The Hyphal Tip: Fungal Genomes and Comparative Genomics

Digesting the fungal genomes

The Hyphal Tip: Fungal Genomes and Comparative Genomics header image 4

Entries Tagged as 'filamentous'

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.

Click to continue reading "Trichoderma reesei genome paper published"

[Read more →]

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

Fusarium graminearum genome published

Posted on September 8th, 2007 by Jason Stajich · 1 Comment

The genome of the wheat and cereal pathogen Fusarium graminearum was published in Science this week in an article entitled "The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specializationtion". The project was a collaboration of many different Fusarium research groups.
Click to continue reading "Fusarium graminearum genome published"

[Read more →]

Categories: RIP · filamentous · fusarium · genome · genome annotation · genome sequencing · plant pathogen

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.
Click to continue reading "Evolution of PEX genes"

[Read more →]

Categories: aspergillus · cell biology · comparative · evolution · filamentous · fungi · peroxisome

More Euriotiomycete genomes

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

P.marneffeiThe genome sampling in the Eurotiomycota clade just keeps getting better. The new J. Crag Venter Institute (TIGR) deposited WGS Assemblies of the human pathogens Penicillium marneffei and Talaromyces stipitatus. P. marneffei is a thermally dimorphic fungus endemic to South-East Asia found in bamboo rats. It is studied by a number of
Click to continue reading "More Euriotiomycete genomes"

[Read more →]

Categories: euriotiomycetes · filamentous · fungi · genome · news

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
Click to continue reading "Clusters of genomes"

[Read more →]

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".
Click to continue reading "Fungal Genetics 2007 details"

[Read more →]

Categories: bioinformatics · chytridomycota · cryptococcus · dothideomycetes · euriotiomycetes · filamentous · glomeromycota · homobasidiomycota · horizontal gene transfer · neurospora · news · sordariomycetes · zygomycete

Hello, do I know you?

Posted on March 21st, 2007 by Jason Stajich · No Comments

Blogging about Peer-Reviewed ResearchSelf and non-self recognition is important for fungi when hyphae interact fuse if they should compartmentalize and undergo apoptosis to kill the heterokaryoton or exchange nutrients. This process is part of cell defense and to limit to the movement of mycoviruses. A paper in PLOS ONE describes the Genesis of Fungal Non-Self Repertoire.
Click to continue reading "Hello, do I know you?"

[Read more →]

Categories: evolution · filamentous · fungi · neurospora · repeats