Fungal Evolutionary Genomics

Some twitter updates for 2010-08-31

Jason Stajich — Wed, 01 Sep 2010 07:16:00 +0000

Fellowship app writing – reminds of all the things up in the air… Plenty else to do but waiting for data from collaborators and sequencer. #

Some published papers this last month

Jason Stajich — Tue, 31 Aug 2010 20:33:12 +0000

We had a productive period over the last year and finally saw set of papers representing this work come out in the last month. This represents great collaborations with several different groups. In addition to the Coprinus genome, we were involved in the publication of two other genome sequences thus summer. One a basidiomycete mushroom and one for an oomycete and pathogen of plants, both with a host of collaborating labs. Two papers on Neurospora also appeared as part of collaborations with Hanna Johannesson‘s group and Michael Freitag, Michael Brunner, and Deb Bell-Pedersen. A fifth paper on Coprinopsis meiotic genes is in press but will post about it when it appears.

Transcription factors in light and circadian clock signaling networks revealed by genome-wide mapping of direct targets for Neurospora WHITE COLLAR COMPLEX. Smith KM, Sancar G, Dekhang R, Sullivan CM, Li S, Tag AG, Sancar C, Bredeweg EL, Priest HD, McCormick RF, Thomas TL, Carrington JC, Stajich JE, Bell-Pedersen D, Brunner M, Freitag M. Eukaryot Cell. 2010 Jul 30.
Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Lévesque CA, Brouwer H, Cano L, Hamilton JP, Holt C, Huitema E, Raffaele S, Robideau GP, Thines M, Win J, Zerillo MM, Beakes GW, Boore JL, Busam D, Dumas B, Ferriera S, Fuerstenberg SI, Gachon CM, Gaulin E, Govers F, Grenville-Briggs L, Horner N, Hostetler J, Jiang RH, Johnson J, Krajaejun T, Lin H, Meijer HJ, Moore B, Morris P, Phuntmart V, Puiu D, Shetty J, Stajich JE, Tripathy S, Wawra S, van West P, Whitty BR, Coutinho PM, Henrissat B, Martin F, Thomas PD, Tyler BM, De Vries RP, Kamoun S, Yandell M, Tisserat N, Buell CR. Genome Biol. 2010;11(7):R73. Epub 2010 Jul 13.
Genome sequence of the model mushroom Schizophyllum commune. Ohm RA, de Jong JF, Lugones LG, Aerts A, Kothe E, Stajich JE, de Vries RP, Record E, Levasseur A, Baker SE, Bartholomew KA, Coutinho PM, Erdmann S, Fowler TJ, Gathman AC, Lombard V, Henrissat B, Knabe N, Kües U, Lilly WW, Lindquist E, Lucas S, Magnuson JK, Piumi F, Raudaskoski M, Salamov A, Schmutz J, Schwarze FW, Vankuyk PA, Horton JS, Grigoriev IV, Wösten HA. Nat Biotechnol. 2010 Jul 11.
Conflict between reproductive gene trees and species phylogeny among heterothallic and pseudohomothallic members of the filamentous ascomycete genus Neurospora. Strandberg R, Nygren K, Menkis A, James TY, Wik L, Stajich JE, Johannesson H. Fungal Genet Biol. 2010 Jul 1.

Our work on the cover

Jason Stajich — Tue, 29 Jun 2010 17:37:43 +0000

Our work on the mushroom genome of Coprinopsis cinerea is featured on the cover of this week’s PNAS. Check out the blog post and the article.

A sendoff for the lab visitor

Jason Stajich — Thu, 27 May 2010 00:21:39 +0000

We bid farewell last weekend to our lab visitor, Nastassa Gioti, who is headed back to Sweden after 6 fun weeks in Riverside. We learned from her, and she got to dig into her genome datasets for Neurospora in the context of the comparative and genome annotation tools we have, so it was fun all around!

This also marked the second get together (but the first where we remembered to bring a camera). Since we gathered at a local mexican restaurant with whimsical and amazing sculptures and art from recycled material, it was fitting we document it with pictures.

A whirlwind spring

Jason Stajich — Fri, 07 May 2010 18:21:21 +0000

Spring is flying along. We’ve been presenting some of our work at conferences and getting ready for a full summer of meetings and Divya preparing for her qualifying exam.

A few papers have come out or are now accepted. One I’ll highlight here is the publication of the Sordaria macrospora genome. This was a fun collaboration with groups in Germany, France, Oregon State, and Edinburgh where we sequenced Sordaria with 454 and Illumina sequence and assembled the genome using de novo assembler and comparative scaffolding to the available Neurospora genomes. Sordaria is an important model system for sexual development and provides a great evolutionary not-too-distant outgroup to the Neurospora clade for evolutionary genomic analyses we are trying to finish off.

Also have had a chance to interact with colleagues at the JGI User meeting, the Neurospora conference, and a special treat of speaking at the PBoFF symposium at Texas A&M.

Everyone is getting their projects underway in the lab and we’ve had two visitors come to work on Neurospora and Chytrid genome project analyses so a busy but exciting time for us.

Several more weeks left in the quarter where I’m teaching introductory biology and then the Gordon Conference, MSA, and IMC9 will be conferences to finish preparing for. The lab will also be represented at Evolution meetings in Portland as John attending.

Fusarium mobile chromosomes

Jason Stajich — Wed, 17 Mar 2010 23:51:26 +0000

Congrats to graduate student Divya Sain a co-author on a paper published in Nature on mobile chromosomes in Fusarium, stemming from her work her work during a rotation in the Borkovich laboratory.

The work highlights the important aspect of how pathogenicity factors can be exchanged via mobile chromosomes and can be an important pathway for adaptive evolution and acquisition of new function through whole chromosome exchange between strains.

Back from Ireland

Jason Stajich — Tue, 09 Mar 2010 21:52:26 +0000

I am back from a short trip to Ireland where I gave a seminar at National University of Ireland, Maynooth and spend some time with folks interested in evolution or fungi like David Fitzpatrick, James McInerney, Davide Pisani. I also learned about a new spinoff company from one of the faculty producing media that will help Bee immune systems. In my chats with some of the faculty I found out that I had lots in common with Sean Doyle on Aspergillus and some basidiomycete genomics questions and also much in common with Gary Jones working on prions in yeast. After my trip to Maynooth, I spent a few days in Dublin afterwards to see the town which included a visit with some Dublin yeast researchers Ken Wolfe and Geraldine Butler who took me out to see Newgrange.

I learned that there is an abundance of yeast research in Ireland. In addition to the researchers there is a whole shop devoted to Yeast.

And my visit to the Guinness Brewery at St. James Gate taught me that that Yeast is a national treasure in Ireland.

Complete with an important safe for insuring there are backup strains. I have to assume there is a -80 freezer somewhere in the Guinness complex holding old strains as well.

Did you know one of the master brewers at Guinness was also the inventor of the Student’s T-test? Here’s the proof

So it was great to visit and look forward to going back at least in 2012 when SMBE will be held in Dublin.

PLoS Pathogens Pearl published

Jason Stajich — Fri, 29 Jan 2010 19:17:17 +0000

PLoS Pathogens has a short review format called Pearls. We were invited to write a short summary on Batrachochytrium which was published in the January issue.

Rosenblum, E., Voyles, J., Poorten, T., & Stajich, J. (2010). The Deadly Chytrid Fungus: A Story of an Emerging Pathogen PLoS Pathogens, 6 (1) DOI: 10.1371/journal.ppat.1000550

Lab news for January

Jason Stajich — Thu, 28 Jan 2010 07:22:16 +0000

A quick January update. Jason was appointed to a two year term as Councilor for Genetics/Molecular Biology for the Mycological Society of America, began a term on the editorial board of Eukaryotic Cell, and was also profiled in the GSA reporter. Finishing grants and working towards completing manuscripts from postdoc-land while we are computing results on from genome and RNA-Seq datasets. Working to getting our laboratory production up and running to generate more of our data.

Currently the lab is four strong with 3 graduate students. They are Divya Sain and Yi (Zoe) Zhou who have joined for the long haul of doing a PhD in the GGB program, and Yizhou Wang, a rotation student from Plant Biology. Divya is working on a project that uses bioinformatics and phylogenetics to reconstruct history of the genes involved in the fungal cell wall across the fungi. Zoe is using bioinformatics and phylogenetics to focus on duplicated gene evolution and is exploring other aspects of duplication in fungal genomes. Yizhou will be getting going in the laboratory learning how to grow Neurospora and preparing some RNA extractions for some transcriptomics and RT-PCR validation.

In February John Abramyan will join us as a postdoctoral scholar to work on some molecular biology and genomics work on at least two fungi along with applying bioinformatic analyses of these data.

I also setup the Gbrowse2 for Sordaria and Coprinopsis, worked on some new template themes for the blogs, and we setup a bioinformatics group website at UCR (which is still coming together). Hoping the rest of Jan and Feb will be clearing a few more to do things off the list and getting a chance to do a bit more research blogging on the Hyphal Tip.

Down to San Diego

Jason Stajich — Sun, 10 Jan 2010 21:34:17 +0000

Although I’m not going to be at PAG this year, I’ll be in San Diego for the BioPerl and part of the GMOD meeting on Wed and Thursday.