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JGI to Provide Sequencing and Analysis for New Microbial, Plant, Fungal Research

NEW YORK (GenomeWeb News) – The US Department of Energy's Joint Genome Institute will provide genome sequencing and analysis to 29 research projects that will delve into problems and questions that are in line with DOE's aim to develop new biofuel and carbon capture technologies.

The projects receiving the 2013 Community Sequencing Program (CSP) awards will involve metagenomics analyses of microbes, will study niche microbial communities, and investigate plant-microbe interactions, generating as much as 30 terabases, or "the microbial, fungal, and plant equivalent of 10,000 human genomes," JGI said Tuesday.

Some of the projects will involve large-scale studies using RNA sequencing, transposon mutagenesis, and DNA synthesis, and one will aim to create a fungus-focused version of the Encyclopedia of DNA Elements (ENCODE) program, and another aims to fill in gaps in the Tree of Life effort.

These 29 research teams will study organisms from a range of environments, including microbes that subsist two miles down in a South African gold mine, ocean-dwelling bacteria living off of west Antarctica, potential biofuel and biomass crops that could be grown in several areas in the US, and fungal pathogens that threaten the yields of energy crops.

The CSP aims to encourage large-scale research projects that will make use of JGI's sequencing and analysis capabilities and will advance sequence-based research from a range of disciplines. The institute chooses these projects based on their scientific merit and relevance to alternative energy production, global carbon cycling, and biogeochemistry.

All of the newly-awarded projects will combine the use of sequence data with large-scale experiments and computational capabilities to provide functional genome annotations.

Two of the projects will focus on DNA synthesis. One project, headed by Jef Boeke of Johns Hopkins University, will aim to design and replace the native genome of baker's yeast with a fully synthetic genome. To support the Synthetic Yeast genome project, JGI will synthesize the largest chromosome of the 12 million-base yeast genome.

Five of the new CSP projects will look at a variety of plants. One of these, the Gene Atlas Project, led by Director of the University of Missouri Center for Sustainable Energy Gary Stacey, will seek to develop a comprehensive index of gene expression for several plant species, including soybean, poplar, foxtail millet, an algae, and one moss.

Another project chosen for an award will focus on the symbiotic relationship between a fungus and its algal partner. Led by Duke University researcher Kathryn Picard, the effort will sequence the genomes of the fungus Rhizidium phycophilum and the alga Bracteacoccus with the aim of identifying algal genes that could be used to help increase algal biomass for biofuel applications.

One of the seven projects that focus on fungal genomics is the Fungal Nutritional ENCODE project. Led by University of California, Berkeley researcher N. Louise Glass, the effort seeks to comprehensively map the nutritional and metabolic regulatory networks of Neurospora crassa, which could be used to improve the productivity of cellulases for use as biofuel.

The new crop of CSP awards also will fund 15 microbial and metagenomics studies, many of which will use single-cell genomics approaches to study microbes that are difficult to culture and will use metatranscriptiomics to study the parts of the genome that encodes gene expression.

One of these, the Functional Encyclopedia of Bacteria and Archaea (FEBA) project, will use a high-throughput approach called transposon mutagenesis and sequencing to discover gene functions in the genomes of 40 microbes that are relevant to DOE's mission.

A full list of the new CSP award projects is available at JGI's website.

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