The Hyphal Tip: Fungal Genomes and Comparative Genomics

Just noticed that the [[JGI]] has released the Cochliobolus heterostrophus genome sequence at their site predicting 9,633 protein-coding genes.  Torrey Mesa Research Institute had access to a sequence many years ago, but it isn't until now that public version of this genome is available.  Cochliobolus is has been a model plant pathogen system and its production of T-Toxin by a PKS gene (Yang et al).

A year ago researchers at James Madison University discovered that, Pedobacter cryoconitis, a bacteria first found on the skin of red backed salamanders, was found to prevent the growth of the chytrid B. dendrobatidis, which is currently decimating frog populations.

Spread of wheat rust Puccinia strain Ug99 and consequences on already strained food supplies is discussed in an Op-Ed piece covered in GeneticMaize

A paper in Science from Jason Crawford and colleagues explores the function of polyketide synthetases (PKS) in the synthesis of the secondary metabolite and carcinogen aflatoxin. Previous work (nicely reviewed in the fungi by Nancy Keller and colleagues) has shown the the PKS genes have several domains. These domains include acyl carrier protein (ACP), transacylase (SAT), ketosynthase (KS), malonyl-CoA:ACP transacylase (MAT), “product template” PT, Aand thioesterase/Claisen cyclase (TE/CLC).

Hyphoid logic points out that it is appropriate to discuss about the oomycete Phytophthora infestans on St. Patrick's Day and mentions a NYT article "The fungus that conquered Europe" that is worth a look.

It is also worth thinking about another blight, well rust, that is spreading through the middle east and could threaten wheat crops worldwide. New Scientist has excellent coverage of Puccinia

What delineates species boundaries in fungi? Much work has been done on biological and phylogenetic species concepts in fungi. Some concepts are reviewed in Taylor et al 2006 and in Taylor et al 2000, and applications can be seen in several pathogens such as Paraccocidiodies, Coccidioides, and the model filamentous (non-pathogenic) fungus Neurospora

A 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.

The Stagonospra nodorum (teleomorph Phaeosphaeria nodorum) genome is now published in Plant Cell, "Sequencing and EST Analysis of the Wheat Pathogen Stagonospora nodorum". The paper describes the sequencing and analysis of this Dothideomycete fungus. The analyses included identifying genes likely involved in pathogenecity such as PKS and NRPS genes and enabled the discovery of new genes like ToxA. A couple of surprising findings:

• The genome was found to have both Class 1 and Class 2 Hydrophobin genes. Class 2 are normally restricted to basidiomycetes.
• Secreted proteins were not clustered in the genome
  • There appeared to be more secreted proteins shared with the plant pathogen M. grisea and N. crassa indicating some even though they are equidistant to S. nodorum although this analysis would need more sampled genomes of saprotrophic and biotrophic fungi to really support this hypothesis.

The paper has a few more observations about genome organization and synteny conservation, EST analyses of the fungus during infection, and a potential role for horizontal transfer among fungi to exchange pathogenic genes that make it worth taking a look.

Robin reviews recent Nature paper by Ilan Wapinski et al describing the orthogroups they built from multiple fungal genomes. I've been remiss in reviewing the paper myself, but they've created an important resource in the SYNERGY tool for orthology identification and a database of orthologs of some ascomycete fungi. I am excited there is a level of interest in the properties of gene duplication and how this may be an important aspect of adaptation and evolution. The Cornell Mushroom blog has a nice treatment of the maize pathogen and Mexican delicacy Ustilago maydis corn smut. Chris and Tom took some more Coprinus pictures while I was away from the lab.

A paper in PLoS Biology from Sandy Johnson's lab entitled "Interlocking Transcriptional Feedback Loops Control White-Opaque Switching in Candida albicans" discusses phenotype switching in the human pathogenic fungus Candida albicans. Why is the important?