The Hyphal Tip

Digesting the fungal genomes

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Attend Fungal Genetics 2009!

Posted on September 5th, 2008 by Jason Stajich · 2 Comments

If you are interested in fungal genetics and genomics, comparative biology, and of course dancing with fungal geneticists, plan to attend the 25th Fungal Genetics Meeting held at the beautiful Asilomar Conference Grounds in Pacific Grove, California. Below is info sent out from the Policy Committee and registration opens in a little over a month.  Budding (and conidiating) artists can also submit a Logo design

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Categories: Fungal Genetics · news
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Papers on our desk

Posted on August 24th, 2008 by Jason Stajich · 2 Comments

A quick post of some recent comparative genomics papers on our desk that are worth a look.

Khaldi N, Wolfe KH (2008) Elusive Origins of the Extra Genes in Aspergillus oryzae. PLoS ONE 3(8): e3036. doi:10.1371/journal.pone.0003036. This was a cool but somewhat controversal [...]

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Categories: ascomycota · bioinformatics · comparative · fungi · sexual reproduction · zygomycete
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A word about databases

Posted on July 27th, 2008 by Jason Stajich · 1 Comment

Logo for fungal GenomesReport concludes that a fungal genome database is of “the highest priority”.

This is the title as listed in PubMed for this article from Future Medicine about the AAM report on charting future needs and avenues of research on the fungal kingdom.

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Categories: opinion
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Penicillium marneffei project

Posted on June 3rd, 2008 by Jason Stajich · 4 Comments

P.marneffeiWe’re excited that a Penicillium marneffei grant to Mat Fisher and collaborators has been funded by the Welcome Trust. It includes a collaboration with University College London, our lab, JCVI, and Univ of Melbourne. This project will explore functional and comparative genomics approaches to studying the fungus

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Categories: aspergillus · euriotiomycetes · news
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Trichoderma reesei genome paper published

Posted on May 12th, 2008 by Jason Stajich · 1 Comment

TrichodermaThe [[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.

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Categories: filamentous · gene family · genome · genome annotation · genome sequencing · trichoderma
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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

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Categories: comparative · genome · genome sequencing · neurospora · sordariomycetes
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Aspergillus comparative transcriptional profiling

Posted on March 12th, 2008 by Jason Stajich · 1 Comment

ResearchBlogging.org

Researchers from Technical University of Denmark published some interesting results from comparing expression across the very distinct Aspergillus species.

Kudos also goes to making it Open Access. I am posting a few key figures below the fold because I can! They grew the fungi in bioreactors fermenting glucose or xylose. After calibrating the growth curves they were able to sample the appropriate time points for comparison of gene expression across these three species. They found a set of genes commonly expressed.

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Categories: aspergillus · evolution · gene regulation · microarray
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Some links

Posted on March 3rd, 2008 by Jason Stajich · 2 Comments

ResearchBlogging.org

I’ve been too busy to post much these last few days, but here are a few links to some papers I found interesting in my recent browsing.

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Categories: basidiomycota · database · extremophiles · molecular evolution · pathogens · zygomycete
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Comparing development

Posted on February 17th, 2008 by Jason Stajich · No Comments

PZ Meyers has a post summarizing of an older paper from Elliot Meyerowitz (2002) that comapares plant and animal development. In particular there is are some major themes summarized about how plants and animals form patterns and cell to cell signaling as part of development. What’s missing is what we’ve learned about within group comparisons where there are multiple lineages of single-celled and multicelled

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Categories: comparative · evolution · genome
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S.pombe telomerase RNA identified

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

Blogging on Peer-Reviewed Research Webb, C.J., Zakian, V.A. (2008). Identification and characterization of the Schizosaccharomyces pombe TER1 telomerase RNA. Nature Structural & Molecular Biology, 15(1), 34-42. DOI: 10.1038/nsmb1354

Leonardi, J., Box, J.A., Bunch, J.T., Baumann, P. (2008). TER1, the RNA subunit of fission yeast telomerase. Nature Structural & Molecular Biology, 15(1), 26-33. DOI: 10.1038/nsmb1343

Two papers in Nature Structural & Molecular Biology identify the telomerase RNA in Schizosaccharomyces pombe. Telomerase is a multi-unit enzyme that has both protein and RNA components. While the protein subunit is highly conserved and identifiable through sequence comparisons of eukaryotes, the RNA subunit has a variable size and sequence making identification through comparative means more difficult. The S. pombe telomerase RNA subunit, or TER1, was discovered by two labs applying similar biochemical approaches to identify the locus.

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Categories: cell biology · s.pombe
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