Category Archives: genome

Not one, but two Aspergillus niger genome sequences

Blogging about Peer-Reviewed ResearchA.niger growing on plate (this is not the sequenced strain)The JGI has previously released A. niger strain ATCC 1015 sequence in November 2005. ATCC 1015 is used in industrial production of citric acid as it is one of the best producers of citric acid. In Nature Biotechnology a Dutch team has published the sequence of another strain, CBS 513.88 which is an early ancestor of ATCC 1015 used in industrial enzyme production.

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.

All hail the rusts

pucciniaThe FGI and the Broad Institute have released the 7X genome assembly of Puccinia graminis f. sp tritici in roughly 4500 contigs. This represents the first rust fungus to be sequenced and the second Urediniomycete that has been sequenced, Sporobolomyces roseus being the first. This rust fungus is “the causal agent of stem rust, has caused serious disease of small cereal grains (wheat, barley, oat, and rye) worldwide.”

Phycomyces Genome Release 1

phycomycesThe JGI has released the Phycomyces blakesleeanus genome. This represents the second Zygomycete genome sequence that has been released in addition to Rhizopus oryzae that was released by the Broad Institute last year. We are now getting a better look at the basal fungal genomes including the Chytrids and Zygomycetes. Much more on specifics of Phycomyces biology and history are on this site run by the group organizing the genome analysis.

I find one of the most interesting things about P. blakesleeanus is its phototropism. We know light sensing is controlled, in part, by the gene white-collar 1. A homolog of this gene in Neurospora crassa is involved as an oscillator circadian rhythm. Of course many more genes are involve in pathways for light sensing including some really old proteins like phytochromes.

There will be a lot of cool analyses to do with this genome beyond phototropism. I am looking forward to seeing what gene families are unique and expanded in this species relative to the other zygomycete. It also looks like it is quite intron rich much like the Basidiomycetes, further supporting the idea that fungi had intron rich ancestors.