The Hyphal Tip

Digesting the fungal genomes

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Entries Tagged as 'genome sequencing'

Jelly fungus Tremella genome available at JGI

Posted on July 2nd, 2009 by Jason Stajich · No Comments

The Tremella mesenterica genome portal is live on the JGI site. Tremella is a Basidiomycete jelly fungus and an interesting study system from the perspective of discovery of novel lignin degrading enzymes. It also occupies an interesting phylogenetic position being an outgroup to the human pathogenic yeast Cryptococcus neoformans and C. gattii.

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Categories: cryptococcus · genome sequencing
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For your reading pleasure

Posted on May 26th, 2009 by Jason Stajich · 1 Comment

Too much on my plate as of late, so I’m woefully behind on posting much on interesting papers or news.  Here’s a short list of links and papers that are worth a look though.

“Evolution of pathogenicity and sexual reproduction in eight Candida genomes” published (Nature)
NYT Science article sort of summarizing the good, bad, and ugly of fungi [...]

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Categories: candida · neurospora · news · resequencing
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Schizophyllum genome portal live at JGI

Posted on March 16th, 2009 by Jason Stajich · No Comments

In preparation for Asilomar, JGI is releasing lots of the genome sequencing project portals. The Schizophyllum commune Genome Portal is now publicly available. Go get your white-rot gene investigation on! (Though please respect the community rules for 1st rights to publication of the genome-wide analyses).

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Categories: Agaricomycota · genome · genome annotation · genome sequencing
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Aspergillus has a posse

Posted on March 12th, 2009 by Jason Stajich · 1 Comment

aspergillusposseShepard Fairley has gotten alot of notice lately for his Obama art that has been replicated pretty much everywhere. In homage to his earlier street art we’ll discuss the growing Aspergillus genome posse.

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Categories: aspergillus · database · genome sequencing
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Yeast population genomics

Posted on March 1st, 2009 by Jason Stajich · No Comments

ResearchBlogging.org
I cheered the Sanger-Wellcome SGRP group work to generate multiple Saccharomyces cerevisiae and S. paradoxus strain genome sequences. They submitted a version of the manuscript to Nature precedings and it is now published in Nature AOP showing that submitting to a preprint server doesn’t necessarily hurt your manuscript getting published in this instance. The research groups explored the impact of domestication (as was also recently done for the sake and soy sauce worker fungus, Aspergillus oryzae) on the Saccharomyces genome by comparing individuals from wild strains of S. paradoxus.

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Categories: SGRP · bioinformatics · comparative · genome annotation · population genomics · resequencing · saccharomyces · short-read
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First release of N.tetrasperma and N.discreta

Posted on February 9th, 2009 by Jason Stajich · 5 Comments

The JGI in collaboration with our lab at Berkeley have released the Neurospora tetrasperma (mat A) and N. discreta (mat A) genome sequences and annotation after about two years of work.  These are two closely related species to the well studied laboratory workhorse Neurospora crassa.
The N.tetrasperma assembly (8X) has an N50 of 976kb and is [...]

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Categories: database · genome annotation · genome sequencing · neurospora
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Brown rotting fungal genome published

Posted on February 5th, 2009 by Jason Stajich · No Comments

Postia placenta genome is now published in early edition of PNAS. Brown rotting fungi are import part of the cellulose degrading ecology of the forest as well (hopefully) providing some enzymes that will help in the ligin to biofuels process. Brown rotters cannot break down lignin while white rotters (like the previously sequenced Phanerochaete chrysosporium). This fungus was chosen for sequencing as it is another potentially helpful fungus in the war on sugars (turning them into fuels) including recently published Trichoderma reesei and 1st basidiomycete genome Phanerochaete (all incidentally with the Diego Martinez as first author – go Diego!).

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Categories: LC/MS · basidiomycota · biofuels · genome annotation · genome sequencing · news
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Coprinopsis cinereus genome annotation updated

Posted on January 21st, 2009 by Jason Stajich · No Comments

The Broad Institute in collaboration with many of the Coprinopsis cinereus (Coprinus cinerea) community of researchers have updated the genome annotation for C. cinereus with additional gene calls based on ESTs and improved gene callers. The annotation was made on the 13 chromosome assembly produced by work by SEMO fungal biology group and collaborators across [...]

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Categories: Agaricomycota · basidiomycota · database · genome annotation · genome sequencing
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Updated Cryptococcus serotype A annotation

Posted on December 9th, 2008 by Jason Stajich · 1 Comment

A new and improved annotation of Cryptococcus neoformans var grubii strain H99 (serotype A) has been made available in GenBank and the Broad Institute website. This update is collaboration between several groups providing data and analyses and the annotation team at Broad’s gene calling pipeline.

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Categories: cryptococcus · genome · genome annotation · genome sequencing · human pathogen
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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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