Schizophyllum genome portal live at JGI

In preparation for Asilomar, JGI is releasing lots of the genome sequencing project portals. The Schizophyllum commune Genome Portal is now publicly available. Go get your white-rot gene investigation on! (Though please respect the community rules for 1st rights to publication of the genome-wide analyses).

Aspergillus has a posse


Shepard Fairley has gotten alot of notice lately for his Obama art that has been replicated pretty much everywhere. I mocked up a homage to his earlier street art — here we’ll discuss the growing Aspergillus genome posse.

But the work from mainly the JCVI, Broad Institute, JGI, NITE, and Sanger centre has generated an excellent collection of genome sequences for the Eurotiales clade (feel free to get a login for the wiki and add other that are missing).  The Aspergillus community now has a AGD – Aspergillus Genome Database project that includes a curator of genome annotation (they are hiring) and presumably literature in the SGD and CGD model of curation.

I think a lot of other projects have a Posse too (or maybe just a loosely organized band) in terms of a community of people working on related species and willing to work together to coordinate.  As these sort of “clade” databases start to develop we will have better clusters of information that can be mapped among multiple species.

Eventually I hope this will spur efforts for more coordinated genome databases for comparative genomic and transfer of known gene and functional information between experimental systems.  The efforts really require coordination or centralization of the data so that gene models can be updated as well as orthologs and phylogenomic inference of function.

On the content of (petri plate) Media

ResearchBlogging.orgAn avid reader pointed out that I was not entirely thorough in describing that we don’t enough about the V8 agar media that is used to induce mating in Cryptococcus. In fact a great deal of work on mating in this fungus had focused on identifying what pathways are induced by V8 agar that induce mating.  It was shown that inositol stimulates mating through use of defined media containing inositol (Xue et al, 2007).  This paper interestingly explores plant-fungal interactions and Cryptococcus suggesting that mating may occur preferentially on plants in cases where inositol is abundant.

It is also worth noting that V8 media contains a high level of copper ions and it was also pointed out to me that Jef Edman’s lab showed that melanin mutants have mating defects, and both phenotypes are suppressed by copper. And more recently (Lin et al, PLOS Genetics 2006) found that alleles of the Mac1 copper regulated transcription factor are a QTL influencing hyphal growth and melanin production, and showed that copper can enhance hyphal growth.

So the role of copper and interplay with V8 agar media and how this induces mating is actually quite known.

C XUE, Y TADA, X DONG, J HEITMAN (2007). The Human Fungal Pathogen Cryptococcus Can Complete Its Sexual Cycle during a Pathogenic Association with Plants Cell Host & Microbe, 1 (4), 263-273 DOI: 10.1016/j.chom.2007.05.005

Scientific program for Fungal Genetics

The scientific program is up on the FGSC website. Plan out your dash between sessions, or where you will get that coffee break meeting. This will be the largest attended fungal genetics meeting yet so will be fun to see so many people enthusiastic about the field. Look forward to seeing some of the blog readers and encouraging some guest post contributions in the future as well.

Fill-er-up with Myco-diesel?

ResearchBlogging.orgSo this is actually old-ish news, but I saw this press release about paper published last year describing the ability of the fungus Gliocladium roseum to naturally synthesizes diesel compounds. The paper from Gary Strobel @Montana State and collaborators describes that G. roseum produces volatile hydrocarbon on cellulose media. Extracts from the host plant (Eucryphia cordifolia) were also able to support growth of the fungus alone. This production of products have been dubbed “myco-diesel”. G. roseum is an endophyte of E. cordifolia I wonder what kinds of advantages it might provide for the fungus or the plant to produce these hydrocarbons.

I wonder if it is better to focus on these organisms that have already evolved a way to make these hydrocarbons directly from cellulose rather than the multistep process of making easy to process sugars from different starting plant materials and then ethanol or other hydrocarbons from yeast or bacteria growing on that sugar. Growth rates, amenability to grow in bioreactors, etc certainly are considerations in building production systems, but I wonder whether these kind of finding represent inroads to solving our problems or if they are peripheral to the current bioengineering approaches that are underway.

Some of the earlier press releases I had missed it seems:

G. A. Strobel, B. Knighton, K. Kluck, Y. Ren, T. Livinghouse, M. Griffin, D. Spakowicz, J. Sears (2008). The production of myco-diesel hydrocarbons and their derivatives by the endophytic fungus Gliocladium roseum (NRRL 50072) Microbiology, 154 (11), 3319-3328 DOI: 10.1099/mic.0.2008/022186-0

Yeast population genomics
I have cheered the Sanger-Wellcome SGRP group work to generate multiple Saccharomyces cerevisiae and S. paradoxus strain genome sequences.   The group had previously submitted a version of the manuscript to Nature precedings and it is now published in Nature AOP showing that submitting to a preprint server doesn’t necessarily hurt your manuscript getting published…  The research groups explored the impact of domestication (as was also recently done for the sake and soy sauce worker fungus, Aspergillus oryzae) on the Saccharomyces genome by comparing individuals from wild strains of S. paradoxus.

This paper addressed several challenges including methodology for light genome sequencing for population genomics. This data represents in a way, a pilot project on for genome resequencing projects and using draft genome sequencing with next generation sequencing tools. Of course with the pace of sequencing technology development, any project more than a couple months old will be using outdated technology it seems, but this work represents some important progress.  Tools like MAQ were also developed and tuned as part of the project.  In addition to the methods development it also provided a new look at evolutionary dynamics of a well-studied fungus.

Genome assembly
The authors apply several different quality controls and utilize a new tool called PALAS (Parallel ALignment and ASsembly)  to assemble all the strains at the same time using a graph-based approach that utilized the reference genome sequences for each species. This is different than a full-blown WGA approach like PCAP, Phusion or Arachne because this is deliberately low-coverage sequencing pass.  The authors are trying impute missing sequence via Ancestral Recombination Graphs as implemented in the Margarita system.   They also use MAQ to align sequence from Illumina/Solexa sequencing to these assemblies made by PALAS.

Since this project was on two species of SaccharomycesS. cerevisiae and S. paradoxus they needed good reference assemblies for each of these species. The previously availably S.paradoxus assembly wasn’t complete enough for this study so they did an addition 4.3 X coverage with sanger/ABI sequencing and 80X coverage with Illumina.

Population genomics and domestication

The sequencing data also provided a framework for population genetic investigations. Some simple findings showed that geographic isolates within each species were more genetically similar to each other.  The main geographic regions of samples for S.paradoxus data included the UK, American, and Far East samples, some of which had been analyzed in a very nice study on Chromosome III.  For the S. cerevisiae samples there were individuals from around Europe, at least 10 European wine strains, Malaysian, Sake brewing strains, West Africa, and North America. From these data it was possible to discover that there are several of strains with mosiac genomes meaning that pieces of the genome match best with the sake fermentation strains and other parts from the wine/European samples.

Efforts to detect the effects of natural selection that may be linked to domestication of these strains explored two different approaches. The McDonald-Kreitman test did not identify any loci under positive selection while Tajima’s D was negative in the S.cerevisiae global and wine strain populations indicating an excess of singleton polymorphisms – though they draw little conclusions from that.  The authors also observed a sharper decay of linkage disequilibrium in S.cerevisiae (half maximum of 3kb) than S.paradoxus (half maximum 9kb) suggesting that S.cerevisiae is recombining more, either due to increased opportunities or a great frequency of recombination events when it does.

In context of the paper title and the idea of exploring the effects of domestication on the genome, the authors observe that the standard paradigm that ‘domesticated’ species have lower diversity levels is simply not the case in these samples.  This isn’t to say there isn’t evidence of the selection for fermentation production from these strains based on the stress response conditions they were tested on, but that there is still ample evidence of maintaining diversity within the populations presumably through various amounts of outcrossing.

We are also interested in these results as we apply similar questions to population genomics of the human pathogenic fungus Coccidioides where 14 strains have been sequenced with sanger sequencing technology.  Hopefully some of these lessons will resonate in our analyses and also that this era of population genomics will see ever more extensive collections to address aspects of migration, phylogeography, and local adaptations within populations of fungi and other microbes.

Gianni Liti, David M. Carter, Alan M. Moses, Jonas Warringer, Leopold Parts, Stephen A. James, Robert P. Davey, Ian N. Roberts, Austin Burt, Vassiliki Koufopanou, Isheng J. Tsai, Casey M. Bergman, Douda Bensasson, Michael J. T. O’Kelly, Alexander van Oudenaarden, David B. H. Barton, Elizabeth Bailes, Alex N. Nguyen, Matthew Jones, Michael A. Quail, Ian Goodhead, Sarah Sims, Frances Smith, Anders Blomberg, Richard Durbin, Edward J. Louis (2009). Population genomics of domestic and wild yeasts Nature DOI: 10.1038/nature07743