Resources for Fungal Comparative Genomics: Annotations and Tools

This website is intended to provide genome annotation data for the available fungal genomes. Additional genome annotations, homology searching, and best reciprocal orthologous genes have been generated for the available species and will be made downloadable this fall. Analyses of orthologous gene relationships, gene trees, and gene structures will follow shortly.

A tree representing the phylogenetic relationships of the sequenced species is available.

Tools for gene comparisons are available. These include BLAST and extracting sub-sequence sequences from the genome.

Genome annotations

Ascomycota

Hemiascomycota
Saccharomyces cerevisiae S288C	Gbrowse	GFF	CDS	AA	DNA	Saccharomyces Genome Database
Saccharomyces cerevisiae RM11-1a	Gbrowse	GFF	CDS	AA	DNA	Broad Institute
Saccharomyces cerevisiae YJM789	Gbrowse	GFF	CDS	AA	DNA	Stanford
Saccharomyces paradoxus	Gbrowse	GFF	CDS	AA	DNA	Broad Institute, Saccharomyces Genome Database
Saccharomyces mikatae	Gbrowse	GFF	CDS	AA	DNA	Broad Institute, WUSTL, Saccharomyces Genome Database
Saccharomyces kudriavzevii	Gbrowse	GFF	CDS	AA	DNA	WUSTL, Saccharomyces Genome Database
Saccharomyces bayanus	Gbrowse	GFF	CDS	AA	DNA	WUSTL, Saccharomyces Genome Database
Saccharomyces castellii	Gbrowse	GFF	CDS	AA	DNA	WUSTL, Saccharomyces Genome Database
Candida glabrata	Gbrowse	GFF	CDS	AA	DNA	Genolevures
Kluyveromyces waltii	Gbrowse	GFF	CDS	AA	DNA	Broad Institute,SGD
Ashbya gossypii	Gbrowse	GFF	CDS	AA	DNA	Ashbya Genome Database
Saccharomyces kluyveri	Gbrowse	GFF	CDS	AA	DNA	WUSTL, Saccharomyces Genome Database
Kluyveromyces lactis	Gbrowse	GFF	CDS	AA	DNA	Genolevures
Debaryomyces hansenii	Gbrowse	GFF	CDS	AA	DNA	Genolevures
Candida albicans	Gbrowse	GFF	CDS	AA	DNA	Stanford
Candida dubliniensis	Gbrowse	GFF	CDS	AA	DNA	Sanger Centre
Candida tropicalis	Gbrowse	GFF	CDS	AA	DNA	Broad Institute
Candida lusitaniae	Gbrowse	GFF	CDS	AA	DNA	Broad Institute
Candida guilliermondii	Gbrowse	GFF	CDS	AA	DNA	Broad Institute
Yarrowia lipolytica	Gbrowse	GFF	CDS	AA	DNA	Genolevures

S.cerevisae
Image courtesy SGD

A.gossypii
Image courtesy P.Philippsen

C.albicans
Image courtesy Whitehead Institute, Fink Lab

Euascomycota
Sordariomycota
Neurospora crassa	Gbrowse	GFF	CDS	AA	DNA	Broad Institute
Magnaporthe grisea	Gbrowse	GFF	CDS	AA	DNA	Broad Institute
Fusarium graminearum	Gbrowse	GFF	CDS	AA	DNA	Broad Institute
Fusarium verticillioides	Gbrowse	GFF	CDS	AA	DNA	Broad Institute
Trichoderma reesei	Gbrowse	GFF	CDS	AA	DNA	DOE Joint Genome Institute
Podospora anserina	Gbrowse	GFF	CDS	AA	DNA	CNRS & Genoscope
Chaetomium globosum	Gbrowse	GFF	CDS	AA	DNA	Broad Institute

N.crassa
Image courtesy N. B. Raju

M.grisae

F.graminearum

P.anserina
Image courtesy CNRS

C.globosum
Image courtesy John Taylor

Eurotiomycota
Aspergillus nidulans	Gbrowse	GFF	CDS	AA	DNA	Broad Institute
Aspergillus fumigatus	Gbrowse	GFF	CDS	AA	DNA	TIGR, Sanger Centre
Aspergillus terreus	Gbrowse	GFF	CDS	AA	DNA	Broad Institute
Aspergillus oryzae	Gbrowse	GFF	CDS	AA	DNA	NITE
Botrytis cinerea	Gbrowse	GFF	CDS	AA	DNA	Broad Institute
Sclerotinia sclerotiorum	Gbrowse	GFF	CDS	AA	DNA	Broad Institute

A. fumigatus
Image courtesy Robert Cramer and Charles Lawrence

A. nidulans
Image courtesy Gettysburg College SEM

Histoplasma capsulatum	Gbrowse	GFF	CDS	AA	DNA	WUSTL
Coccidioides immitis	Gbrowse	GFF	CDS	AA	DNA	Broad Institute
Uncinocarpus reesii	Gbrowse	GFF	CDS	AA	DNA	Broad Institute
Stagonospora nodorum	Gbrowse	GFF	CDS	AA	DNA	Broad Institute

C. immitis
Image courtesy Tom Volk

H. capsulatum
Image courtesy Tom Volk

Archeascomycota
Schizosaccharomyces pombe	Gbrowse	GFF	CDS	AA	DNA	Sanger Centre
Pneumocystis carinii (note this a low-coverage assembly)	Gbrowse	GFF	CDS	AA	DNA	U Cincinnati

S. pombe
Image courtesy Paul Young

P. carinii
Image courtesy Mt Sinai Hospital, Toronto CA

Basidiomycota

Also see www.basidiomycetes.org

Cryptococcus
Cryptococcus neoformans var grubii serotype A, strain H99	Gbrowse	GFF	CDS	AA	DNA	Duke, Broad Institute
C. neoformans var neoformans serotype D, strain JEC21	Gbrowse	GFF	CDS	AA	DNA	TIGR, Stanford
Crytococcus gattii serotype B, strain WM276	Gbrowse	GFF	CDS	AA	DNA	BC GSC
C. gattii serotype B/C, strain R265	Gbrowse	GFF	CDS	AA	DNA	Broad Institute
Homobasidiomycota
Coprinus cinereus (Coprinopsis cinerea)	Gbrowse	GFF	CDS	AA	DNA	Duke, Broad Institute
Phanerochaete chrysosporium	Gbrowse	GFF	CDS	AA	DNA	Joint Genome Institute

C. neoformans
Image courtesy J.Lodge

C. cinereus
Image courtesy Mario Cervini

P. chrysosporium
Image courtesy Tom Volk

Ustilaginomycota
Ustilago maydis	Gbrowse	GFF	CDS	AA	DNA	Broad Institute

U. maydis
Image courtesy A.G. Bölker

Zygomycota

Rhizopus oryzae

R.oryzae
Image courtesy David Ellis

Phylogeny

The phylogenetic relationship of the sequenced genomes (not all may be present when new data is added to the system). This is a MrBayes tree for 168 orthologous proteins among the 56 genomes. Corrections to remove fast evolving sites produces the same topology. This is still an in-progress project. Click on the image for a printable PDF.

Please contact Jason Stajich with questions.

Genome Tools

Similarity Searches

Fungal BLAST

a protein sequence versus annotated fungal proteins (BLASTP)
a DNA sequence versus fungal genomes (BLASTN)
a protein sequence versus translated fungal genomes (TBLASTN)
a DNA sequence,translated versus annotated fungal proteins (BLASTX)
a DNA sequence, translated versus fungal genomes, translated (TBLASTX [disabled])

Retrieve a gene sequence

Retrieve CoDing Sequence (CDS)
Retrieve Protein Translation Sequence
Retrieve Genomic Locus
Retrieve Introns

Other tools

Fungal Motifs [old, removed] as per MW Hahn et al.

Gene Prediction Parameter files

SNAP parameter files
Genezilla parameter files
AUGUSTUS parameter files

Resources for Fungal Comparative Genomics