The Hyphal Tip: Fungal Genomes and Comparative Genomics

Digesting the fungal genomes

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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

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

More RIP without sex?

Posted on April 5th, 2008 by Jason Stajich · No Comments

Another asexual species of fungi also has evidence for the meiosis-specific process of Repeat Induced Point-mutations (RIP).
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Categories: RIP · neurospora · sordariomycetes

Mold farm?

Posted on March 31st, 2008 by Jason Stajich · No Comments

Bret has a mold farm of Aspergillus fumigatus in Flight of the Conchords
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Categories: fungi · news

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

Aspergillus comparative transcriptional profiling

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

ResearchBlogging.org

Researchers from Technical University of Denmark published some interesting results from comparing expression across the very distinct Aspergillus species.

Kudos also goes to making it Open Access. I am posting a few key figures below the fold because I can! They grew the fungi in bioreactors fermenting glucose or xylose. After calibrating the growth curves they were able to sample the appropriate time points for comparison of gene expression across these three species. They found a set of genes commonly expressed.

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Categories: aspergillus · evolution · gene regulation · microarray

Beware Aspergillus

Posted on August 18th, 2007 by Jason Stajich · No Comments

Aspergillus fumigatusAspergillus fumigatus can be dangerous, even to those with intact immune systems. A recent article in Discover magazine's Vital Signs describes how dangerous the ubiquitous fungus can be.
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Categories: aspergillus · pathogens

Genomes on the horizon at JGI

Posted on July 4th, 2007 by Jason Stajich · 1 Comment

Several more fungi are on the docket for sequencing at JGI through their community sequencing program. This includes
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Categories: NRPS · aspergillus · basidiomycota · chytridomycota · cryptococcus · dothideomycetes · fungi · genome · genome sequencing · neurospora · pathogens · plant pathogen · rumen · rusts · saccharomyces

Exploring a global regulator of gene expression in Aspergillus

Posted on June 25th, 2007 by Jason Stajich · No Comments

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)...
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Categories: NRPS · aspergillus · gene cluster · gene function · gene regulation · microarray · secondary metabolite

Evolution of PEX genes

Posted on June 7th, 2007 by Jason Stajich · 2 Comments

A nice evolutionary analysis of peroxin genes entitled PEX Genes in Fungal Genomes: Common, Rare, or Redundant in the journal "Traffic" from Kiel et al out of the University of Groningen in The Netherlands. Within a species, the genes in the PEX family are not necessarily phylogenetically related to each other, but instead are all named as to how they were discovered in mutant screens.
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Categories: aspergillus · cell biology · comparative · evolution · filamentous · fungi · peroxisome