Archive for April, 2011

Blast2GO

April 28th, 2011

 

  • Are you working in sequencing projects?
  • Do you have thousands of novel sequences that need functional annotation?
  • Do you need a user-friendly tool to functionally analyze your data?

After last years success the Blast2GO Team is again very pleased to announce:

THIRD INTERNATIONAL COURSE

IN AUTOMATED FUNCTIONAL ANNOTATION AND DATA MINING

In this course you will learn tools and tips for functional annotation, visualization and analysis of novel sequence data making use of Blast2GO. The course will be offered to 30 participants at 2 locations :

  • UC Davis, Davis, California, US: July, 26 to 28, 2011
  • CIPF, Valencia, Spain: September, 28 to 30, 2011

For more information and course registration please visit: http://bioinfo.cipf.es/blast2gocourse

Truffle Genome FGB Special Issue

April 24th, 2011

Scientists studying  the molecular biology and ecology of the mycorrhizal symbiosis have benefited from the description of the T. melanosporum genome (Martin et al., 2010) and equally so from the companion papers compiled in the special issue of New Phytologist. A new cluster of companion papers is now published in a special issue of Fungal Genetics and Biology. The authors of these papers have used the freshly minted truffle genome to begin to probe some of the most intriguing questions in both the biology and ecology of this iconic fungus.

Sequencing the Fungal Tree of Life

April 24th, 2011

Last week, a paper of mine has been published online March 14, 2011 in New Phytologist. I enjoyed drafting this letter titled ‘Sequencing the fungal tree of life (fToL)’ with other long-time DOE JGI fungal genomics collaborators. Since I think it is pretty cool, I would like to  further discuss our on-going fToL projects dealing with comparative genomics of soil fungi and metagenomics of forest soils discussed in this paper.

As you may know, forest soils host diverse microbial communities that impact tree health and productivity, and which play pivotal roles in terrestrial carbon cycling and sequestration, and biogeochemical cycles.

Amongst these microbial communities, soil fungi are undoubtly major players. Traditionally, they have been divided into discrete ecological guilds, such as leaf litter-decomposers, white- and brown-rot wood decayers, parasites and ectomycorrhizal (ECM) symbionts. However, the actual functional properties of individual species, and the synergistic effects among them, are often obscure. Moreover, the basic biodiversity of the vast majority of soil systems (e.g., boreal forests and subartic taiga)  remains unexplored using modern high-throughput DNA barcoding approaches.

We hypothesize that firm distinctions between fungi commonly labeled ECM, parasite, wood decomposer, litter saprotroph are, in some instances, unwarranted, and that crucial ecosystem processes, such as carbon sequestration, litter decay and mutualism, can only be understood in the context of interactions among multiple species representing a functional continuum.

Thanks to the DOE JGI launched Fungal Genomic Program, the number of available fungal genomes has expanded dramatically in recent months (see my previous post ‘Crunching Fungal Genomes at High Speed‘), and this provides unprecedented opportunities to study the functional (and taxonomic) diversity of soil communities. We — David Hibbett, Dan Cullen, Roger Finlay, Cheryl Kuske, Rytas Vilgalys and others — have taken this opportunity to set up a series of projects to elucidate physiological processes taking place along the ‘saprotrophism/mutualism’ continuum encompassing decaying woody debris, soil hyphal networks and ECM symbiosis on major forest ecosystems, using comparative genomics and metatranscriptomic approaches.

As described in the New Phytologist paper, these complementary projects should provide valuable opportunities to investigate two major aspects of the interactions between trees, ECM symbionts and wood/litter decayers, and their role in carbon and nutrient cycling:

  • By studying the transcriptional regulation of genes coding for secreted enzymes, such as plant cell wall polysaccharide degrading enzymes, we would gain a more holistic picture of enzyme secretion and subsequent organic matter turnover than has subsequently been possible.
  • By focusing on transcriptional regulation of fungal genes involved in resource exchange across the ECM/plant and ECM/saprotroph interfaces, we would obtain a better understanding of how mycorrhizal symbiont and the wood decayer communities are altered by changes in nutrient availability.

More exciting times ahead!!!

Another post on this fToL paper: DOE JGI Science Highlights: Toward a Genomic Encyclopedia of Fungi.

F. Martin, D. Cullen, D. Hibbett, A. Pisabarro, J. W. Spatafora, S. E. Baker and I. V. Grigoriev (2011) Sequencing the fungal tree of life. New Phytologist, DOI: 10.1111/j.1469-8137.2011.03688.x

Photo: State Forest of Champenoux © F Martin

JGI Spring 2011 Primer

April 23rd, 2011

The Spring 2011 edition of the JGI newsletter, The Primer, is now available and features:

  • A report from the 6th Annual DOE JGI User Meeting (Genomics of Energy & Environment) including keynotes by Persis Drelland Terry Hazen
  • Cow Rumen Metagenomics
  • Sentinel of Change: Water Flea Genome Improves Environmental Monitoring
  • Battling Brown Tide with Genomics

 

Available for download (along with archived editions) here: http://go.usa.gov/TfF

EUCAGEN

April 12th, 2011
From Zander Myburg (EUCAGEN Coordinator)
It is a pleasure to announce the full release of the E. grandis genome as part of the Phytozome 7.0 update (www.phytozome.net). This update includes the full gene family analysis and integration of the E. grandis gene models in Phytozome. The full release notes and Data Release Policy are available here:http://www.phytozome.net/eucalyptus.php). The genome browser (http://www.phytozome.net/cgi-bin/gbrowse/eucalyptus/) now includes tracks for E. grandis (BRASUZ1) predicted genes (transcripts), alternative transcripts and ESTs. Additional tracks are also available for sibling species ESTs (mostly E. globulus) and Illumina mRNA-Seq reads from the Eucspresso database (http://eucspresso.bi.up.ac.za/).
In addition, I would like to point out the following:
INTEGRATED E. GRANDIS GENOME ANNOTATION
Phytozome currently includes the v1.0 annotation produced by the team at JGI under the leadership of Dan Rokhsar. A parallel annotation was produced at UGent by the research group of Yves van de Peer (available in http://bioinformatics.psb.ugent.be/webtools/bogas/). The JGI and UGent annotation teams are working tirelessly to integrate the two annotations, with a target date of 30 April (or as soon as possible after). The integrated annotation will be made available as the final annotation (predicted gene set) for the genome paper. People that are mapping short reads to the current JGI gene models should take note that these may change with the release of the integrated annotation. The integrated annotation will be made available for manual annotation in the BOGAS database at UGent.
MAIN GENOME PAPER AND ASSOCIATED PAPERS
EUCAGEN members and other interested persons are invited to access the genome data and share information and results that can be used in the main genome paper or associated papers. We are aiming to submit the main paper by the end of 2011, and we are currently exploring the possibility of coordinating the publication of a small number of associated genome papers in a special issue of a plant research journal. A publication schedule and proposed outline for the main genome paper will be posted on the EUCAGEN website by the end of the month. Please contact any of the main project PIs, Zander Myburg (zander.myburg@fabi.up.ac.za), Dario Grattapaglia (dario@cenargen.embrapa.br) or Jerry Tuskan (tuskanga@ornl.gov) to coordinate analyses and contributions. Interested persons are also encouraged to register as members of EUCAGEN (http://www.eucagen.org/).
—-
Photo: Rose gum (Eucalyptus grandis) from Tatiana Gerus from Brisbane, Australia (Wikipedia).

There might be at least one other, previously hidden, domain of life

April 3rd, 2011

Environmental metagenomics is currently generating massive streams of  DNA sequences from almost all ecosystems, including our human body. Most of these new sequences are coded by the genomes of unknown organisms, but belonging to the three major domains of life: Archaea, Bacteria and the Eukaryota. In a recent paper published in PLoS One, Jonathan Eisen and his colleagues mined the vast amount of sequences generated by Craig Venter’s Global Ocean Sampling (GOS) circumnavigation around the world seas and oceans. They sought to address a single, but crucial, question: Are there sequences encoded by this metagenomic data set that represent novel lineages that branch closer to the base of the tree of life (ToL) than any known phylogenetic marker sequences?

They developed an automated screening system (STAP) for detecting ss-rRNA genes that branch very deeply in the ToL (see Jonathan’s blog post discussing this novel approach). It appeared that rRNA genes in metagenomic data sets were not ideally suited for finding phylogenetically very deep branches of the ToL. Due to these difficulties, they used two genes called RecA and RpoB to answer this question. RecA is involved in DNA recombination. RpoB is involved in translating DNA into RNA. Both, like the genes for ribosomal RNA, are old and ubiquitous. When they constructed phylogenetic trees that tracked the evolutionary relationships between all the RecAs and all the RpoBs found in the GOS DNA samples, they discovered clades that did not fit with any known sequences in the databases. Some of these novel gene subfamilies were, nevertheless, similar enough to known branches to be accounted for as ‘known unknowns’. But both RecA and RpoB had one branch (subfamily) that really was an ‘unknown unknown’. Neither of these branches fits in the existing ToL. Assuming the sequences are in fact real, they may belong to some as-yet-unknown group of viruses (e.g. cyanophages). More excitingly, they may come from a new (i.e., fourth) major branch of cellular organisms on the ToL. I liked the fact that the authors do not overinterpret their results and call for additional analyses to support their speculation. Additional metagenomics and phylogenetics analyses are undoubtly required to confirm the existence of these deeply branching lineages.

Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, et al. (2011) Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees.PLoS ONE 6: e18011. doi:10.1371/journal.pone.0018011

Phylogenetic approaches to metagenomic analysis by Jonathan Eisen (slide presentation at Keystone Symposium).

Cartoon: © The Economist: A new domain of life. Plenty more bugs in the sea.