The Hyphal Tip: Fungal Genomes and Comparative Genomics

Digesting the fungal genomes

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Cochliobolus genome released

Posted on July 17th, 2008 by Jason Stajich · No Comments

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).

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Categories: pezizomycota

Trichoderma reesei genome paper published

Posted on May 12th, 2008 by Jason Stajich · No Comments

TrichodermaThe [[Trichoderma reesei]] genome paper was recently published in Nature Biotechnology from Diego Martinez at [[LANL]] with collaborators at [[JGI]], [[LBNL]], and others. This fungus was chosen for sequencing because it was found on canvas tents eating the cotton material suggesting it may be a good candidate for degrading cellulose plant material as part of cellulosic ethanol production.

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Categories: filamentous · gene family · genome · genome annotation · genome sequencing · trichoderma

Will mushrooms save the world?

Posted on May 12th, 2008 by Jason Stajich · 1 Comment

Paul Stamets thinks so and he's done work to make this happen.  The founder of FungiPerfecti and author many books on mushroom cultivation spoke at a TED talk recently that is worth taking a look. 
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Categories: bioremediation · fungi · news

Podospora genome published

Posted on May 11th, 2008 by Jason Stajich · No Comments

P.anserinaThe genome of Podospora anserina S mat+ strain was sequenced by Genoscope and CNRS and published recently in Genome Biology. The genome sequence data has been available for several years, but it is great to see a publication describing the findings.  The 10X genome assembly with ~10,000 genes provides an important dataset for comparisons
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Categories: comparative · genome · genome sequencing · neurospora · sordariomycetes

Fungal remediation of contaminated war zones

Posted on May 8th, 2008 by cellison · No Comments

Depleted uranium (DU) from spent ammunition used in the conflicts in Iraq and the Balkans poses a health risk to the inhabitants of those regions. This paper in Current Biology from Marina Fomina et al shows that several species of fungi including one from the mycorrhizal genus Rhizopogon

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Categories: basidiomycota · bioremediation

Deconstructing aflatoxin biosynthesis

Posted on April 27th, 2008 by Jason Stajich · No Comments

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).
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Categories: PKS · aflatoxin · aspergillus

EMBO workshop on Evolutionary and Environmental Genomics of Yeasts

Posted on April 24th, 2008 by Jason Stajich · No Comments

EMBO Workshop on Evolutionary and Environmental Genomics of Yeasts taking place at EMBL Heidelberg, 1-5 October 2008
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Categories: conferences

Rhizoctonia genome project

Posted on April 23rd, 2008 by Jason Stajich · 1 Comment

Rhizoctonia on cucumberJennifer from the other end of the lab just showed me the Rhizoctonia solani genome project page at JCVI.  Another Basidiomycete genome on the way, yah!
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Categories: basidiomycota · genome sequencing

Coprinus on the heart?

Posted on April 13th, 2008 by Jason Stajich · No Comments

Here's a fungal infection you don't hear much about. One of the fungi we work on, a model for mushroom development as it can be fruited in the lab is Coprinopsis cinerea (previously named Coprinus cinereus). C. cinerea is a saprobric coprophillic fungus so it is usually found on dung.  Although rare in human infections there are a few reports in immunocopromised patients.

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Categories: human pathogen

RIPing in an asexual fungus

Posted on March 23rd, 2008 by Jason Stajich · 3 Comments

ResearchBlogging.orgA.niger conidiophoreA paper in Current Genetics describes the discovery of Repeat Induced Polymorphism (RIP) in two Euriotiales fungi.  RIP has been extensively studied in Neurospora crassa and has been identified in other Sordariomycete fungi Magnaporthe, Fusiarium. This is not the first Aspergillus species to have RIP described as it was demonstrated in the biotech workhorse Aspergillus oryzae.  However, I think this study is the first to describe RIP in a putatively asexual fungus.  The evidence for RIP is only found in transposon sequences in the Aspergillus and Penicillium.  A really interesting aspect of this discovery is RIP is thought to only occur during sexual stage, but a sexual state has never been observed for these fungi.  
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Categories: RIP · aspergillus · fusarium · magnaporthe · neurospora