The Hyphal Tip

Digesting the fungal genomes

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Genome survey sequencing of Witches’ Broom

Posted on November 23rd, 2008 by Jason Stajich · No Comments

Genome survey sequencing (1.9X coverage) was generated for Moniliophthora perniciosa, the cause of witches’ broom disease on cacao plants. The sequence for this basidiomycete plant pathogen was published in BMC Genomics this week. The authors report a higher number of ROS metabolism and P450 genes. Evaluating whether these copy number differences are significantly different [...]

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Categories: P450 · basidiomycota · genome · genome sequencing · plant pathogen
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Attend Fungal Genetics 2009!

Posted on September 5th, 2008 by Jason Stajich · 2 Comments

If you are interested in fungal genetics and genomics, comparative biology, and of course dancing with fungal geneticists, plan to attend the 25th Fungal Genetics Meeting held at the beautiful Asilomar Conference Grounds in Pacific Grove, California. Below is info sent out from the Policy Committee and registration opens in a little over a month.  Budding (and conidiating) artists can also submit a Logo design

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Categories: Fungal Genetics · news
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A word about databases

Posted on July 27th, 2008 by Jason Stajich · 1 Comment

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
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Cochliobolus genome released

Posted on July 17th, 2008 by Jason Stajich · 1 Comment

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

Posted on June 26th, 2008 by Chris Villalta · 3 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
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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
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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 & courses
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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
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Trichoderma reesei genome paper published

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

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
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