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).
Schizophyllum genome portal live at JGI
Posted on March 16th, 2009 by Jason Stajich · No Comments
Categories: Agaricomycota · genome · genome annotation · genome sequencing
Tags: basidiomycete, fruiting body, fungi, genome sequencing, model system, schizopyllum
Lichen genome projects and the power shift prompted by next-gen sequencing
Posted on October 31st, 2008 by Jason Stajich · 1 Comment
Genome Technology highlights the very cool thing about next-gen sequencing – it puts the power in the hands of the researchers to explore genome sequence and doesn’t limit them to projects only funded through sequencing centers. The Genome Technology piece highlights work at Duke to sequence the genome Cladonia grayi, a lichenized fungus, with 454 technology at Duke’s Institute for Genome Sciences and Policy through their next-gen sequencing program.
Categories: bioinformatics · comparative · genome annotation · short-read · symbiosis
Tags: bioinformatics, computational, fungi, genome, genome sequencing, lichen, next-gen, sequencing, training
Platypus genome
Posted on May 8th, 2008 by Jason Stajich · No Comments
Neil has a great summary of the results from the Platypus genome sequencing project.
Categories: genome
Tags: genome sequencing, platypus
More updates on Saccharomyces resequencing project at Sanger
Posted on December 19th, 2007 by Jason Stajich · 1 Comment
I’ve paraphrased an email sent by David Carter to folks interested in Saccharomyces resequencing project.
The latest version of the SGRP data is on the web site and ftp site. This release is somewhat provisional, and motivated more by the fact that we have a paper deadline coming up than by any claim to finality. It should be quite
Categories: population genomics · resequencing · saccharomyces
Tags: cerevisiae, genome sequencing, paradoxus, population genomics, resequencing, saccharomyces
Banana black leaf fungus sequenced
Posted on November 17th, 2007 by Jason Stajich · No Comments
The JGI have released the genome sequence and annotation of the Mycosphaerella fijiensis fungus an important crop pathogen of bananas. This Dothideomycete fungus is one of several in the clade of important plant pathogens that have been sequenced recently including M. gramicola, a relative that causes wheat-blotch.
Categories: dothideomycetes · genome
Tags: fungus, genome sequencing, JGI, plant pathogen
Yes, Ecology can improve Genomics
Posted on October 5th, 2007 by sharpton · 1 Comment
Few organisms are as well understood at the genetic level as Saccharomyces cerevisiae. Given that there are more yeast geneticists than yeast genes and exemplary resources for the community (largely a result of their size), this comes as no surprise.
Categories: bioinformatics · comparative · functional · gene function · gene knockout · genome · genome annotation · genome sequencing · molecular evolution · saccharomyces · yeast
Tags: bioinformatics, comparative, functional, gene function, gene knockout, genome, genome annotation, genome sequencing, molecular evolution, saccharomyces, yeast
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.
Categories: RIP · filamentous · fusarium · genome · genome annotation · genome sequencing · plant pathogen
Tags: filamentous, fusarium, genome, genome annotation, genome sequencing, plant pathogen, RIP
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
- The Dothideomycete leaf streak disease causing fungus Mycosphaerella fijiensis
- Soybean rust Phakopsora pachyrhizi
- The Basidiomycete and jelly fungus Tremella mesenterica proposed by Joe Heitman for use as outgroup to the human pathogen Cryptococcus
- The plant pathogen Cochliobolus heterostrophus proposed by Gillian Turgeon which ironically was already sequenced
Categories: NRPS · aspergillus · basidiomycota · chytridomycota · cryptococcus · dothideomycetes · fungi · genome · genome sequencing · neurospora · pathogens · plant pathogen · rumen · rusts · saccharomyces
Tags: aspergillus, basidiomycota, chytridomycota, cryptococcus, dothideomycetes, fungi, genome, genome sequencing, neurospora, NRPS, pathogens, plant pathogen, rumen, rusts, saccharomyces
Genome of Postia placenta
Posted on June 12th, 2007 by Jason Stajich · 1 Comment
The JGI has released the genome sequence and annotation of the Basidiomycete brown rot Postia placenta. Brown rotters can only break down cellulose but do not degrade lignin that white rotters (like Phanerochaete chrysosporium).
Using total genomic DNA from dikaryotic strain MAD-698, the JGI generated 571,000 reads that assembled into 1243 haplotype scaffolds, with 85 of these scaffolds covering half of the genome sequence.
Categories: basidiomycota · genome · genome sequencing
Tags: basidiomycota, genome, genome sequencing
More Neurospora genomes
Posted on April 24th, 2007 by Jason Stajich · 1 Comment
We got word last week from the JGI that our DNA for Neurospora tetrasperma and N. discreta have passed QC and library QC and are on their way to being sequenced. The center also plans to do some EST sequencing to improve gene calling abilities.
Why more Neurospora genomes? The sequencing proposal discussed these species as a model system for evolutionary and ecological genetics.
Categories: genome · genome sequencing · neurospora
Tags: genome, genome sequencing, neurospora
