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PRIMER Winter 2010 Volume 7 Issue 1 the PRIMER Winter 2010 Volume 7 Issue 1 Revealing the Soybean also in this issue Sequence: A Series of Firsts Cassava genome spurs research grant . 2 The soybean, one of the energy, protein, and nutrients IMG update released . 2 most important global sources for human and animal use,” Probing life in oceanic “dead zones” . 3 of protein and oil, has become said Anna Palmisano, Soybean's sequence supplied . 4 the first legume to have a pub- Associate Director of the DOE lished complete draft genome Office of Science’s Office of A Guide called GEBA . 6 sequence. In the January 14 Biological and Environmental Tracking projects in progress. 7 issue of the journal Nature, a Research. “This opens the Delft University Chancellor visits . 7 team of researchers from the door to crop improvements U.S. Department of Energy that are sorely needed for Joint Genome Institute (DOE energy production, sustainable JGI), the U.S. Department of human and animal food pro- Agriculture-Agricultural duction, and a healthy environ- Research Service (USDA-ARS), mental balance in agriculture the National Science worldwide.” Foundation (NSF), the Briefly setting aside the list University of Missouri, Purdue of potential applications to be Photo by Roy Kaltschmidt, LBNL University, and a dozen other derived from the sequence, institutions described the Jeremy Schmutz, the study’s sequence and how the infor- first author and a DOE JGI sci- mation might be applied to entist at the HudsonAlpha agricultural strategies and Institute for Biotechnology in biodiesel production. Alabama, noted two other key “The soybean genome’s bil- points about the complete lion-plus nucleotides afford us draft genome. “The soybean a better understanding of the sequence project is the largest plant’s capacity to turn sun- plant project done to date at light, carbon dioxide, nitrogen the Joint Genome Institute,” and water, into concentrated he said. “It cont. on page 4 Now Available: Microbial Genomes Encyclopedia, Vol. 1 Nearly 2,000 microbes the ribosomal RNA Tree of Life, the 40 major phyla. The same sequenced 100 bacterial and have been sequenced out of which allows researchers to trend holds for archaea, archaeal genomes that repre- the estimated nonillion (1030) track and understand how organ- eukaryotes and viruses. The sent little-studied branches of in, on and around the Earth. isms are related to each other. solution is to use the tree to the Tree of Life. The work, con- And while the information is “We’ve done a very poor job guide us, going through phylo- sidered the first “volume” of a significantly impacting almost of sampling across the tree in genetic diversity to explicitly fill Genomic Encyclopedia of all aspects of microbiology, microbial studies,” said Eisen. in missing branches of the Bacteria and Archaea or GEBA, said DOE JGI Phylogenomics “If you look at phylogenetic tree with actual data.” was published in the December Program Head and University diversity in the bacterial king- To remedy the problem of 24, 2009 issue of the journal of California, Davis professor dom, most of the available insufficient phylogenetic diver- Nature. Jonathan Eisen, it is bypassing genomes come from just 3 of sity, Eisen and his colleagues The GEBA cont. on page 6 2 / the PRIMER Winter 2010 Volume 7, Issue 1 The Integrated Microbial Genomes sequencing project. Among these regulatory interactions on the transcrip- (IMG) system, featured in a recent edition genomes, 4,650 are finished genomes, tional and posttranscriptional levels in of Nucleic Acids Research* serves as a and 904 are draft genomes, and four are prokaryotic genomes, that contains experi- community resource for comparative permanent draft (i.e., will never be fin- mental data and predicted sites published analysis and annotation of all publicly ished) genomes. Twenty-seven new fungal in scientific journals. available genomes from three domains of genomes have been also included in IMG IMG 3.0 also contains proteomic data life in a uniquely integrated context. IMG 3.0. Compared with IMG 2.9, IMG 3.0 from recent Arthrobacter chlorophenolicus, 3.0, the 18th release, went live on contains 7,540,500 genes, an increase of Cryptobacterium curtum, and December 21, 2009. 1,026,256 genes. Brachybacterium faecium studies. MetaCyc and KEGG pathways in IMG The User Interface for IMG 3.0 has 3.0 have been updated with MetaCyc ver- been extended with Scaffold Cart tools sion 13.5 and KEGG version 52.0 respec- that facilitate the analysis of genomes at IMG 3.0 tively. The Pfam collection of protein the level of individual scaffolds and con- domain families has been updated based tigs, such as individual chromosomes and Goes Live on Pfam version 24.0, and Pfam clans plasmids. ACT (Artemis Comparison Tool), have been added as an additional classifi- a viewer based on Artemis for pair-wise cation of Pfam domain families. genome DNA sequence comparisons, has The content of IMG 3.0 has been In addition, chromosomal gene cas- also been added to IMG’s suite of synteny updated with new microbial genomes settes† have been recomputed together viewers. available in RefSeq version 37 (June 02, with estimates of their conservation For additional information: see What’s 2009) and contains a total of 5,558 across IMG genomes. New and Using IMG: http://img.jgi.doe.gov. genomes consisting of 1,748 bacterial, Genes in IMG involved in regulatory 77 archaeal, 76 eukaryotic genomes, interaction experiments controlling their *Nucleic Acids Research, 2010, Vol.38: http:// 2,606 viruses (including bacterial expression are now linked to RegTransBase nar.oxfordjournals.org/cgi/reprint/gkp887v1 phages), and 1,051 plasmids that did not (http://regtransbase.lbl.gov). RegTransBase †PLoS ONE 4(11): http://www.plosone.org/article/ come from a specific microbial genome- is a database of regulatory sequences and info%3Adoi%2F10.1371%2Fjournal.pone.0007979 Cassava draft genome sequence spurs Gates Foundation funding news Not long after the first draft of the improved resistance annotated cassava genome sequence to CBSD and other was made available on the DOE JGI’s diseases. Claude Phytozome.net in November, the Bill & Fauquet, chair and Melinda Gates Foundation announced a co-founder of the $1.3 million grant to fund the develop- Global Cassava ment of a genome variation database that Partnership and a will help farmers grow more disease-resis- researcher at the tant and nutritious varieties of the root Danforth Center, crop in less time. said having the A third of the cassava harvest in Africa genome sequence of is lost because of pathogens such as cassava will benefit the international food DOE JGI, the University of Maryland and cassava brown streak disease. A staple security situation as well as help improve 454 Life Sciences, in collaboration with food for more than 750 million people the farmers’ health and economic growth. researchers in Kenya, Uganda and around the world, cassava was Several varieties of cassava will be Tanzania, to identify genes that corre- sequenced by the DOE JGI as part of CSP sampled by an international consortium spond to important traits and develop a 2007 to help develop a variety with that includes the University of Arizona, the genetic markers database. the PRIMER / 3 Winter 2010 Volume 7, Issue 1 Studying life in a “Dead Zone” For researchers at the University of The project is part of the DOE JGI’s metabolism. Additionally, a comparative British Columbia (UBC), the Saanich Inlet Community Sequencing Program estab- analysis revealed that 35 percent of the off the coast of British Columbia, Canada lished in 2004 to tackle mission-relevant SUP05 genome is unique and is involved is an ideal “living lab” to study the micro- genomics projects that support the goals in helping the bacteria adapt to changing bial communities in low oxygen waters. As of the U.S. Department of Energy to devel- environmental conditions such as the sea- these so-called “dead zones” expands in op clean, sustainable bioenergy sources sonal increase and decrease of oxygen oceans worldwide, so does interest in and characterize biological and environ- levels in Saanich Inlet, and the shifting understanding how the microorganisms mental processes such as biogeochem- balance of the nitrate and sulfide levels that thrive in these regions affect and are istry and carbon cycling. that are its key energy resources. impacted by the changes to their ecosys- Susannah Tringe, a metagenomics sci- “Just as cyanobacteria play an essen- tems. entist at the DOE JGI, said that oxygen tial role in producing atmospheric oxygen; In the October 23, 2009 issue of the minimum zones (OMZs) are sinks for an in future oceans this could be one of journal Science, a team of UBC and DOE essential nutrient that marine organisms those organisms that play similarly inte- JGI researchers described the results of a need to survive—nitrogen—as well as gral roles, albeit with different ecological study conducted over several seasons on sources for the greenhouse gases outcomes,” said Hallam. He noted that the microbial communities of Saanich methane and nitrous oxide. “By studying the SUP05 microorganism and its rela- Inlet, which led to the identification of the the genomes of the uncultivated microbes tives will become increasingly important most abundant organism called SUP05. found in OMZs, we can better understand as OMZs continue to expand, providing Study senior author and UBC professor how they participate in global geochemical researchers with a biological indicator Steven Hallam noted that the team cycles such as the carbon and nitrogen useful in monitoring the changing state of obtained enough sequence coverage to cycles,” she said. the global ocean. assemble what they called “the SUP05 Hallam described SUP05 as a paradoxi- “Global warming is changing the chem- metagenome, a composite of the entire cal organism, one that fixes carbon diox- istry of the oceans and one of the byprod- SUP05 population spanning the various ide and removes toxic sulfides, but which ucts of change is that the ocean pH is environmental samples that we might also be producing nitrous oxide, a becoming acidic,” Hallam said.
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