The Hyphal Tip: Fungal Genomes and Comparative Genomics

Digesting the fungal genomes

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Entries from March 2007

Proteins Evolve Differentially in Saccharomyces

Posted on March 30th, 2007 by sharpton · 2 Comments

Blogging about Peer-Reviewed ResearchPerhaps not a surprise to anyone that has dabbled in evolutionary analysis of proteins, Kawahara and Imanishi (BMC Evolutionary Biology 2007) confirm that not every protein evolves via a molecular clock in Saccharomyces sensu scricto. Using everyone's favorite evolutionary tool, PAML, the authors identify protein lineages via a whole genome scan that evolve relatively slow or
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Categories: comparative · evolution · fungi · genome · phylogeny · saccharomyces · speciation

maple syrup fungus

Posted on March 29th, 2007 by Jason Stajich · No Comments

Kathie Hodge has a nice description with cool photos of a fungus growing in maple syrup. I guess I better make sure our syrup is in the fridge!
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Categories: fungi

Fungal Genetics 2007 details

Posted on March 28th, 2007 by Jason Stajich · 1 Comment

I'm including a recapping as many of the talks as I remember. There were 6 concurrent sessions each afternoon so you have to miss a lot of talks. The conference was bursting at the seams as it was- at least 140 people had to be turned away beyond the 750 who attended. If there was any theme in the conference it was "Hey we are all using these genome sequences".
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Categories: bioinformatics · chytridomycota · cryptococcus · dothideomycetes · euriotiomycetes · filamentous · glomeromycota · homobasidiomycota · horizontal gene transfer · neurospora · news · sordariomycetes · zygomycete

Fungal Genetics 2007 summary

Posted on March 26th, 2007 by Jason Stajich · 1 Comment

A Fungal Genetics 2007 summary. Wow. What a meeting! I am still exhausted and not just because of the very late Saturday night dancing at the close of the conference. I will just say anyone who thinks scientists are boring people should witness the passion researchers have for their science and in sharing it with other people.
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Categories: news

Hello, do I know you?

Posted on March 21st, 2007 by Jason Stajich · No Comments

Blogging about Peer-Reviewed ResearchSelf and non-self recognition is important for fungi when hyphae interact fuse if they should compartmentalize and undergo apoptosis to kill the heterokaryoton or exchange nutrients. This process is part of cell defense and to limit to the movement of mycoviruses. A paper in PLOS ONE describes the Genesis of Fungal Non-Self Repertoire.
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Categories: evolution · filamentous · fungi · neurospora · repeats

At Asilomar

Posted on March 21st, 2007 by Jason Stajich · 2 Comments

We're at Asilomar mtg for Fungal Genetics 2007. We'll try and blog a bit about the interesting talks and data. I'm curious how many fungal geneticists are in fact reading blogs like these and if this medium will work for idea dissemination.
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Categories: news

Genome resources for Candida species

Posted on March 18th, 2007 by Jason Stajich · 1 Comment

The Candida clade of Hemiascomycete fungi have received much attention from funding bodies so that many genomic and experimental resources are available address questions of pathogenecity and industrial applications of these species.

The Candida genus

Traditionally, species of yeasts that were thought to be asexual were given the genus name Candida. This has lead to Candida being a sort of taxonomic rubbish bin.
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Categories: candida · comparative · phylogeny · saccharomyces

Yeast resequencing data updated

Posted on March 15th, 2007 by Jason Stajich · 3 Comments

Image from http://www.bath.ac.uk/bio-sci/wheals2.htmThe Saccharomyces Genome Resequencing Project has completed " ABI sequencing of 32 S. cerevisiae strains and 27 S. paradoxus strains to a depth of between 1x and 3x". This is in collaboration with Ed Louis' group who have been working on number of really interesting fungal biology.
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Categories: resequencing · saccharomyces

SGD community annotation

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

The Saccharomyces Genome Database has deployed a wiki for gene annotation from the community.  This should be an interesting experiment in how information can flow from the community into these databases.
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Categories: database · genome annotation · saccharomyces · wiki

Yeast keeps to itself

Posted on March 7th, 2007 by Jason Stajich · No Comments

Cliff Zeyl and Sally Otto present a nice review on research from the Kruglyak lab regarding evidence that Saccharomyces is primarily a selfer in nature as it outbreeds very infrequently (once in 50,000 generations). The implications of this work has relevance on the importance of sexual reproduction and recombination in natural populations.
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Categories: evolution · recombination · saccharomyces · yeast