Tag Archives: release

FungiDB 2.3 released with 52 genomes

The latest release of FungiDB (2.3) is now live and includes 52 genomes, 11 of which are new for this release. This was a longer than expected release cycle due to reintegration with the EuPathDB software team. Programmers Raghu Ramamurthy and Edward Liaw at UC Riverside did nearly all the Fungal specific work, collaborating closely with the EuPathDB team who provided many site-specific corrections and assistance in running the workflow. This is a joint collaborative project between the UCR,Oregon State (FungiDB) and U Penn, Univ of Georgia (EuPathDB) and the work in this release was funded through grants from the Burroughs Welcome Fund, the Alfred P. Sloan Foundation, and the USDA-NIFA.

An announcement for FungiDB 2.3 is here and included below.

New genomes included in this release include

Botrytis cinerea
Sclerotinia sclerotiorum
Aspergillus carbonarius
Neosartorya fischeri
Trichoderma reesei
Schizosaccharomyces japonicus
Schizosaccharomyces octosporus
Phanerochaete chrysosporium
Sporisorium reilianum
Malassezia globosum
Mucor circinelloides f. lusitanicus
Mitochondrial genomes were added for the following organisms

Aspergillus fumigatus
Neurospora crassa
Saccharomyces cerevisiae
Schizosaccharomyces japonicus
Schizosaccharomyces octosporus
New genomics data available in this release include additional RNA-Seq experiments for Coprinopsis cinerea. High Throughput SNP (HTS) discovery module have been addded for Aspergillus fumigatus and a population of 23 strains from JCVI.

Data fixes and update

Updated in this release include new versions of annotation for

Aspergillus fumigatus – s03-m02-r18 from AspGD
Aspergillus nidulans – s09-m05-r03 from AspGD
Fusarium oxysporum f. sp. lycopersici – correcting some annotation problems in Broad v2
Neurospora discreta – correcting some annotation problems from JGI
Saccharomyces cerevisiae version from 2012-11-20
The current annotation for N. crassa is still v10 release and does not reflect the V12 release made March 2013. The updated version will be available in the 3.0 release of FungiDB.

Corrections

The Coccidioides RNA-Seq data in the previous release had flipped the labels of the spherule and mycelium results, this has been corrected.

Errors in previous loading of gene product information for P. sojae had left many genes without sufficient product information and description. This has been corrected.

Synteny results between several species were not properly loaded in the previous release. This has been corrected.

Data summary tables of genomes and gene metrics have been updated to reflect the current state of the database.

Known errors

Alternative splicing and starting/ending non-coding exons may not be properly represented in GBrowse and in the GFF files available for download.

Dermatophyte genome sequences

The first of several dermatophyte fungal genomes, Microsporum gypseum, has been released at the Broad’s Dermatophyte site.  Two Tricophyton species and another Microsporum genome should follow soon. These dermatophyte fungi are Onygenales (Ascomycota) fungi (like Coccidioides and Histoplasma), although their placement in the phylogenies shown in the whitepaper and related review paper is a bit ambiguous. I’m sure that can be improved with a few more gene sequences gleaned from the genomes.

The 23 Mb M. gypseum genome is a bit smaller than the sizes of C. immitis (28 Mb), H. capsulatum (32 Mb), or Paracoccidioides brasiliensis (29 Mb).  While no annotation is currently available for the M. gypseum genome, this genome will help in establishing what genes were ancestral in the Onygenales and comparing patterns of gene family gains and losses in fungi that specialize on animal hosts.

Some more comparison across different kinds of dermatophyte fungi that are very distantly related like dandruff causing fungus Malasezzia globosa (Basidiomycota) will be really interesting as well.

Thanks Joe H and FGI folks for passing along announcement and to the Broad/FGI folks for the work to make this sequence available.