By Jason Stajich, on January 12th, 2010
These papers got lost in my drafts of things to write about. Grants and overdue manuscripts are keeping me away from the blog.
Published work from Gary Foster’s lab in Applied Env Micro show progress on genetic engineering tools to express introduced genes in the basidiomycete mushroom system Clitopilus passeckerianus. C. passeckarianus produces an antibiotic, pleuromutilin, an [...]
By Jason Stajich, on June 13th, 2009
Genome sequencing is underway on several early branches in the Opisthokont and some related linages as part of the “Origins of Multicellularity” project at the Broad Institute (BI) include some recently made available assemblies for:
Allomyces macrogynus (Blastocladiomycota “Chytrid”)
Capsaspora owczarzaki (Ichthyosporea)
Already available data from
Monosiga brevicolis (JGI)
Batrachochytrium dendrobatidis (JGI, BI) (Chytridiomycota)
Still in progress (BI)
Amastigomonas sp
Amoebidium parasiticum
Nuclearia simplex
Salpingoeca or [...]
By Jason Stajich, on March 16th, 2009
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 [...]
By Jason Stajich, on March 12th, 2009
The Mucormycotina (formerly Zygomycota) fungus Mucor circinelloides Genome Portal is now publicly available at http://genome.jgi-psf.org/Mucci1/Mucci1.home.html.
If you are planning to attend the Fungal Conference in Asilomar, there will be a JGI Workshop on March 19, 2009 at noon in Chapel to show how to use the manual curation tools.
By Jason Stajich, on December 9th, 2008
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 [...]
By Jason Stajich, on November 23rd, 2008
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 [...]
By Jason Stajich, on September 30th, 2008
BBC news and GTO report the sequence of P. chrysogenum, will be published in October in Nat Biotechnology in a project based at the biotech company DSM. P. chrysogenum being the mold that fortuitously contaminated Dr Fleming’s bacterial plates.
The 13,500 reported genes in the press release is quite bit larger than relatives in the [...]
By Chris Villalta, on June 26th, 2008
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.
By Jason Stajich, on May 26th, 2008
This 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 [...]
By Jason Stajich, on May 12th, 2008
The [[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 [...]