Category Archives: euriotiomycetes

Phytopathogenic Fungi: what have we learned from genome sequences?

ResearchBlogging.orgA review in Plant Cell from Darren Soanes and colleagues summarizes some of the major findings about evolution of phytopathogenic fungi gleaned from genome sequencing highlighting 12 fungi and 2 oomycetes. By mapping evolution of genes identified as virulence factors as well as genes that appear to have similar patterns of diversification, we can hope to derive some principals about how phytopathogenic fungi have evolved from saprophyte ancestors.

They infer from phylogenies we’ve published (Fitzpatrick et al, James et al) that plant pathogenic capabilities have arisen at least 5 times in the fungi and at least 7 times in the eukaryotes. In addition they use data on gene duplication and loss in the ascomycete fungi (Wapinski et al) to infer there large numbers of losses and gains of genes have occurred in fungal lineages.

Continue reading Phytopathogenic Fungi: what have we learned from genome sequences?

Coccidioides in the news

The NY Times has an article on the high rate of Coccidioides incidence at the state prison in Pleasant Valley, California. The infection rate has been documented by Pappagianis et al in an in-depth study of Coccidioidomycosis in the California state prisons. The disease has stalled some plans for constructing a new prison the edge of the San Joaquin Valley so the state is definitely taking note.

Cocci map
Also see Figure here with prettier links.

Thanks Liz!

Flaxseed antifungals

Blogging about Peer-Reviewed ResearchCareful eating those old noodles left in the fridge, lots of fungi probably have made a home in the starch rich environment. But can food be inoculated with some inherent antifungal properties to help it last longer. A recent paper in the Intl Journal of Food Microbiology “Fungistatic activity of flaxseed in potato dextrose agar and a fresh noodle system.” describes work to test whether flaxseed can stop fungi from growing as a potential food preservation agent. Strains of Penicillium chrysogenum, Aspergillus flavus,moldy noodles Fusarium graminearum, and other Penicillium sp isolated from moldy noodles were used in a test assay for fungistatic activity of flaxseed. Flaxseed has a whole host of health benefits that have lead to is use in many foods, cereals, and baked goods. The authors test to see what type of antifungal properties flaxseed has as well to test if it can provide a role in food preservation and be edible (or even healthy). Some other edible antifungals include spices like cinnamon, cloves, and mustard. These authors have also investigated the stability of the antifungal properties of flaxseed in another paper.

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.

Evolution of aflatoxin gene cluster

Blogging on Peer-Reviewed ResearchIgnazio Carbone and colleagues published a recent analysis of the evolution of the aflatoxin gene cluster in five Aspergillus fungi entitled “Gene duplication, modularity and adaptation in the evolution of the aflatoxin gene cluster” in BMC Evolutionary Biology. The authors were able to identify seven modules pairs of genes whose history of duplication were highly correlated. Several genomes of Aspergillus have been sequenced along with more Eurotioales fungi. Continue reading Evolution of aflatoxin gene cluster

Genomes on the horizon at JGI

Several more fungi are on the docket for sequencing at JGI through their community sequencing program. This includes

This complements an ever growing list of fungal genome sequences which is probably topping 80+ now not including the several dozen strains of Saccharomyces that are being sequenced at Sanger Centre and a separately funded NIH project to be sequenced at WashU.

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

Exploring a global regulator of gene expression in Aspergillus

Blogging about Peer-Reviewed ResearchWhen first discovered, the gene LaeA was thought to be a master switch for silencing of several NRPS secondary metabolite gene clusters in Aspergillus. NRPS and PKS are important genes in filamentous fungi as they produce many compounds that likely help fungi compete in the ecological niche mycotoxins (e.g. aflatoxin, gliotoxin), plant hormone (e.g. Gibberellin), and a potential wealth of additional undiscovered activities.

A recent paper from Nancy Keller’s lab entitled Transcriptional Regulation of Chemical Diversity in Aspergillus fumigatus by LaeA has followed up previous studies with whole genome expression profiling of a LaeA knockout strain to explore the breadth of the genome that is regulated by this transcriptional regulator. Continue reading Exploring a global regulator of gene expression in Aspergillus