The Hyphal Tip: Fungal Genomes and Comparative Genomics

Digesting the fungal genomes

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A word about databases

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

Logo for fungal GenomesReport concludes that a fungal genome database is of "the highest priority".

This is the title as listed in PubMed for this article from Future Medicine about the AAM report on charting future needs and avenues of research on the fungal kingdom.

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Categories: opinion

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

AAM Releases "The Fungal Kingdom" Report

Posted on July 9th, 2008 by Jason Stajich · 2 Comments

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

Theobroma cacao to be sequenced, Oompa Loompa genome to follow.

Posted on June 26th, 2008 by Chris Villalta · 2 Comments

Looks like the USDA, Mars (the candy company), and IBM are partnering up to sequence the Cacao plants genome for everyone to use. Here is the article over at BBC News.
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Categories: genome

Will you always be able to satisfy that chocolate craving?

Posted on June 15th, 2008 by Jason Stajich · No Comments

Crinipellis_perniciosa_mushroomNPR had a story this weekend on Cocoa plantation collapse and the ecological aftermath of the changes the witches' broom fungus [[Moniliophthora perniciosa]] has wreaked. The genome sequence project for this Homobasidiomycete fungus is underway.

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Categories: genome sequencing · homobasidiomycota · plant pathogen

Basidiomycete genomes galore

Posted on June 1st, 2008 by Jason Stajich · Comments Off

Just finished attending Genetics and Cell Biology of Basidiomycetes in Cape Girardeau, MO which was an intimate gathering of basidiomycetaphiles.  I learned about systems that are used for studying fruiting body development, genetic mapping, pheromone and mating genes, kinesin dynamics, meoitic gene regulation, and a host of topics.  I'm happy I got a chance to meet more folks in the community and learned about where informatics is needed

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Categories: conferences

Chlamy genome investigations

Posted on May 26th, 2008 by Jason Stajich · No Comments

Chlamy coverThis month's Genetics has a series of articles exploring the genome (published last year & freely available at Science) of the green algae [[Chlamydomonas reinhardtii]]. These manuscripts are primarily genome analyses making for a very bioinformatics focused issue of Genetics. Some of the highlights include:

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Categories: bioinformatics · comparative · evolution · gene family · genome · genome annotation

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

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 · pezizomycota · sordariomycetes

Fungal Genetics 2007 details

Posted on March 28th, 2007 by Jason Stajich · 2 Comments

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