The Hyphal Tip: Fungal Genomes and Comparative Genomics

Digesting the fungal genomes

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AAM Releases "The Fungal Kingdom" Report

Posted on July 9th, 2008 by Jason Stajich · 1 Comment

AAM The Fungal Kindgom Report CoverThe American Academy of Microbiology has released a report (PDF) on the Fungal Kingdom outlining importance of research in the kingdom and recommending several areas of priority for future areas of research.

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Categories: news · science policy

Penicillium marneffei project

Posted on June 3rd, 2008 by Jason Stajich · 3 Comments

P.marneffeiWe're excited that a Penicillium marneffei grant to Mat Fisher and collaborators has been funded by the Welcome Trust. It includes a collaboration with University College London, our lab, JCVI, and Univ of Melbourne. This project will explore functional and comparative genomics approaches to studying the fungus

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Categories: aspergillus · euriotiomycetes · news

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

B. dendrobatidis strain JAM81 released

Posted on March 6th, 2008 by Jason Stajich · No Comments

B.dendrobatidis zoosporeThe following is an announcement to the B.dendrobatidis and fungal community at large from Alan Kuo at JGI. This is the JAM81 strain (Jess Morgan collected from a frog in the California Sierra Nevada). The JEL423 (Joyce Longcore, collected in Panama) strain genome sequence and annotation is available from the Broad Institute.

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Categories: chytridomycota · genome · news

Some links

Posted on March 3rd, 2008 by Jason Stajich · 1 Comment

ResearchBlogging.org

I've been too busy to post much these last few days, but here are a few links to some papers I found interesting in my recent browsing.

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Categories: basidiomycota · database · extremophiles · molecular evolution · pathogens · zygomycete

Yes, Ecology can improve Genomics

Posted on October 5th, 2007 by sharpton · 1 Comment

Blogging on Peer-Reviewed ResearchFew organisms are as well understood at the genetic level as Saccharomyces cerevisiae. Given that there are more yeast geneticists than yeast genes and exemplary resources for the community (largely a result of their size), this comes as no surprise.
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Categories: bioinformatics · comparative · functional · gene function · gene knockout · genome · genome annotation · genome sequencing · molecular evolution · saccharomyces · yeast

Gene knockouts in Candida parapsilosis

Posted on September 18th, 2007 by Jason Stajich · 1 Comment

Cparapsilosis from G.ButlerA recent paper "Targeted gene deletion in Candida parapsilosis demonstrates the role of secreted lipase in virulence", from the Nosanchuk lab at Yeshiva University, shows the role of secreted lipases in virulence of this pathogen.
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Categories: candida · functional · gene function · gene knockout · human pathogen · pathogens

That was a lot of work

Posted on April 3rd, 2007 by sharpton · No Comments

I've never worked with Magnaporthe grisea, the fungus responsible for rice blast, one of the most devastating crop diseases, but I do know that its life cycle is complicated and that knocking out roughly 61% of the genes in the genome and evaluating the mutant phenotype to infer gene function is not trivial. In their recent letter to Nature, Jeon et al did what many
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Categories: functional · fungi · gene function · genome · genome annotation · magnaporthe · plant pathogen

Approaching 100% coverage for GO assignments in S.pombe

Posted on March 4th, 2007 by Jason Stajich · 2 Comments

S. pombe taken from http://www.steve.gb.com/science/spectroscopy.htmlA paper by Martin Aslett and Val Wood indicate that the fission yeast community is approaching 100% coverage of a GO annotation for every gene in the S. pombe genome. Only Ashbya gossypii has a smaller genome in the fungi (see a recent paper
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Categories: functional · genome annotation · s.pombe

Making the Revolution Work for You

Posted on January 30th, 2007 by sharpton · No Comments

In a recent Microbiology Mini-Review, Meriel Jones catalogs both the potential benefits and problems that arise from fungal genome sequencing.
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Categories: aspergillus · comparative · database · functional · fungi · genome