The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) has selected 35 new genomic sequencing projects for its 2011 Community Sequencing Program (CSP)—a targeted sampling of the planet’s biodiversity—to be characterized for bioenergy and environmental applications.
Supported by the Office of Biological and Environmental Research in the DOE Office of Science, the DOE JGI’s Community Sequencing Program enables scientists from universities and national laboratories around the world to probe the hidden world of microbes and plants for innovative solutions to the nation’s major challenges in energy, climate, and environment. This year’s portfolio is composed mostly of large-scale projects, which DOE JGI Director Eddy Rubin said was in keeping with the facility’s mission of large-scale genomics and analysis, and that meet the DOE missions of bioenergy, carbon cycling and biogeochemistry.
“Advances in sequencing technologies are really changing the landscape and have dramatically increased data output,” he said. “This has led to enormous changes which have impacted the science we produce. In the past year alone, the JGI’s sequence output has increased fivefold to five terabytes or five trillion nucleotides. Connected with the increased productivity, we’re beginning to position the JGI to work on projects of tera- and peta- or quadrillion-base scale. Our mission hasn’t changed; what is changing is the scale and complexity of the projects – which will increase. This highlights one of the directions genomics is going as data output begins to rival the output of the high-energy physics and astronomy communities.”
To highlight the directional shift, the CSP 2011 call urged researchers to submit proposals for projects that advance capabilities in fields such as large-scale resequencing, single-cell genomics and metatranscriptomics.
A total of 35 proposals were approved from the 127 submitted, selected from the 145 letters of intent originally received. Of the approved proposals, two involve plant genomes and two involve algal genomes; 10 are fungal projects; nine are microbial projects, six of which involve single-cell genomics; and 12 are metagenome (microbial communities) or metatranscriptome projects. The projects approved by an outside review panel and vetted by the DOE make the most of the DOE JGI’s increased sequencing capacity, allocating 10 trillion bases (TB or terabases), a 30-fold increase compared with last year’s one-third of a trillion nucleotides.
One of the microbial projects approved builds upon a previous CSP project to realize the evolutionary diversity of bacteria and archaea in nature. Since its inception, more than 100 microbes have been sequenced as part of the Genome Encyclopedia of Bacteria and Archaea (GEBA) to provide information on unrepresented branches of the Tree of Life. An analysis of the first 56 genomes from the GEBA project was published in the December 24, 2009 edition of the journal Nature. Now the team, led by the DOE JGI and UC Davis researcher Jonathan Eisen, plans to sequence another 61 bacteria and archaea not just to increase the phylogenetic reference genomes but to also identify new proteins and subfamilies that could be useful to the DOE missions.
The single largest project, and the Institute’s largest to date, involves sequencing barley, which has an anticipated five-billion base genome. Proposed by Gary Muehlbauer of the University of Minnesota, barley ranks fifth in the world among all crops cultivated and is grown on four million acres in the United States alone. The crop can be used to produce ethanol from the grain or for cellulosic ethanol from the straw.
One of the projects approved for CSP 2011 involves resequencing the wild grass Brachypodium distachyon. Resequencing, as the name suggests, revisits previously sequenced genomes but focuses on comparing new data with a reference model. Earlier this year, the genome sequence of this plant was published in the journal Nature to help researchers develop grasses tailored to serve as feedstocks for biofuel production. Led by John Vogel of the US Department of Agriculture Agricultural Research Service, the project involves sequencing 50 inbred lines of the grass to further develop genomic resources for Brachypodium and carry out comparisons of their gene sets to enable identification of candidate genes involved in traits such as drought tolerance that are of interest to the DOE.
Researchers at the DOE JGI have been among the pioneers of the methodology known as single-cell genomics in which the DNA isolated from a lone cell is amplified allowing researchers to study organisms that have not or cannot be cultured in a laboratory setting. This is a critically important capability as it is well known among microbiologists that 99 percent of the microbial world is difficult to grow in culture and thus very difficult to study. Two-thirds of the approved CSP 2011 microbial projects involve the use of single cell genomics to learn more about uncultured microbes found in ecosystems such as deep-sea hydrothermal vents and terrestrial subsurface aquifers.
For example, Stefan Sievert from the Woods Hole Oceanographic Institute is interested in using single-cell genomics to sequence nearly a dozen genomes of uncultivated bacteria that are found in deep-sea hydrothermal vents to learn about their roles in the global carbon, sulfur and nitrogen cycles. Additionally, the genomic information could be used to reduce sulfur emissions and resulting smog and acid rain.
Another project that involves the application of single cell genomics focuses on the microbial diversity in the methane-rich environment of western Greece’s Etoliko lagoon, which essentially supports two ecosystems by having both an oxygen-rich area and a distinct oxygen-poor zone. The anoxic zone is noted for having increased levels of sulfides and salinity. Led by George Tsiamis of Greece’s University of Ioannina, the proposal calls for sequencing nearly two-dozen microbes to learn more about the microbial diversity in the lagoon, and the genomic information collected will also enrich the DOE JGI’s ongoing GEBA project.
Metatranscriptomics focuses on the complex region of the complete genetic code that is transcribed into RNA molecules and provides information on gene expression and gene function. Half of the projects that look at the genomes of microbial communities (metagenomes) also involve plans to study their transcriptomes.
One of the algal projects is noteworthy partly due to the stated intent of involving student participation to boost undergraduate education in genomics and informatics. A team including DOE JGI’s Education head Cheryl Kerfeld, who was recently honored by the American Society for Biochemistry and Molecular Biology, plans to study algal strains from isolated acidic waters to understand their role in the carbon cycle, specifically how they can fix carbon under these conditions under these conditions.
“While integrating educational opportunities into the data generated by the proposal is not a stipulation of the CSP program, this is truly is a commendable effort and it serves as a further metric of the dedication these authors obviously have for the work,” noted one reviewer regarding the proposal submitted.
Several fungal projects were also selected. One of them focuses on Aureobasidium pullulan, the genetic information from which could lead to the development of drought-tolerant and salt-tolerant crops. Proposed by Martina Turk and Nina Gunde-Cimerman of the University of Ljubljana in Slovenia, the fungus thrives in a variety of environments and has been found on plants, PVC pipes and even on the walls of the Chernobyl nuclear power plant. The genomic information could help researchers studying ionizing radiation to develop new methods of assessing radiation effects. Additionally, as recent studies indicate, a strain of this fungus has been found in Arctic glaciers, and researchers hope to learn more about its role in the carbon cycle, especially as these glacial habitats are being affected by climate change. From a bioenergy perspective, the yeast-like fungus may hold enzymes that can help break down biomass, underscoring the metabolic versatility of fungi and relevance to and the DOE mission.
Another fungal project is focused on developing a comparative transcriptomics pipeline and is led by Antonio Pisabarro of Spain’s Public University of Navarre. Using several brown rot and white rot fungi whose genomes either have been or are in the process of being sequenced by the DOE JGI for their relevance to bioenergy and carbon cycling, Pisabarro and his collaborators want to improve the process by which gene expressions and gene functions of these fungi are compared.
Finally, one of the metagenome projects involves the so-called termite of the sea, the shipworm. As a wood-boring bivalve, the shipworm has two bacterial populations that can break down — one in the gut and the other in a specialized organ in the gills. The DOE JGI sequenced the only shipworm species adapted to cold water — Bankia setacea – as part of the CSP 2009 portfolio to identify the enzymes in these microbes involved in breaking down wood for cellulosic biofuel production. Now DOE JGI collaborator Daniel Distel of the Ocean Genome Legacy Foundation has proposed studying both microbial communities in different species of shipworm, including Lyrodus pedicellatus, a shipworm species adapted to warm water. Wood-boring bivalves are the only marine animals known to sustain normal growth and reproduction feasting solely on wood.