
Eubacteria
29828638_Streptomyces_avermitilis_MA−4680
117927390_Acidothermus_cellulolyticus_11B
29831527_Streptomyces_avermitilis_MA−4680
72163322_Thermobifida_fusca_YX
162450460_Sorangium_cellulosum_So_ce_56
18
32141278_Streptomyces_coelicolor_A3
92
21219204_Streptomyces_coelicolor_A3
.5._Scco238097_Schizophyllum_commune
71
.5._CC1G_12361_Coprinus_cinereus
50
.5._Phch125669_Phanerochaete_chrysosporium
92
.5._Popl113670_Postia_placenta
29
94
.5._Phch138715_Phanerochaete_chrysosporium
100.5._Phch138345_Phanerochaete_chrysosporium
.5._Scco254944_Schizophyllum_commune
.5._Pa_2_4290_Podospora_anserina
40
.5._MGG_05464_Magnaporthe_grisea
.5._MGG_14243_Magnaporthe_grisea
8
.5._Pa_4_4530_Podospora_anserina
13
100
.5._NCU07130_Neurospora_crassa
.5._MGG_15430_Magnaporthe_grisea
35
.5._Pa_5_12430_Podospora_anserina
6
51
.5._CHG00030_Chaetomium_globosum
50
.5._Neha25306_Nectria_haematococca
99
100 .5._FGSG_10411_Fusarium_graminearum
53
60
.5._FOXG_04992_Fusarium_oxysporum
.5._VDBG_06231_Verticillium_albo−atrum
.5._NCU04997_Neurospora_crassa
.5._PTRG_08785_Pyrenophora_tritici−repentis
98
69
92 .5._SNU03593_Stagonospora_nodorum
.5._Cohe70947_Cochliobolus_heterostrophus
.5._VDAG_08273_Verticillium_dahliae
62
98
.5._Neha86582_Nectria_haematococca
97
.5._Myfi54093_Mycosphaerella_fijiensis
48
95
.5._Mygr61141_Mycosphaerella_graminicola
87
.5._Mygr94846_Mycosphaerella_graminicola
45
.5._SNU01776_Stagonospora_nodorum
25
.5._AB06192_Alternaria_brassicicola
89
60
.5._Cohe20996_Cochliobolus_heterostrophus
100
.5._PTRG_03943_Pyrenophora_tritici−repentis
100 .5._FGSG_06445_Fusarium_graminearum
2
.5._FVEG12502_Fusarium_verticillioides
.5._ATEG_03410_Aspergillus_terreus
93
.5._Afu6g13610_Aspergillus_fumigatus
72 .5._ACLA086910_Aspergillus_clavatus
.5._SS1G_12191_Sclerotinia_sclerotiorum
99.5._BC1G_01778_Botrytis_cinerea
62
.5._Crpa40682_Cryphonectria_parasitica
.5._NCU08189_Neurospora_crassa
8
Phca34804_Phytophthora_capsici
100Phra74308_Phytophthora_ramorum
97
Phca77900_Phytophthora_capsici
22
100 Phra74319_Phytophthora_ramorum
Phra85409_Phytophthora_ramorum
100
100
7
Phso140368_Phytophthora_sojae
Phca21832_Phytophthora_capsici
4
84
PITG_17055_Phytophthora_infestans
53
74 PITG_17054_Phytophthora_infestans
24
Phca65367_Phytophthora_capsici
43
Phso140369_Phytophthora_sojae
31
60
35
100 Phra83134_Phytophthora_ramorum
Phra83132_Phytophthora_ramorum
24
Phso108296_Phytophthora_sojae
20
.5._ATEG_07190_Aspergillus_terreus
100
97.5._NFIA061880_Neosartorya_fischeri
.5._Afu3g15210_Aspergillus_fumigatus
.5._AB04088_Alternaria_brassicicola
.5._Pist35732_Pichia_stipitis
.5._CC1G_04646_Coprinus_cinereus
.5._UM03411_Ustilago_maydis
41
.5._AB03077_Alternaria_brassicicola
73
.5._PTRG_09530_Pyrenophora_tritici−repentis
100
.5._Cohe25415_Cochliobolus_heterostrophus
17
92
.5._AFL06449_Aspergillus_flavus
14
.5._ACLA048770_Aspergillus_clavatus
14
.5._Scco15936_Schizophyllum_commune
2
.5._SS1G_00509_Sclerotinia_sclerotiorum
6
.5._Trvi56652_Trichoderma_virens
89
100.5._Trat88310_Trichoderma_atoviride
.5._FVEG11849_Fusarium_verticillioides
100 .5._CHG00304_Chaetomium_globosum
60
.5._SNU15934_Stagonospora_nodorum
.5._Trre120229_Trichoderma_reesei
31
100
.5._Trvi53264_Trichoderma_virens
83
.5._VDBG_09510_Verticillium_albo−atrum
38
.5._FOXG_14504_Fusarium_oxysporum
58
.5._FGSG_11487_Fusarium_graminearum
97
.5._Neha39302_Nectria_haematococca
PGTG_17529_Puccinia_graminis s
95
Mela103920_Melampsora_laricis−populina
90
Mela67094_Melampsora_laricis−populina
79
Mela111031_Melampsora_laricis−populina
117927581_Acidothermus_cellulolyticus_11B
152964519_Kineococcus_radiotolerans_SRS30216
99
72163190_Thermobifida_fusca_YX
32476146_Rhodopirellula_baltica_SH_1
Mobr25499_Monosiga_brevicollis
125974464_Clostridium_thermocellum_ATCC_27405
100
148269989_Thermotoga_petrophila_RKU−1
15642845_Thermotoga_maritima_MSB8
159901317_Herpetosiphon_aurantiacus_ATCC_23779
Emhu246479_Emiliania_huxleyi
100
Emhu108619_Emiliania_huxleyi
Phtr47398_Phaeodactylum_tricornutum
100
Fig. 1.27
Support for within Fungi
Support for with Fungi
Oomycetes
Fungi
100
100
49
69
60
63
95
.5._Nectria haematococca [EEU43424.1]
23
38
30
100
97
0.3
56
Nagr74952_Naegleria_gruberi
83
97
.5._Aspergillus clavatus [XP_001270532.1]
.5._Aspergillus nidulans [XP_660796.1]
.5._Aspergillus terreus [XP_001215975.1]
.5._Aspergillus flavus [XP_002379891.1]
.5._Laccaria bicolor [XP_001876907.1]
Phca4256__Phytophthora_capsici
Phra75147_Phytophthora_ramorum
44
.5._Botryotinia fuckeliana [XP_001560790.1]
.5._Sordaria macrospora [CBI55317.1]
.5._Gibberella zeae [XP_385227.1]
100
.5._Nectria haematococca [EEU40139.1]
.5._Verticillium albo-atrum [EEY16858.1]
Nagr71630_Naegleria_gruberi
70
86
33
45
Nagr46110_Naegleria_gruberi
n20540089_Homo_sapiens
Macaca fascicularis BAE01391.1
75Homo sapiens [Q86W34.1]
73
Pongo abelii [NP_001127001.1]
n75812978_Mus_musculus
30 Equus caballus XP_001494377
45
Ailuropoda melanoleuca [EFB17332.1]
Ornithorhynchus anatinus [XP_001508130.1]
Taru608065_Takifugu_rubripes
Ciin274284_Ciona_intestinalis
Teth2791_Tetrahymena_thermophila
18
18
16
38
10
21
13
22
12
44
46
8
31
2
76
13
43
48
100
82
96
81
92
81
52
0.3
Fig. 1.28
Support for within Fungi
Support for with Fungi
Oomycetes
Fungi
arabinogalactan endo−1_[YP_003153861.1]
Arabinogalactan endo−1_[ZP_06271000.1]
arabinogalactan endo−1_[NP_822499.1]
100
arabinogalactan endo−1_[ZP_05529357.1]
63
Streptomyces scabiei 8722_[CBG75302.1]
arabinogalactan endo−1_[ZP_05010254.1]
145299340_Aeromonas_salmonicida_subsp_salmonicida_A449
116691394_Burkholderia_cenocepacia_HI2424
100
arabinogalactan endo−1_[YP_001818930.1]
Clostridium cellulovorans 743B_[ZP_04803725.1]
Arabinogalactan endo−1_[XP_002535419.1]
97
ararbinogalactan endo−1_[ACY02856.1]
86
Clostridium thermocellum ATCC 27405_[YP_001037824.1]
54
Arabinogalactan endo−1_[YP_003125778.1]
Pectobacterium atrosepticum SCRI1043_[YP_048962.1]
90
Arabinogalactan endo−1_[YP_003016330.1]
100
Vibrio mimicus VM603_[ZP_05721770.1]
Arabinogalactan endo−1_[YP_003013430.1]
116618168_Leuconostoc_mesenteroides_subsp_mesenteroides_ATCC_8293
50812295_Bacillus_subtilis_subsp_subtilis_str_168
92
100
15614586_Bacillus_halodurans_C−125
Arabinogalactan endo−1_[YP_002883086.1]
30
36
Jonesia denitrificans DSM 20603_[YP_003160357.1]
21
23
23464860_Bifidobacterium_longum_NCC2705
Coprococcus eutactus ATCC 27759_[ZP_02208215.1]
YBAB_BACCI RecName Full=Uncharacterized protein in bgaB 5’region AltName Full=ORF1_[P48843.1]
100 15643957_Thermotoga_maritima_MSB8
148270678_Thermotoga_petrophila_RKU−1
Arabinogalactan endo−1_[YP_002352752.1]
arabinogalactan endo−1_[YP_002428099.1]
glycosyl hydrolase_[ZP_03055277.1]
arabinogalactan endo−1_[ZP_05656968.1]
Yersinia pestis KIM_[NP_670537.1]
95
Serratia odorifera 4Rx13_[ZP_06190082.1]
58
Arabinogalactan endo−1_[YP_003003621.1]
62
Klebsiella pneumoniae subsp rhinoscleromatis ATCC 13884_[ZP_06017098.1]
100
54
Cronobacter turicensis_[YP_003208911.1]
Arabinogalactan endo−1_[YP_003018520.1]
76
arabinogalactan endo−1_[YP_001142175.1]
arabinogalactan endo−1_[YP_003153874.1]
arabinogalactan endo−1_[YP_003153873.1]
92
arabinogalactan endo−1_[ZP_04853513.1]
Bryantella formatexigens DSM 14469_[ZP_05344897.1]
100
Roseburia inulinivorans DSM 16841_[ZP_03755773.1]
47
Coprococcus eutactus ATCC 27759_[ZP_02206114.1]
.5._Popl112732_Postia_placenta
97
.5._Scco15841_Schizophyllum_commune
65
.5._Phch138710_Phanerochaete_chrysosporium
35
.5._CC1G_03507_Coprinus_cinereus
.5._Cohe24653_Cochliobolus_heterostrophus
99
.5._SNU11649_Stagonospora_nodorum
73
62
.5._AB04106_Alternaria_brassicicola
12
.5._FOXG_17412_Fusarium_oxysporum
27
.5._Mygr51381_Mycosphaerella_graminicola
.5._NFIA017780_Neosartorya_fischeri
100
.5._Afu1g06910_Aspergillus_fumigatus
67
95
.5._ATEG_02927_Aspergillus_terreus
.5._Asni187227_Aspergillus_niger
85
72
.5._AN5727_Aspergillus_nidulans
48
.5._AFL09135_Aspergillus_flavus
48
.5._Crpa72924_Cryphonectria_parasitica
57
.5._Crpa45201_Cryphonectria_parasitica
83
100 .5._BC1G_16209_Botrytis_cinerea
.5._SS1G_11585_Sclerotinia_sclerotiorum
70
.5._MGG_09726_Magnaporthe_grisea
.5._VDAG_09288_Verticillium_dahliae
58
.5._FGSG_11048_Fusarium_graminearum
97
98
.5._FVEG11697_Fusarium_verticillioides
95
47
.5._Neha40212_Nectria_haematococca
.5._NCU11198_Neurospora_crassa
90
.5._Pa_1_16660_Podospora_anserina
84
.5._CHG05856_Chaetomium_globosum
.1._BC1G_03991_Botrytis_cinerea
100
.1._SS1G_01216_Sclerotinia_sclerotiorum
89
.1._Mygr25958_Mycosphaerella_graminicola
81
.1._Myfi5258_Mycosphaerella_fijiensis
100
Phso131883_Phytophthora_sojae
Phca17588_Phytophthora_capsici
79
PITG_09910_Phytophthora_infestans
100
Phca14305_Phytophthora_capsici
39
Phra76943_Phytophthora_ramorum
68
100
Phra76942_Phytophthora_ramorum
36
Phra76940_Phytophthora_ramorum
99
Hyp702954_Hyaloperonospora_parasitica
48
73
Phso131878_Phytophthora_sojae
57
Phca13457_Phytophthora_capsici
Phra76944_Phytophthora_ramorum
99
Phca33646_Phytophthora_capsici
33
Phso131879_Phytophthora_sojae
Physcomitrella patens subsp patens_[XP_001762057.1]
100
Physcomitrella patens subsp patens_[XP_001781259.1]
158314089_Frankia_sp_EAN1pec
arabinogalactan endo−1_[YP_001818047.1]
182413864_Opitutus_terrae_PB90−1
64
14
91
26
35
25
6
18
85374319_Erythrobacter_litoralis_HTCC2594
70730824_Pseudomonas_fluorescens_Pf−5
EC851785 HAE00002312 Home−made _[EC851785.1]
98
116625037_Solibacter_usitatus_Ellin6076
118469296_Mycobacterium_smegmatis_str_MC2_155
88
118467431_Mycobacterium_smegmatis_str_MC2_155
Pist30010_Pichia_stipitis
100
157692893_Bacillus_pumilus_SAFR−032
114569664_Maricaulis_maris_MCS10
148557074_Sphingomonas_wittichii_RW1
.1._Crpa62614_Cryphonectria_parasitica
.1._FGSG_00051_Fusarium_graminearum
38
.1._AFL10930_Aspergillus_flavus
58
.1._Asni211815_Aspergillus_niger
.1._BC1G_01922_Botrytis_cinerea
39
100
.1._BC1G_14773_Botrytis_cinerea
.1._SS1G_01652_Sclerotinia_sclerotiorum
86
100 .1._MGYG_05305_Microsporum_gypseum
55
.1._MCYG_07433_Microsporum_canis
49 .1._TEQG_07123_Trichophyton_equinum
57
22
.1._AB08652_Alternaria_brassicicola
93
.1._Neha80653_Nectria_haematococca
93
.1._FVEG11942_Fusarium_verticillioides
97
20
.1._CHG09937_Chaetomium_globosum
43
20
.1._NCU01838_Neurospora_crassa
63
.1._SS1G_10174_Sclerotinia_sclerotiorum
.1._Trre65106_Trichoderma_reesei
78
.1._Trat46232_Trichoderma_atoviride
63
.1._ACLA076410_Aspergillus_clavatus
49
28
.1._Cohe98429_Cochliobolus_heterostrophus
Phra77558_Phytophthora_ramorum
100
Phso108252_Phytophthora_sojae
100 Phso142055_Phytophthora_sojae
93
.1._Trre65190_Trichoderma_reesei
49
.1._Myfi57691_Mycosphaerella_fijiensis
96
.1._Mygr70166_Mycosphaerella_graminicola
.1._ACLA087720_Aspergillus_clavatus
85
.1._Asni46258_Aspergillus_niger
92 49
.1._Afu2g17500_Aspergillus_fumigatus
27
100
.1._AFL02869_Aspergillus_flavus
26
.1._AN11114_Aspergillus_nidulans
.1._SS1G_13754_Sclerotinia_sclerotiorum
.1._Crpa84265_Cryphonectria_parasitica
64
64
.1._NCU04697_Neurospora_crassa
78
.1._AB07771_Alternaria_brassicicola
91 83
83 .1._Cohe78162_Cochliobolus_heterostrophus
70
.1._PTRG_00659_Pyrenophora_tritici−repentis
.1._MGG_10714_Magnaporthe_grisea
62
.1._FVEG05759_Fusarium_verticillioides
29
.1._Trat34934_Trichoderma_atoviride
100
.1._Trvi48875_Trichoderma_virens
47
.1._FGSG_06480_Fusarium_graminearum
94
.1._A020000571_Aspergillus_oryzae
42
.1._Neha51531_Nectria_haematococca
40
100
.1._ATEG_07252_Aspergillus_terreus
.1._Afu8g01780_Aspergillus_fumigatus
29
.1._Trre64996_Trichoderma_reesei
80
.1._FOXG_14488_Fusarium_oxysporum
91784632_Burkholderia_xenovorans_LB400
66043278_Pseudomonas_syringae_pv_syringae_B728a
17
Fungi
33
124266186_Methylibium_petroleiphilum_PM1
34
Oomycetes
148553910_Sphingomonas_wittichii_RW1
15
55
146341448_Bradyrhizobium_sp_ORS278
Support for with Fungi
54025238_Nocardia_farcinica_IFM_10152
Support for within Fungi
11
89056226_Jannaschia_sp_CCS1
61
27381513_Bradyrhizobium_japonicum_USDA_110
Emhu415168_Emiliania_huxleyi
76800744_Natronomonas_pharaonis_DSM_2160
100
55376903_Haloarcula_marismortui_ATCC_43049
Pa_3_5180_Podospora_anserina
98
CHG09518_Chaetomium_globosum
71
PTRG_11878_Pyrenophora_tritici−repentis
100
66
SNU10152_Stagonospora_nodorum
NCU00437_Neurospora_crassa
Fig. 1.29
28
14
Outgroup
9
Outgroup
74
0.4
100
100
42
55
81
65
75
92
65
45
0.4
100
82
Support for within Fungi
Fig. 1.30
Paenibacillus sp JDR−2_[YP_003013953.1]
Bacteroides dorei DSM 17855_[ZP_03299015.1]
Pedobacter heparinus DSM 2366_[YP_003092569.1]
80
Parabacteroides merdae ATCC 43184_[ZP_02031901.1]
69
Parabacteroides distasonis ATCC 8503_[YP_001302701.1]
Victivallis vadensis ATCC BAA−548_[ZP_06241603.1]
Thermobaculum terrenum ATCC BAA−798_[YP_003323765.1]
94
Thermomicrobia bacterium PRI−1686_[AAR96047.1]
100
Paenibacillus sp JDR−2_[YP_003010242.1]
Opitutaceae bacterium TAV2_[ZP_03725668.1]
31
Opitutus terrae PB90−1_[YP_001820591.1]
Bacteroides sp 2_2_4_[ZP_04551260.1]
100
Bacteroides sp 1_1_6_[ZP_04845599.1]
100
Ruminococcus obeum ATCC 29174_[ZP_01964696.1]
100
Pediococcus acidilactici 7_4_[ZP_06196645.1]
62
Enterococcus faecium DO_[ZP_00602679.1]
45
Lactobacillus plantarum_[ACR19007.1]
Thalassiosira pseudonana CCMP1335_[XP_002297169.1]
97
Victivallis vadensis ATCC BAA−548_[ZP_06242335.1]
172060271_Burkholderia_ambifaria_MC40−6
66
116688192_Burkholderia_cenocepacia_HI2424
Catenulispora acidiphila
BC1G_07101_Botrytis_cinerea
Afu3g02880_Aspergillus_fumigatus
100 NFIA004560_Neosartorya_fischeri
100
68
ATEG_05089_Aspergillus_terreus
99
AFL07340_Aspergillus_flavus
55
35
Asni176718_Aspergillus_niger
CHG06672_Chaetomium_globosum
56
Trvi68030_Trichoderma_virens
Catenulispora acidiphila
96
Stigmatella aurantiaca D4/3−1_[ZP_01461681.1]
.2._50551131_Yarrowia_lipolytica
98
.2._50421633_Debaryomyces_hansenii
23
Phra82832_Phytophthora_ramorum
100
Phso132256_Phytophthora_sojae
100
Phra82838_Phytophthora_ramorum
35
.1._Crpa64851_Cryphonectria_parasitica
.1._AFL01780_Aspergillus_flavus
100
83
.1._Asni170172_Aspergillus_niger
99
100
.1._NFIA022970_Neosartorya_fischeri
100
.1._Afu1g01660_Aspergillus_fumigatus
.1._SNU10370_Stagonospora_nodorum
57
88
.1._PTRG_05955_Pyrenophora_tritici−repentis
88
.1._Cohe110857_Cochliobolus_heterostrophus
100
.1._Myfi43770_Mycosphaerella_fijiensis
94
33
52
.1._Mygr69329_Mycosphaerella_graminicola
.1._Crpa52455_Cryphonectria_parasitica
.5._AB00100_Alternaria_brassicicola
94
.5._Cohe45960_Cochliobolus_heterostrophus
.5._AN10277_Aspergillus_nidulans
98
98
.5._VDAG_07955_Verticillium_dahliae
63
.5._Afu1g06130_Aspergillus_fumigatus
.5._ATEG_03018_Aspergillus_terreus
53
.5._Asni42916_Aspergillus_niger
24
36
.5._SS1G_13501_Sclerotinia_sclerotiorum
43
71
.5._Crpa64882_Cryphonectria_parasitica
50
.5._Myfi40556_Mycosphaerella_fijiensis
.5._VDAG_04642_Verticillium_dahliae
.5._Scco59132_Schizophyllum_commune
48
100
.5._Scco55069_Schizophyllum_commune
94
Fungi
.5._Popl52078_Postia_placenta
94
.5._Popl51992_Postia_placenta
Oomycetes
SS1G_04541_Sclerotinia_sclerotiorum
100
MGG_05246_Magnaporthe_grisea
57
Trvi69065_Trichoderma_virens
Support for with Fungi
93
Trat43821_Trichoderma_atoviride
59
Trre58887_Trichoderma_reesei
Acidobacterium capsulatum ATCC 51196_[YP_002753889.1]