Tag Archives: onygenales

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.

Onygenales genome cluster

I’m excited about our projects to tackle the evolution of the Onygenales fungi.

I just remembered to look and see what was going on with the Blastomyces genome sequencing at WashU.  I checked and the Blastomyces dermatitidis genome sequence assembly version 3 was released in October 2007 and ESTs via 454 and ABI technologies are all available from WUSTL Genome Sequencing Center.

With the Broad Institute release this week of the Paracoccidioides genome sequence, the 10 Coccidioides strain genomes + 1 C. posadasii strain from JCVI/TIGR, 3 strains of Histoplasma capsulatum (both WUSTL and Broad), and the in-progress dermatophyte for Trichophyton and Microsporum sequences that are being generating through the FGI at Broad we have incredible genome coverage of this group of dermatophyte, keratin loving, and often animal pathogenic fungi.

I know I’ve been accused of being too positive announcing these things, but I do think analyses here are going to be as rich for comparisons as any old 12 flies.

More Cocci genomes

The Broad Institute has made available additional genomes of strains of Coccidioides immitis and C. posadasii. There are now genome sequences for 4 strains of C. immitis sequenced and 3 strains of C. posadasii including the C735 strain from the JCVI/TIGR. including the reference strain RS that is assembled into 7 supercontigs (there are probably 5 chromosomes) and annotated with ~10,000 genes. However we think at least ~1-2k of the annotated genes in strain RS are likely reptitive sequences and not real genes based on comparisons with the TIGR annotations of C. posadasii C735 strain and de novo repeat finding and analysis – John talked about this in his talk at Asilomar.

Thse available strain sequences are going to allow for some interesting analyses that have yet to be applied in fungi. This includes doing some whole genome scans for selection using more sensitive population genetic tests than the gross-level non-synonymous /synonymous ratio tests that we’ve been relegated to with the current comparisons and it is starting to feel a bit like when “all you have is a hammer…”. Now all we have to do is get the whole genome multi-strain alignment quirks worked out and probably have to do our own quick annotation since only the two reference strains are annotated.

Cocci arthrocondia

Genomes of honeybee pathogens

A.apisBlogging about Peer-Reviewed ResearchThe Baylor sequencing center has published the genome of two honey bee pathogens. Recently Baylor and collaborators published a slew of honey bee genome papers and it is great that they have also chosen to follow up on the parasites as well.

The group published the genomes of the bacteria pathogen Paenibacillus larvae and fungal pathogen Ascosphaera apis. A. apis is in the Onygenales clade which also includes the fungal human pathogens Coccidioides, Histoplasma, and Blastomyces.

Currently the genome annotation is limited to the bacterial genome where many ab initio gene prediction programs exist and no annotation is provided for A. api. We should be able to apply gene prediction parameters trained from other Onygenales fungi to get a resonable annotation. Study of this pathogenic genome may also provide insight into the evolution of this clade of fungi which contains most of the primary fungal pathogens of humans.