The Hyphal Tip

Tremella mesenterica (from K. Findley)

The Tremella mesenterica genome portal is now live at the JGI. The genome is ~28Mb and the JGI annotation group predicted 8,313 genes, a significantly larger number of peptides predicted for C. neoformans (~7000; 18Mb genome) which may represent new and interesting genes or aspects of gene loss in the Cryptococcus yeast lineage.

Tremella is a Basidiomycete jelly fungus and an interesting study system from the perspective of discovery of novel lignin degrading enzymes.  It also occupies an interesting phylogenetic position being an outgroup to the human pathogenic yeast Cryptococcus neoformans and C. gattii. Comparative genomics on this system may also provide insight into the interesting evolution of the large mating-type locus that was formed through various rearrangements resulting in conversion from a tetrapolar to biopolar mating system.

Tremella may also be an important source of understanding wood degradation and how it differs in jelly fungi from the more distantly related Agaricomycotina (mushroom forming). The fungus is reasonably easy to grow in the laboratory and also to collect from nature. It can handle some desiccation to survive during a dry period only to swell up after  moisture is available.  It is also called Witch’s butter and Tom Volk has a summary of its features on his FOTM page.  It can often be confused with a phylogenetically distinct jelly fungus named Dacyromyces, usually the differences can be best be determined microscopically.  See what kinds of Tremella people have been finding at the Mushroom Observer.

See also

• Fraser et al, PLoS Biology 2004. doi: 10.1371/journal.pbio.0020384
• Hseuh et al, PLoS Genetics, 2006. doi: 10.1371/journal.pgen.0020184
• Hseuh et al, Euk Cell, 2008. doi: 10.1128/EC.00271-08

• Annotate the pizza mushroom genome – Mike Challen posts about Agaricus bisporus genome progress http://bit.ly/6Vzxp & community coordination #

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• Gbrowse2 up and running. http://gb2.fungalgenomes.org/gb2/gbrowse/yeast/ #

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Genome sequencing is underway on several early branches in the Opisthokont and some related linages as part of the “Origins of Multicellularity” project at the Broad Institute (BI) include some recently made available assemblies for:

• Allomyces macrogynus (Blastocladiomycota “Chytrid”)
• Capsaspora owczarzaki (Ichthyosporea)

Already available data from

• Monosiga brevicolis (JGI)
• Batrachochytrium dendrobatidis (JGI, BI) (Chytridiomycota)

Still in progress (BI)

• Amastigomonas sp
• Amoebidium parasiticum
• Nuclearia simplex
• Salpingoeca or Codosiga sp.
• Sphaeroforma arctica
• Stephanoeca or Acanthocopis sp.
• Mortierella verticulata
• Spizellomyces punctatus

Still in progress (Other centers)

• Monosiga ovata (WashU)
• Physarum polycephalum (WashU)

Alan Muskat raps about mushrooms in “A Fist Full of Mushrooms” (small) (large)

- From the Bay Area Mycological Society website

• Updating Bio-Graphics and reloading wiggle data to hopefully get rid of the blocky xyplot data for the highdensity numerical data. #

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Too much on my plate as of late, so I’m woefully behind on posting much on interesting papers or news.  Here’s a short list of links and papers that are worth a look though.

• “Evolution of pathogenicity and sexual reproduction in eight Candida genomes” published (Nature)
• NYT Science article sort of summarizing the good, bad, and ugly of fungi and human interactions
• Attempts to save amphibians from chytridiomycosis “Riders of a Modern-Day Ark” (PLoS Biology)
• Looks like Scott Baker with the JGI are in the process of resequencing several classical mutant strains of Phycomyces, Neurospora and Cochliobolus, Cryphonectria for sequence-based mapping of mutants (i.e. here and here and here).

• Mark your calendars: Neurospora 2010 meeting April 8-11 http://bit.ly/bcO3b Call for award nominations http://bit.ly/F9e6p & session chairs. #

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• Inoculate frogs with with skin-associated bacteria to fight Bd? Hmm… http://bit.ly/5gNqb #
• Added link to Rosenblum lab postdoc focusing on amphibian and Chytrid (Bd) genomics http://bit.ly/18lmJU #
• re-setting up rsync of ncbi genomes repository. Now if they actually had all the fungal genomes really organized, many are not kept there. #
• AutoMsg: Server starting #

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• Fixed local GD::SVG problems, Gbrowse SVG image generation is now working again. #

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