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 As always, please contact the lead contact and PI associated with unpublished 1KFG genomes for permission prior to the use of any data in publications.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.
I just returned from the "1 Fungus = ? Genes" symposium, which was hosted by the Centraalbureau voor Schimmelcultures (CBS) and held at the Dutch Royal Academy in Amsterdam. The meeting (April 10-11, 2013) was excellent and the program included numerous internationally renowned speakers including Joe Heitman, Christina Cuomo, David Geiser, Ulrich Kuck, Francois Lutzoni and many more. The energy around the meeting is comparable to the early Fungal Genetics Conferences, and the CBS meeting is rapidly becoming the annual meeting for Fungal Taxonomy, Systematics and Biodiversity. After the conference, there were two days (April 12-13) of barcoding talks, which were held at CBS in Utrecht. One of the big themes that came out of these talks was the increased use of MALDI-TOF for rapidly diagnosing lab and clinical strains of pathogenic fungi.
I gave a talk on "1000 Fungal Genomes: Gaining Momentum". It was well received and there seems to be a lot of enthusiasm around the project. Be sure and visit the nomination page for 1KFG and help edit the taxonomy and nominate genomes for sequencing.
Greetings from Nancy, France! I'm having a wonderful time in the lab of Francis Martin at the Institut National de la Recherche Agronomique (or INRA). Much of their research has focused on understanding the symbiosis formed between mycorrhizal fungi and their plant hosts, and they have led the genomic sequencing projects of many truffles (Tuber spp.).You can learn more about the Lab of Excellence ARBRE, Francis, and his lab group by visiting his blog at http://mycor.nancy.inra.fr/blogGenomes/.
I'm here for 2 months to assemble the genome of Elaphomyces granulatus, the "false-truffle" producing, ectomycorrhizal species which is a host for my study organism, Elaphocordyceps ophioglossoides. The sequence data that I have for this truffle, E. granulatus, is in some ways a metagenome because sporocarp or fruiting body tissue was used for sequencing as this species does not grow in culture. Because members of the Martin group have experience assembling this type of genomic data from sporocarp (from the white truffle or Tuber magnatum), I am here to learn the assembly techniques they are using. Some of things we hope to examine from this assembly are to determine what kind of bacterial community is associated with E. granulatus, compare the genome structure and content to other sequenced ascomycotan ectomycorrhizal species (e.g. Tuber spp.), and determine if there is any evidence for horizontal gene transfer between the truffle host and Elaphocordyceps pathogen.
On Tuesday, I had the opportunity to join Francis, Claude Murat, and their colleagues for a day examining some field sites and "trufficulture" or the practice of propagating truffles in tree plantations for the sake of harvesting truffles. In the photo you can see a Hazelnut orchard, planted 24 years ago for the purpose of growing truffles (and the sweetest truffle dog you'll ever meet, on the left). Some of the trees now produce Tuber aestivum var. mesentericum, but the managers (working with Francis and Claude) have learned a lot in the past couple of decades about the kinds of conditions that seem to favor truffle production in the area, such as the density of trees, watering regime, etc. And Claude is the first author on a nice paper coming out soon examining genetic structure and mating type distribution of Tuber melanosporum at one of the sites we visited.
It has been a busy month for the Spatafora lab. Here is a quick update.
The lab had a very successful Fungal Genetics Conference in Asilomar, CA. All lab members gave great presentations. We drove down in a van and had a lot of fun with stops for milk shakes, olives, and even olive milk shakes.
I returned home for a week and then headed to Thailand, where I participated in Sing's defense. Sing was a visiting student from Prince Songkla University in Thailand. She works works on endophytes of seagrasses as a source of biologically active natural products. She successfully defended her thesis and will graduate in May! As always, Thailand was amazing. This time we were mostly in the south in Hat Yai near the Malaysian border.
Teppo our visiting graduate student from Finland via Norway completed his 3 month visit and has gone back to Norway with his family. We really enjoyed having him as part of the lab and will miss him and his family.
Alisha is in Nancy, France for two months. She is visiting Francis Martin's lab where she is learning some metagenomic assembly approaches for Elaphomyces. Sounds like she has hit the ground running. Perhaps she will contribute to blog from Nancy (hint hint).
We also welcome our newest lab member, Dabao Sun Lu. He is a Fulbright scholar from Norway and is in a MS program in Botany and Plant Pathology. Welcome Dabao!!
Kathryn, Derek and Alija are holding down the fort while I am gone. I have a great lab who keep things running despite me. Thanks so much to all of them.
And now I am in Amsterdam for the CBS 1 Fungus = Which Genes conference. Should be a good one. WiFi willing, I will post and tweet
Latest paper out of the Schardl lab on evolutionary genomics of the "grass endophytes" and the evolution of ergot biosynthesis ( Schardl CL, Young CA, Hesse U, Amyotte SG, Andreeva K, et al. (2013) Plant-Symbiotic Fungi as Chemical Engineers: Multi-Genome Analysis of the Clavicipitaceae Reveals Dynamics of Alkaloid Loci. PLoS Genet 9(2): e1003323. doi:10.1371/journal.pgen.1003323). Great paper that details the distribution, diversification and evolution of ergot biosynthesis. They argue that these secondary metabolite gene clusters are found in transposon-derived, AT-rich repeat blocks, which are implicated in gene losses, duplications, and diversification. In addition to the insights into secondary metabolism, the result showing that Periglandula species, which were recently described from morning glories, group phylogenetically with mycoparasites of Tyrranicordyceps and Verticillium is another important sampling point in understanding the evolution of host affiliation.
Ryan Kepler and Steve Rehner just published some nice work (Molecular Ecology Resources Volume 13, Issue 2, pages 210–217, March 2013) on genome-assisted marker development for the Metarhizium anisopliae complex. Using the genome sequences of M. acridum and M. robertsii, they identified a number of conserved, intergenic regions that are both more variable and more informative for phylogenetics of the M. anisopliae complex than current nuclear markers that are most frequently used in fungal systematics. Undoubtedly, this approach will become more common and become part of genomic barcoding.