Joint Genome Institute releases upgraded Integrated Microbial Genomes data management system

The U.S. Department of Energy Joint Genome Institute (JGI) announces it has released a powerful set of computational tools established to ease the visualization and exploration of genomes flooding the public domain. The tools are bundled in IMG Version 2.3 - the Integrated Microbial Genomes (IMG) data management system, which is publicly available. The JGI is at the forefront of genetic research into energy crops and organisms used for the conversion of biomass.

The content of IMG 2.3, upgraded with new microbial genomes from the Version 23 release of the National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) collection, now includes fungi, protists (eukaryotic unicellular organisms), and plant genomes to enhance the breadth of comparative analysis. A new addition of particular interest to DOE is Pichia stipitis CBS 6054, a fungus with the exceptional capability to ferment xylose, five-carbon wood sugar, and yield high levels of ethanol.

Using comparative approaches is a powerful means to increase our understanding of gene function. My research is centered on fungi, so I am employing IMG 2.3 to advance our efforts to identify relevant pathways in fungi for bioenergy applications. - Scott Baker, Senior Research Scientist on the Fungal Biotechnology Team at Pacific Northwest National Laboratory.

Baker and his colleagues, building on the pioneering work on fungal model systems that led to such biotechnology workhorses as Aspergillus niger, are currently investigating Aspergillus terreus, now incorporated in IMG 2.3, for its ability to produce itaconic acid. Products generated from itaconic acid via chemical catalysis could be used to displace petroleum-derived chemicals. This and other organic acids that can be produced by fungi and other microbes are highlighted in the DOE Energy Efficiency and Renewable Energy (EERE) Office of the Biomass Program sponsored Top Value-Added Chemicals From Biomass [*.pdf] study performed jointly by PNNL and the National Renewable Energy Laboratory.

Fungal genomes offer an expansive repertoire of enzymes needed for the deconstruction of plant biomass into its component sugars. The cost-effective production of cellulosic biofuels will undoubtedly involve fungal enzymes, and the ability to compare complements of enzyme families across organisms, with the tools packaged in IMG 2.3, will be essential to those researchers engaged in this effort.

The new version of IMG (image shows user interface, click to enlarge) contains a total of 2,878 genomes consisting of 729 bacterial, 46 archaeal, 40 eukaryotic, and 1,661 bacterial phage genomes, and 402 plasmids that did not come from a specific microbial genome sequencing project. Among these genomes, 2,609 are finished and 269 are draft genomes. IMG 2.3 contains 236 microbial genomes sequenced at DOE JGI, consisting of 157 finished and 79 draft genomes:
energy :: sustainability :: biomass :: bioenergy :: biofuels :: biocoversion :: microorganisms :: genomics :: bioinformatics ::

IMG 2.3 extensions include an expanded controlled vocabulary of IMG terms, representing over 2,300 curated product names, and a growing collection of IMG pathways that form the foundation for composite IMG networks. IMG terms, pathways, and networks are used for improving the functional characterization of genes in ongoing studies related to carbohydrate utilization, cofactor biosynthesis, and methanogenesis.

Responding to the needs of the DOE JGI user community, IMG 2.3 provides enhanced support through "MyIMG Annotations," which enables users to associate related genes of interest with their curated annotations, including product name, and enzyme number. Other user interface extensions include reorganization of the organism and gene details pages and additional genome, gene, and function search capabilities.

IMG, accessible to the public here, is a collaborative effort between DOE JGI and the Lawrence Berkeley National Laboratory Biological Data Management and Technology Center (BDMTC). IMG is updated on a quarterly basis with new public and DOE JGI genomes. The next update is scheduled for December 2007.

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.

Image: user interface map of the Integrated Microbial Genomes data management system. Credit: JGI.

References:
Pacific Northwest National Laboratory (PNNL), National Renewable Energy Laboratory (NREL): Top Value Added Chemicals from Biomass. Volume I—Results of Screening for Potential Candidates from Sugars and Synthesis Gas [*.pdf], U.S. Department of Energy Energy Efficiency and Renewable Energy, Office of Biomass Program (EERE), August 2004.

Joint Genome Institute: Integrated Microbial Genomes system.