The Hyphal Tip: Fungal Genomes and Comparative Genomics

Digesting the fungal genomes

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Entries from May 2007

Melaninized fungi use ionizing radiation for energy

Posted on May 29th, 2007 by Jason Stajich · 2 Comments

Blogging about Peer-Reviewed ResearchA recent paper in PLoS One entitled Ionizing Radiation Changes the Electronic Properties of Melanin and Enhances the Growth of Melanized Fungi describes some pretty amazing results that have gotten some press lately. The lead author, Dr Dadachova, spoke on NPR's Science Friday last week.
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Categories: bioremediation · extremophiles · melanin

Multiple Losses of sex within Microsporidia

Posted on May 27th, 2007 by Jason Stajich · No Comments

Blogging about Peer-Reviewed ResearchA recent paper I found interesting (and I am sure was interesting to Dr Logsdon) about Multiple losses of sex within a single genus of Microsporidia. In the paper Joseph Ironside describes multiple instances of loss of sex within the Nosema/Vairimorpha group testing the hypothesis that the ancestral lineage was asexual.
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Categories: evolution · fungi · genome reduction · microspordia · pathogens

More Euriotiomycete genomes

Posted on May 25th, 2007 by Jason Stajich · No Comments

P.marneffeiThe genome sampling in the Eurotiomycota clade just keeps getting better. The new J. Crag Venter Institute (TIGR) deposited WGS Assemblies of the human pathogens Penicillium marneffei and Talaromyces stipitatus. P. marneffei is a thermally dimorphic fungus endemic to South-East Asia found in bamboo rats. It is studied by a number of
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Categories: euriotiomycetes · filamentous · fungi · genome · news

Yeast genome: Known knowns, and known unknowns

Posted on May 20th, 2007 by Jason Stajich · 1 Comment

From Genetics this week a review discusses Why are there still 1000 Uncharacterized Yeast genes? Poor Yeast - so many more genes have no known function, while S. pombe has nearly 100% coverage in functional annotation. I'll also point out that the 1000 genes refers to protein-coding genes, not ncRNA genes which may mean that there is alot more that is unknown.
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Categories: gene function · genome annotation · saccharomyces · yeast

Fungal tree of life papers

Posted on May 15th, 2007 by Jason Stajich · No Comments

Lots of papers in Mycologia (subscription required) this month of different groups analyzing the fine-scale relationships of many different fungal clades using the loads of sequences that were generated as part of the Fungal Tree of Life project.
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Categories: basidiomycota · chytridomycota · euriotiomycetes · fungi · glomeromycota · phylogenetics · s.pombe · saccharomyces · yeast · zygomycete

Clusters of genomes

Posted on May 14th, 2007 by Jason Stajich · No Comments

As announced at the Fungal Genetics meeting, the FGI at the Broad Institute is focusing on clusters of genomes rather than single ones. Some of genome projects are already grouped.
  • Coccidioides has 3 strains already plus the outgroup Uncinocarpus and conceivable one could include Histoplasma in there. This resources will grow to 14 strains (which comprise two species) of Coccidioides contributed by FGI and
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Categories: aspergillus · cryptococcus · filamentous · fungi · fusarium · genome

Pyrenophora tritici-repentis

Posted on May 14th, 2007 by Jason Stajich · No Comments

The genome of Pyrenophora tritici-repentis, the fourth sequenced Dothideomycete genome, was released by the FGI at the Broad Institute this spring (March 2007). P. tiritici-repentis was sequenced for its role as the cause of tan spot on wheat and as a research model for other Pyrenophora sp. that are pathogens of several grasses. The 6X assembly contains 37.8 Mb of sequence similar to the other Dothideomycetes
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Categories: dothideomycetes · genome

Would a Beetle by another name smell as sweet?

Posted on May 13th, 2007 by Jason Stajich · No Comments

I read this blurb in the New Scientist about a PNAS paper (subscription required for next 6 months) on how hive beetles (Aethina tumida) are able to infest bee hives by throwing off the bees because they are producing isopentyl acetate which is thought to be produced and used by bees to signal an alarm.
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Categories: co-evolution · fungi · honeybee · saccharomyces · symbiosis · yeast