Additional File 1: fungal genomes used for alignment based fungal gene prediction

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Additional File 1: fungal genomes used for alignment based fungal gene prediction.

For each species is given the classification according to the NCBI Taxonomy browser (12/06/2012). The source indicates the sequence repository from which the genome data were downloaded. Species from which unigenes were used to benchmark the performance of the ABDGP method are indicated

Fungal species	Phylum \| Class \| Order	Source^a	Unigenes^b
Aspergillus flavus	Ascomycota \| Eurotiomycetes \| Eurotiales	BROAD
Aspergillus nidulans	Ascomycota \| Eurotiomycetes \| Eurotiales	BROAD	GI5
Aspergillus niger	Ascomycota \| Eurotiomycetes \| Eurotiales	BROAD
Aspergillus oryzae	Ascomycota \| Eurotiomycetes \| Eurotiales	BROAD
Botrytis cinerea	Ascomycota \| Leotiomycetes \| Helotiales	BROAD
Candida albicans	Ascomycota \| Saccharomycetes \| Saccharomycetales Saccharomycetales	BROAD
Cladosporium fulvum	Ascomycota \| Dothideomycetes \| Capnodiales	JGI
Cochliobolus heterostrophus C5	Ascomycota \| Dothideomycetes \| Pleosporales	JGI	JGI
Coccidioides immitis RS	Ascomycota \| Eurotiomycetes \| Onygenales	BROAD
Cryptococcus neoformans grubii h99	Basidiomycota \| Tremellomycetes \| Tremellales	BROAD
Coccidioides posadasii	Ascomycota \| Eurotiomycetes \| Onygenales	BROAD
Cryphonectria parasitica	Ascomycota \| Sordariomycetes \| Diaporthales	JGI	JGI
Dothistroma septosporum	Ascomycota \| Dothideomycetes \| Capnodiales	JGI	JGI
Fusarium graminearum	Ascomycota \| Sordariomycetes \| Hypocreales	BROAD
Fusarium oxysporum	Ascomycota \| Sordariomycetes \| Hypocreales	BROAD
Fusarium verticillioides	Ascomycota \| Sordariomycetes \| Hypocreales	BROAD	GI8
Histoplasma capsulatum NAm1	Ascomycota \| Eurotiomycetes \| Onygenales	BROAD
Magnaporthe oryzae ^c	Ascomycota \| Sordariomycetes \| Magnaporthales	BROAD	GI6
Mycosphaerella fijiensis	Ascomycota \| Dothideomycetes \| Capnodiales	JGI
Neurospora crassa	Ascomycota \| Sordariomycetes \| Sordariales	BROAD	GI4
Nectria haematococca	Ascomycota \| Sordariomycetes \| Hypocreales	JGI	JGI
Puccinia graminis tritici	Basidiomycota \| Pucciniomycetes \| Pucciniales	BROAD
Pyrenophora tritici-repentis	Ascomycota \| Dothideomycetes \| Pleosporales	BROAD
Stagonospora nodorum	Ascomycota \| Dothideomycetes \| Pleosporales	BROAD
Sclerotinia sclerotiorum	Ascomycota \| Leotiomycetes \| Helotiales	BROAD
Trichoderma atroviride	Ascomycota \| Sordariomycetes \| Hypocreales	JGI	JGI
Verticillium dahliae VdLs.17	Ascomycota \| Sordariomycetes \| Glomerellales	BROAD
Verticillium albo-atrum VaMs.102	Ascomycota \| Sordariomycetes \| Glomerellales	BROAD
Zymoseptoria tritici ^d	Ascomycota \| Dothideomycetes \| Capnodiales	JGI	JGI

^a BROAD institute (www.broadinstitute.org) and Joint Genome Institute (www.jgi.doe.gov)

^b The Gene Index Project, including version number (compbio.dfci.harvard.edu/tgi/) and Joint Genome Institute (www.jgi.doe.gov)

^c Formerly named Magnaporthe grisea

^d Formerly named Mycosphaerella graminicola