Genome-scale comparative analysis of:
Synapomorphies
B
A
C
C
A
B
C
A novel mode of visual
perception in the fungi…
Gene Fusions
Gene fusions are a hyrbid of two or more
previously separate open reading frames (ORFs).
Mechanism 1: Fission by Separation
Insertion Event
Loss Event
35
Loss Event
Dark
Rate and Types of Gene Fission
500
400
300
29
26
100
24
Light
Light
Light (521nm)
(630nm)
(521nm)
+ HA
Zoospores were exposed to hydroxylamine in a photobleaching
process, as no gene-knockout is available, to test whether the
gene-fusion was involved in photo-taxis.
Localization of BeGC1 to the eye-spot by immunofluorescence
microscopy. From left to the right: zoospore under phase
contrast (DIC image); BeGC1 (green); lipid droplets (nile-red)
of the eyespot.
22
20
18
Rate of Fission
Dark
16
14
12
1 8 9 17 62
10
8
Blastocladiomycota
Chytridiomycota
6
Side body complex - "eye spot"
4
2
0
0
Flagellum
62
Saccharomycotina
These data suggest that gene fission plays
an important and hitherto underestimated
role in gene evolution. Gene fusions,
therefore, are highly labile characters,
and their use for polarizing evolutionary
relationships, without reference to gene
and species phylogenies is limited.
200
0
Sordariomycetes
Number of Zoosporangia
600
Ascomycota
Loss Event
Pezizomycotina
Mechanism 2: Fission by Degeneration
Eurotiomycetes
Light (521nm)
Gene Fissions
Mechanism 3: Fission by Duplication & Differential Loss
12
Dothideomycetes
Gene fusions, therefore, have been suggested to
represent useful tools for polarizing evolutionary
relationships (1-3). This approach follows the logic that
taxa possesing a gene fusion are monophyletic to the
exclusion of taxa that possess unfused orthologs.
Single Gene
One gene fusion, consistent with the
Promoter Region
monophyly of the Blastocladiomycota
Coding Region
includes a novel hybrid-protein that we
Stop Codon
Start Codon
show functions in the visual perception
and phototaxis of Blastocladiella
Gene Fusion
Deletion Event
zoospore.
This light perception is accomplished by
the function of a novel gene fusion (BeGC1) of a
guanylyl cyclase catalytic domain and rhodopsin-like
domain. Full genome sequencing was used to recover
the sequence of the gene-fusion and found no other
true rhodopsin genes.
Phototaxis assays were performed in
agar plates, the resulting vegetative cells found in
the region of the plates exposed, or not, to light
were visualised and counted under a microscope.
Phanerochaete chrysosporium
Phanerochaete carnosa
12 Phlebiopsis gigantea
12 36 Bjerkandera adusta
16 31
12 36 Phlebia brevispora
16 Fomitopsis pinicola
32B
14 Postia placenta
49 Ceriporiopsis subvermispora
12
16 Wolfiporia cocos
13 Ganoderma sp.
32A
Dichomitus
squalens
16
32A 49
Trametes versicolor
13 16 49 Stereum hirsutum
8 12 16
12
36 Heterobasidion annosum
32B 36 56
38 45 Pleurotus ostreatus
12 15 16 32B 36 56 Laccaria bicolor
31 56
12 16 31 32B 56 Schizophyllum commune
36 Gloeophyllum trabeum
12 16 32B Punctularia strigosozonata
16 32B 45 Fomitiporia mediterranea
49
49 16
12 Serpula lacrymans
13 Coniophora puteana
31 56 Coprinus cinereus *
31 45
38
36 Agaricus bisporus
15 31 45 Auricularia delicata
15 Dacryopinax sp.
Tremella mesenterica
51 57
Tremellomycetes
Cryptococcus neoformans
15 17 Wallemia sebi
Rhodotorula graminis
1 15 Sporobolomyces roseus
Pucciniomycotina
17 Puccinia graminis
9 11 Melampsora laricis-populina
Malassezia globosa
11 13
Ustilaginomycotina
5 27 28 29
Ustilago maydis *
14 15
Pyrenophora teres
60
42 55 Pyrenophora tritici-repentis
55 Alternaria brassicicola
42 55
Cochliobolus sativus
59
55 59 Cochliobolus heterostrophus
43 47
Setosphaeria turcica
48 60
Leptosphaeria maculans
Stagonospora nodorum
10 Hysterium pulicare
48 Rhystidhysteron rufulum
Septoria musiva
3
Septoria populicola
Mycosphaerella fijiensis
Dothistroma septosporum
Mycosphaerella graminicola
Baudoinia compniacensis
40 61
Aspergillus fumigatus
Neosartorya fischeri
Aspergillus clavatus
Aspergillus oryzae
40
40
Aspergillus flavus
54 Aspergillus terreus
50 54 61 Aspergillus carbonarius
40 Aspergillus niger
44 50
54 Aspergillus aculeatus
Aspergillus nidulans
54 61
Microsporum canis
Microsporum gypseum
50 54 61
Trichophyton equinum
9
Coccidioides immitis
61 Coccidioides posadasii
44 54 Uncinocarpus reesii
Blastomyces dermatitidis
61 Histoplasma capsulatum
52
10 17
44 Paracoccidioides brasiliensis
58
Sporotrichum thermophile
53
41 Thielavia terrestris
Chaetomium globosum
3 37 Podospora anserina
37
Neurospora
crassa *
37
Neurospora tetrasperma
39 Cryphonectria parasitica
Magnaporthe grisea
Trichoderma reesei
Trichoderma virens
41
46 Trichoderma atoviride
Nectria haematococca
46
Fusarium oxysporum
Fusarium verticillioides
Fusarium graminearum
39
Verticillium dahliae
3 33
Verticillium albo-atrum
Acremonium alcalophilum
Botrytis cinerea
Leotiomycetes
Sclerotinia sclerotiorum
Spathaspora passalidarum
Candida albicans
Pichia stipitis
Debaryomyces hansenii
Candida tenuis
Candida glabrata
4
34
Saccharomyces cerevisiae *
Ashbya gossypii
2 4
34 Wickerhamomyces anomalus
8
Hansenula polymorpha
34
Pichia membranifaciens
Yarrowia lipolytica
34 Candida caseinolytica
8 Lipomyces starkeyi
HGT
Schizosaccharomyces octosporus
Schizosaccharomyces cryophilus
24 34
Schizosaccharomycetes
Schizosaccharomyces pombe *
1 18 19 20 21 22 23 25 26 30
Schizosaccharomyces japonicus
Mucor circinelloides *
Rhizopus oryzae *
Mucoromycotina
9
Phycomyces blakesleeanus
Allomyces macrogynus atcc 38327 *
6 7
Blastocladiella emersonii
Batrachochytrium dendrobatidis *
Spizellomyces punctatus daom br117
56
Basidiomycota
Gene fusions can be used as synapomorphies if they are
shown to be stable and monophyletic; thus the root of a tree
can be excluded from a clade defined by a gene fusion,
allowing phylogenetic relationships to be polarized on a tree.
36
Agaricomycotina
A
B
C
The Fungal Tree of Life
Applying this tool to the Fungi, we identified 63 gene fusions present in two or more genomes.
Using a combination of phylogenetic and comparative genomic analyses,
we then investigated the evolution of these genes across 115
fungal genomes, testing
each gene fusion for
Accounting for these considerable sources of homoplasy, we identified
evidence of
fusion characters that provide support for multiple nodes in the phylogeny
homoplasy,
of the Fungi, including relationships within the deeply derived flagellum-forming
including gene
fungi (i.e. the chytrids)
fission, convergence,
It has been argued that gene fission events occur at a low frequency because
and horizontal
the process requires multiple simultaneous evolutionary occurances at
gene transfer.
selectively viable positions within an ORF (1): i) gain of a stop codon, ii) gain
of a promoter region, and iii) appropriation of a start codon
(Mechanism 1).
Agaricomycetes
B
@guyleonard
To investigate the fidelity of gene fusion characters, we developed an approach for identifying
differentially distributed gene fusions among whole-genome datasets: fdfBLAST.
A shared, derived character is used as a cladistic device,
grouping individual taxa or groups of taxa together
into specific clades.
A
Guy Leonard & Thomas A. Richards
0.1
0.2
Rate of Fusion
0.3
0.4
Mechanism 1: Fission by Separation
Mechanism 2: Fission by Degeneration
Mechanism 3: Fission by Duplication
& Differential Loss
Unknown
0.1
100
80+
50+
} Bootstrap Value
#
#
Fusion
Reversion
Genus species * = fdfBLAST Sampled Proteomes
1 - Stechmann A, Cavalier-Smith T (2002) Rooting the eukaryote tree by using a derived gene fusion. Science 297(5578):89–91.
2 - Philippe H, et al. (2000) Early-branching or fast-evolving eukaryotes? An answer based on slowly evolving positions. Proc Biol Sci 267(1449):1213–1221.
3 - Stechmann A, Cavalier-Smith T (2003) The root of the eukaryote tree pinpointed. Current Biology 13(17):R665–R666.
4 - Leonard, G & RichardsT. A. (2012) Genome-scale comparative analysis of gene fusions, gene fissions, and the fungal tree of life. PNAS 109(52).
5 - Avelar, G M, Schumacher, R I, Zaini, P I, Leonard, G, Richards, T A, Gomes, S L (2013) A novel mode of visual perception in the fungi. Manuscript submitted.