Alisha Owensby, PhD candidate in the lab, was recently awarded an NSF Doctoral Dissertation Improvement Grant (DDIG) for her proposal, "Evolutionary Genomics of Inter-Kingdom Host-Jumping in the Fungal Genus Elaphocordyceps". Way to go! If you follow our blog, you know that Alisha is currently in Nancy, France working in the laboratory of Francis Martin at INRA. She is working on the genome of Elaphomyces, one of the hosts of Elaphocordyceps. This is a particularly challenging project as Elaphomyces does not culture and thus the genomic libraries are prepared from DNA and RNA extracted directly from sporocarps and are metagenomic in nature. The photo is of Alisha working in Francis' lab doing an RNA extraction. Just a few more weeks and she'll be back. Bring wine and cheese!!
An interesting paper out of Antonis Rokas's lab looks at some of the current methods to minimize gene tree incongruence when reconstructing phylogenies using genome scale data. This is relevant to a lot of work that we do, so I thought I would share. Among other things, they argue that using genes with strong signal may be more valuable than sheer concatenation of all available data, and that using bootstrap support is not relevant when using such large data sets. Here's the link: http://www.nature.com.ezproxy.proxy.library.oregonstate.edu/nature/journal/vaop/ncurrent/full/nature12130.html
1KFG is pleased to announce the public release of the Suillus brevipes genome http://genome.jgi.doe.gov/Suibr1/Suibr1.home.html. Suillus brevipes is an ectomycorrhizal species of Suillaceae (Boletales), and was contributed to the 1KFG project by Sara Branco and Tom Bruns from the University of California at Berkeley. As always, please contact the lead contact and PI associated with unpublished 1KFG genomes for permission prior to the use of any data in publications.
Two new genomes were released today as part of the JGI 1000 Fungal Genomes (1KFG) Project. These are Lepidopterella palustris v1.0 (http://genome.jgi.doe.gov/Lpalustris) and Polychaeton citri v1.0 (http://genome.jgi.doe.gov/Pcitri). Both of these taxa are members of the class Dothideomycetes and represent previously unsampled families Argynnaceae and Capnodiaceae, respectively. These taxa were contributed to 1KFG by researchers Pedro Crous, Manfred Binder and Janneke Bloem from the Centraalbureau voor Schimmelcultures in the Netherlands. Annotation and editing privileges remain password-protected but all other tools are now available to the general public. If you use these data, please contact the lead PI and related researchers prior to any plans for publication.
Our lab has been performing more gene tree - species tree reconciliation analyses lately. Especially as they relate to the evolution of modular genes like non-ribosomal peptide synthetases. Just came across this interesting paper that deals with error correction in GT-ST reconciliation analyses. Thought I would pass it on.
"Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence." Chaudhary R, Burleigh JG, Eulenstein O. BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S11. doi: 10.1186/1471-2105-13-S10-S11.