Regulation of pentose utilisation in Eurotiales
Supplementary Information
Supplemental Table 1. Primers used in this study.
Table 1. Primers used in this study.
gene
araR 5’
flank
araR 3’
flank
xlnR
abfA
abfB
ladA
xdhA
xyrA
xkiA
dw
Primer 5’ to 3’
up
GGTACCCTTTGATGTTAGTTG
GGATCCATCGCGGGGAAAC
GCATGCTTAAATTATCTTCCGCC
AAGCTTTCAATTTTTGTGTCTGGAG
CTTGGTTGGTCTCCGTCTG
AGGGTGGCAACTCATCCAG
ACCCGCGCCCTATACAGC
AGATCTCTACCGCAACTGTTCTCG
AGATCTGCACCCAGAACACCAACG
AACAGCGGCTACGACATGC
CATCGGCTTCGACCTCTC
GGGAAGTGCGGAGGGAGTG
GCCAGCACCGTCAACTTG
CTGCTTCGTGCCATCGTTG
CTGCAGTTTAAATCTTCTGACCAG
CTGCAGAATTCTATGAATCGACACC
TCTGCTTCAACCGCTGAGG
CAGTGCTTCCCTTCCTGG
www.studiesinmycology.org
38-S1
38-S2
Ascomycota
http://www.broad.mit.edu/annotation/genome/aspergillus_group/Blast.html
Aspergillus clavatus
Aspergillus fischerianus
Botrytis cinerea
Gibberella zeae
Fusarium graminearum
Ascomycota
http://www.ncbi.nlm.nih.gov/genomeprj
Ascomycota
Mucormycotina
Ascomycota
http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/Home.html
http://www.broad.mit.edu/annotation/genome/rhizopus_oryzae/Home.html
http://www.broad.mit.edu/annotation/genome/schizosaccharomyces_japonicus
Schizosaccharomyces japonicus
Pyricularia oryzae
Rhizopus oryzae
Ascomycota
Basidiomycota
http://podospora.igmors.u-psud.fr/
http://genome.jgi-psf.org/Pospl1/Pospl1.home.html
Podospora anserina
Mucormycotina
http://genome.jgi-psf.org/Phybl1/Phybl1.home.html
Phycomyces blakesleeanus
Postia placenta
Ascomycota
Ascomycota
http://www.ncbi.nlm.nih.gov/genomeprj
http://www.ncbi.nlm.nih.gov/genomeprj
Penicillium marneffei
Talaromyces stipitatus
Magnaporthe oryzae
Ascomycota
http://genome.jgi-psf.org/Mycfi1/Mycfi1.home.html
Penicillium chrysogenum
Ascomycota
http://www.broad.mit.edu/annotation/genome/neurospora/Home.html
Mycosphaerella fijiensis
Neurospora crassa
Paracercospora fijiensis var. difformis
Mucorales
Mucormycotina
Ascomycota
http://genome.jgi-psf.org/Mucci1/Mucci1.home.html
http://genome.jgi-psf.org/Necha1/Necha1.home.html
Mucor circinelloides
Agaricales
Basidiomycota
http://genome.jgi-psf.org/Lacbi1/Lacbi1.home.html
Hypocreales
Schizosaccharomycetales
Mucorales
Magnaporthales
Polyporales
Sordariales
Mucorales
Eurotiales
Eurotiales
Eurotiales
Capnodiales
Sordariales
Hypocreales
Onygenales
Ascomycota
Ascomycota
http://www.broad.mit.edu/annotation/genome/fusarium_group/MultiHome.html
Hypocreales
Hypocreales
Tremellales
Agaricales
Onygenales
Saccharomycetales
Saccharomycetales
Helotiales
Eurotiales
Eurotiales
Eurotiales
Eurotiales
Eurotiales
Eurotiales
Eurotiales
Eurotiales
order
http://www.broad.mit.edu/annotation/genome/histoplasma_capsulatum/Home.html
Ascomycota
Ascomycota
http://www.broad.mit.edu/annotation/genome/fusarium_group/MultiHome.html
http://www.broad.mit.edu/annotation/genome/fusarium_group/MultiHome.html
Basidiomycota
Basidiomycota
http://www.broad.mit.edu/annotation/genome/coprinus_cinereus/Home.html
http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans/Home.html
Ascomycota
Ascomycota
http://www.broad.mit.edu/annotation/genome/saccharomyces_cerevisiae/Home.html
http://www.broad.mit.edu/annotation/genome/coccidioides_group/MultiHome.html
Ascomycota
Ascomycota
Nectria haematococca
Laccaria bicolor
Gibberella moniliformis
Ajellomyces capsulatus
Fusarium verticillioides
Histoplasma capsulatum
Fusarium oxysporum
Coprinopsis cinerea
Filobasidiella neoformans
Coprinus cinereus
Saccharomyces cerevisiae
Botryotinia fuckeliana
Cryptococcus neoformans
Coccidioides immitis
Candida robusta
Candida albicans
http://www.broad.mit.edu/annotation/genome/botrytis_cinerea/Home.html
Ascomycota
Ascomycota
http://www.broad.mit.edu/annotation/genome/aspergillus_group/Blast.html
http://www.broad.mit.edu/annotation/genome/aspergillus_group/Blast.html
Aspergillus oryzae
Aspergillus terreus
http://www.broad.mit.edu/annotation/genome/candida_group/MultiHome.html
Ascomycota
http://www.broad.mit.edu/annotation/genome/aspergillus_group/Blast.html
Aspergillus niger JGI
Ascomycota
Ascomycota
http://www.broad.mit.edu/annotation/genome/aspergillus_group/Blast.html
http://www.broad.mit.edu/annotation/genome/aspergillus_group/Blast.html
Aspergillus fumigatus
Aspergillus nidulans
Emericella nidulans
Ascomycota
Ascomycota
http://www.broad.mit.edu/annotation/genome/aspergillus_group/Blast.html
http://www.broad.mit.edu/annotation/genome/aspergillus_group/Blast.html
Aspergillus flavus
Neosartorya fischeri
(sub)phylum
Species teleomorph
website
Species anamorph
Table 2. Fungal genomes used for the phylogenetic analysis.
Battaglia et al.
Supplementary Information
Phanerochaete chrysosporium
Hypocrea jecorina
Hypocrea virens
Septoria tritici
Sporotrichum pruinosum
Trichoderma reesei
Trichoderma virens
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Ustilaginales
Basidiomycota
Ascomycota
http://www.broad.mit.edu/annotation/genome/ustilago_maydis/Home.html
http://www.broadinstitute.org/annotation/genome/verticillium_dahliae/MultiHome.html
Ustilago maydis
Onygenales
Ascomycota
http://www.broad.mit.edu/annotation/genome/uncinocarpus_reesii/Home.html
Hypocreales
Hypocreales
Hypocreales
Ascomycota
Ascomycota
Corticiales
http://genome.jgi-psf.org/Trire2/Trire2.home.html
Basidiomycota
http://genome.jgi-psf.org/Phchr1/Phchr1.home.html
order
Capnodiales
http://genome.jgi-psf.org/Trive1/Trive1.home.html
(sub)phylum
Ascomycota
website
http://genome.jgi-psf.org/Mycgr1/Mycgr1.home.html
Verticillium albo-atrum
Uncinocarpus reesii
Species teleomorph
Mycosphaerella graminicola
Species anamorph
Table 2. (Continued).
Regulation of pentose utilisation in Eurotiales
Supplementary Information
38-S3
Battaglia et al.
Supplemental Figure 1. Maximum Parsimony bootstrap tree (1000 bootstraps) of pentose catabolic pathway
genes. XDH = xylitol dehydrogenase, LAD = L-arabitol dehydrogenase, XKI = D-xylulose kinase, XYR =
D-xylose reductase.
Supplementary Information
Fig. 1. Maximum Parsimony bootstrap tree (1000 bootstraps) of pentose catabolic pathway genes. XDH = xylitol dehydrogenase, LAD = L-arabitol dehydrogenase, XKI =
D-xylulose kinase, XYR = D-xylose reductase.
38-S4
Regulation of pentose utilisation in Eurotiales
Supplementary Information
Fig. 1. (Continued).
www.studiesinmycology.org
38-S5