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Enabled by New Sequencing Techs, JGI Projects 300 GB of Data for 2010 Community Sequencing Program


By Julia Karow

Both 454's and Illumina's sequencing technologies will play important roles in 71 new genomic sequencing projects that the Department of Energy's Joint Genome Institute announced yesterday for its 2010 Community Sequencing Program.

According to a statement from the Walnut Creek, Calif.-based institute, JGI's "recent transition to new sequencing technologies" has almost quintupled the amount of sequencing allocated to the program, from more than 60 gigabases for CSP 2009 to about a third of a terabase for CSP 2010.

A JGI spokeswoman told In Sequence that about half that data is expected to be produced on 454's sequencing platform, and the other half on Illumina's.

The new projects selected for CSP 2010, listed here, comprise 15 eukaryote genomes, six eukaryotes to be resequenced using short-read sequencing technologies, two transcriptome sequencing projects, 20 microbes, 20 metagenomes of microbial communities, and eight bacterial isolates to be resequenced.

JGI said it will employ "a variety of sequencing methods," including whole-genome shotgun sequencing to produce high-quality draft sequences, next-generation sequencing technologies, and single-cell sequencing techniques "that allow access to genomes when only minute quantities of DNA are available."

According to the spokeswoman, both eukaryote and bacterial resequencing projects will primarily use the Illumina technology, while eukaryote de novo and metagenome sequencing projects will predominantly use the 454 technology.

Earlier this year, JGI scientists, in collaboration with the Bigelow Laboratory for Ocean Sciences, published a proof-of-principle study in PLoS One, in which they generated high-quality draft genome assemblies of two uncultured flavobacteria using multiple displacement amplification of DNA from single cells followed by sequencing. According to the spokeswoman, this approach will be used in at least one of the CSP 2010 projects.

The institute currently has 50 Applied Biosystems 3730xl, eight 454 GS FLX, and seven Illumina Genome Analyzer instruments installed and plans to retire 35 of its 3730xl sequencers in fiscal year 2010, she said.

During the first and second quarters of fiscal year 2009, these platforms produced a total of 321 gigabases of sequence data for all of JGI's activities, according to the institute's website — already about a third more than JGI had projected for all of fiscal 2009. Of those, almost 250 gigabases, or 77 percent, were produced on the Illumina Genome Analyzer; more than 60 gigabases, or 19 percent, on the 454 GS FLX; and almost 12 gigabases, or 3.7 percent, by Sanger sequencing.

The Community Sequencing Program, established in 2005 and supported by the Office of Biological and Environmental Research in the DOE Office of Science, is "the largest genomic sequencing effort" that is focused on non-medical organisms, according to JGI. This year, it was scheduled to make up approximately 50 to 60 percent of JGI's overall sequencing activities (see In Sequence 7/8/2008).

The CSP provides the scientific community with free access to high-throughput sequencing at JGI "for projects of relevance to DOE missions." Projects are chosen based on scientific merit and relevance to bioenergy, global carbon cycling, and biogeochemistry.

Besides sequencing services, JGI also provides assembly, annotation, and genome analysis services for the 71 CSP projects.