Fungal Genomes and Comparative Genomics

Digesting the fungal genomes

Fungal Genomes and Comparative Genomics header image 1

Podospora genome published

Posted on May 11th, 2008 by Jason Stajich · No Comments

P.anserinaThe 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
Click to continue reading "Podospora genome published"

Categories: comparative · genome · genome sequencing · neurospora · sordariomycetes

→ No Comments

Fungal remediation of contaminated war zones

Posted on May 8th, 2008 by cellison · No Comments

Depleted uranium (DU) from spent ammunition used in the conflicts in Iraq and the Balkans poses a health risk to the inhabitants of those regions. This paper in Current Biology from Marina Fomina et al shows that several species of fungi including one from the mycorrhizal genus Rhizopogon

Click to continue reading "Fungal remediation of contaminated war zones"

Categories: basidiomycota · bioremediation

→ No Comments

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

→ No Comments

Deep EST sequencing = RNA-Seq

Posted on May 6th, 2008 by Jason Stajich · No Comments

The transcriptional landscape of yeast has been (further) defined with Solexa sequencing in a method deemed "RNA-Seq", but what I would call "deep EST sequencing".  This approach for transcriptional profiling by sequencing alone is sure to be used by many labs looking for lower and more complete ways to describe and quantitate the full population of transcripts in an organism.

Click to continue reading "Deep EST sequencing = RNA-Seq"

Categories: genome sequencing · saccharomyces · yeast

→ No Comments

Dioxin cleanup with fungi

Posted on May 1st, 2008 by Jason Stajich · No Comments

Pleurotus

NYT article on the work of Paul Stamets using fungi like Pleurotus for Dioxin cleanup in Ft Bragg, CA.

Thanks for the link Pat!

Click to continue reading "Dioxin cleanup with fungi"

Categories: bioremediation · fungi · homobasidiomycota

→ No Comments

Stem rust

Posted on April 29th, 2008 by Jason Stajich · 2 Comments

Spread of wheat rust Puccinia strain Ug99 and consequences on already strained food supplies is discussed in an Op-Ed piece covered in GeneticMaize
Click to continue reading "Stem rust"

Categories: plant pathogen · rusts

→ 2 Comments

Deconstructing aflatoxin biosynthesis

Posted on April 27th, 2008 by Jason Stajich · No Comments

A paper in Science from Jason Crawford and colleagues explores the function of polyketide synthetases (PKS) in the synthesis of the secondary metabolite and carcinogen aflatoxin. Previous work (nicely reviewed in the fungi by Nancy Keller and colleagues) has shown the the PKS genes have several domains. These domains include acyl carrier protein (ACP), transacylase (SAT), ketosynthase (KS), malonyl-CoA:ACP transacylase (MAT), “product template” PT, Aand thioesterase/Claisen cyclase (TE/CLC).
Click to continue reading "Deconstructing aflatoxin biosynthesis"

Categories: PKS · aflatoxin · aspergillus

→ No Comments

EMBO workshop on Evolutionary and Environmental Genomics of Yeasts

Posted on April 24th, 2008 by Jason Stajich · No Comments

EMBO Workshop on Evolutionary and Environmental Genomics of Yeasts taking place at EMBL Heidelberg, 1-5 October 2008
Click to continue reading "EMBO workshop on Evolutionary and Environmental Genomics of Yeasts"

Categories: conferences

→ No Comments

Rhizoctonia genome project

Posted on April 23rd, 2008 by Jason Stajich · 1 Comment

Rhizoctonia on cucumberJennifer from the other end of the lab just showed me the Rhizoctonia solani genome project page at JCVI.  Another Basidiomycete genome on the way, yah!
Click to continue reading "Rhizoctonia genome project"

Categories: basidiomycota · genome sequencing

→ 1 Comment

Phytophthora work highlighted

Posted on April 22nd, 2008 by Jason Stajich · No Comments

A link to the story about Matteo Garbelotto's work on Phytophthora ramorum and showing that the source in California is likely from ornamentals from a nursery. The work is to appear soon in Molecular Ecology but alas is not available yet.

A recent paper on updated Phytophthora phylogeny from Jamie Blair and co-authors is also out in FGB.

Click to continue reading "Phytophthora work highlighted"

Categories: phytophora · plant pathogen

→ No Comments