The Hyphal Tip

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 [...]

[Read more →]

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).

[Read more →]

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.

[Read more →]

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.

[Read more →]

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 [...]

[Read more →]

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 [...]

[Read more →]

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.

[Read more →]

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 include:

[Read more →]

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 production.

[Read more →]

The genome of Podospora anserina S mat+ strain was sequenced by Genoscope and CNRS and published recently in Genome Biology. The genome sequence data has been available for several years, but it is great to see a publication describing the findings.  The 10X genome assembly with ~10,000 genes provides an important dataset for comparisons

[Read more →]