WALNUT CREEK, CA–As interest in the rising number of newly characterized microbial genomes mounts, powerful computational tools become critical for the management and analysis of these data to enable strategies for such challenges as harvesting the potential of carbon-neutral bioenergy sources and coping with global climate change.
The Integrated Microbial Genomes (IMG) data management system developed by the U.S. Department of Energy Joint Genome Institute (DOE JGI) addresses this challenge with the release of version 2.1. Released on the two-year anniversary of its launch, the content of IMG 2.1 is updated with new microbial genomes from National Center for Biotechnology Information’s (NCBI) Reference Sequence collection (RefSeq) latest release, Version 21. Other enhancements feature model eukaryotic genomes, including several well-characterized yeast species, and plasmids, the double-stranded circular DNA molecules independent of any sequenced microbes–significantly expanding the utility of the system for comparative genome analysis.
“Over two very productive years the community has adopted IMG as a mainstay genome analysis tool and have supported and contributed to the continuous growth and improvement of the system,” said Nikos Kyrpides, head of DOE JGI’s Genome Biology program and IMG’s scientific lead.
In the last year alone, IMG’s contribution has been cited dozens of publications. Recently, an article in the Journal of Bacteriology (2007 Mar;189:2477-86), featured research led by Kyrpides, Athanasios Lykidis, and other DOE JGI colleagues in which the genome sequence of Thermobifida fusca, a soil bacterium that is a major degrader of plant cell walls was generated and analyzed. Thermobifida has been used as a model organism for the study of secreted, heat-stable cellulases. These cellulases are among the growing portfolio of enzymes being explored for their potential to be incorporated into industrial-scale processes for the breakdown of cellulose to sugars that, in turn, can be ferment into ethanol and other biofuels.
“We continue to expand IMG’s functionality in response to the demand in the rapidly growing microbial genomics domain,” said Victor Markowitz, Lawrence Berkeley National Laboratory Biological Data Management and Technology Center (BDMTC) head and IMG’s system development lead. “The outstanding computing and data management expertise and infrastructure at DOE’s national labs have contributed to our success to date and will sustain IMG’s future growth.”
“While IMG is already used for teaching microbiology courses in several universities, we are now developing the necessary features and tutorials for incorporating IMG into DOE JGI’s educational outreach program,” said Kyrpides.
“IMG has become a major resource my graduate course focusing on integrating genomics into microbial ecology research,” said Mary Ann Moran of the Department of Marine Sciences at University of Georgia in Athens. “The students find the tools intuitive and easy to use, and I’ve developed a suite of exercises that makes use of the IMG’s various analysis capabilities.”
“We are delighted that the new version of IMG incorporates the genomes of plasmids,” said Anne Summers of the Department of Microbiology, also at the University of Georgia, “We picked IMG to become the ‘mobile genetic element home’ on the basis of its user-friendly cataloging of bacterial genomes and viruses, its commitment to ongoing development of its tools, and the fact that the developers are willing to work closely with the mobile genetic element community. We look forward to a continuing collaboration with IMG in making the plasmid component of their database a valuable tool, especially for the rapidly growing study of horizontal gene transfer and for applications in genetic engineering.”
IMG 2.1 comprises a total of 2,782 genomes–661 bacterial, 34 archaeal, 24 eukaryotic genomes, 1,661 bacterial phages, and 402 plasmids. Among these genomes, 2,524 are finished and 258 are draft. Compared to version 2.0, IMG 2.1 contains 481 new public microbial, eukaryotic, and plasmid genomes. IMG 2.1 includes 108 finished and 94 draft genomes sequenced by DOE JGI, bringing this total to 202 microbial genomes generated in-house.
IMG, accessible to the public at http://img.jgi.doe.gov/, is the result of a collaboration between the DOE JGI and BDMTC. IMG is updated on a quarterly basis with new public and DOE JGI genomes.
The DOE Joint Genome Institute, supported by the DOE Office of Science, unites the expertise of five national laboratories, Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest, along with the Stanford Human Genome Center to advance genomics in support of the DOE mission related to clean energy generation and environmental characterization and clean-up. DOE JGI’s Walnut Creek, Calif. Production Genomics Facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges.