The Hyphal Tip: Fungal Genomes and Comparative Genomics

Digesting the fungal genomes

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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

Cryptococcus species deliniation

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

ResearchBlogging.org 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

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Categories: cryptococcus · human pathogen · phylogenetics · phylogeny · speciation

When Microorganisms attack: Protect your historical heritage!

Posted on February 1st, 2008 by Jason Stajich · No Comments

ResearchBlogging.orgAn article in Applied Environmental Biology describes work characterizing microorganisms that degrade materials used to preserve cultural heritage objects. These are some heavy duty synthetic compounds which are commonly used to preserve or treat wood, cover objects to protect them from moisture, light, and avoid direct attack by microbes. This article describes some interesting findings of the types of organisms that attack these preservation materials. Table 1 lists fungi like Aureobasidium pullulans which can degrade Polyvinyl chloride, Chaetomium globosum which has enzymes (someone make sure and describe all of these in the genome sequence) to dissolve Polyurethane, several wood degrading fungi that break down Nylon (Phanerochaete can break down diesel fuel), and melanin producing fungi (like Cryptococcus?) that destroy acrylics.

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Categories: bioremediation · fungi · melanin

Haunted Woods

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

Eucalyptus is an utilitarian tree, so it's no surprise that several organizations are interested in genetically engineering it. Indeed, its genome sequence is slated for release, which should facilitate a GE market for the species. One company in particular - ArborGen (they have a very interesting mission statement) - is using genetic engineering, cloning and classic hybridization techniques to make a cold tolerant variety.
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Categories: cryptococcus · fungi · genome

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

Clusters of genomes

Posted on May 14th, 2007 by Jason Stajich · No Comments

As announced at the Fungal Genetics meeting, the FGI at the Broad Institute is focusing on clusters of genomes rather than single ones. Some of genome projects are already grouped.
  • Coccidioides has 3 strains already plus the outgroup Uncinocarpus and conceivable one could include Histoplasma in there. This resources will grow to 14 strains (which comprise two species) of Coccidioides contributed by FGI and
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Categories: aspergillus · cryptococcus · filamentous · fungi · fusarium · genome

Fungal Genetics 2007 details

Posted on March 28th, 2007 by Jason Stajich · 1 Comment

I'm including a recapping as many of the talks as I remember. There were 6 concurrent sessions each afternoon so you have to miss a lot of talks. The conference was bursting at the seams as it was- at least 140 people had to be turned away beyond the 750 who attended. If there was any theme in the conference it was "Hey we are all using these genome sequences".
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Categories: bioinformatics · chytridomycota · cryptococcus · dothideomycetes · euriotiomycetes · filamentous · glomeromycota · homobasidiomycota · horizontal gene transfer · neurospora · news · sordariomycetes · zygomycete

Evolving a new pathway

Posted on February 10th, 2007 by Jason Stajich · No Comments

A paper* this week from the Huffnagle lab argues that even though the human pathogenic fungus Cryptococcus neoformans can produce an oxylipin similar to prostaglandin, the authors were unable to identify any homologous cyclooxygenase genes in the genome.
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Categories: cryptococcus