DOE JGI

The Genome Sequencing Center began collaborating with the Department of Energy’s Joint Genome Institute in the fall of 1999 at Stanford University (SHGC).  At that time, the Production Genomics Facility of the JGI in Walnut Creek (JGI-PGF) had just been established, and while the JGI was building sequencing capacity, they needed a center with a proven track record to finish the human chromosomes that the PGF was shotgun sequencing for the DOE’s allocated portion of the human genome.  Since the completion of the sequencing of the human genome, the JGI has rapidly expanded its scientific goals in several DOE mission-relevant areas.

At the JGI-HAGSC, we have kept pace with this rapid expansion of projects with our focus on assessing, assembling, improving and finishing eukaryotic whole genome shotgun (WGS) projects for which the shotgun sequence is generated JGI-PGF.  We follow this by combining the draft WGS with genomic resources generated at JGI-HAGSC or in collaborator laboratories (including BAC end sequences, genetic maps and FLcDNA sequences) to produce an improved draft sequence.  For eukaryotic genomes important to the DOE mission, we then add further information from directed experiments to produce reference genomic sequences that are publicly available for any scientific researcher.  Also, we have continued our program for producing BAC-based finished sequence, both for adding information to JGI genome projects and for small BAC-based sequencing projects proposed through the JGI sequencing programs.  We have now improved our computational expertise in WGS assembly and analysis and have moved eukaryotic genome assembly from the JGI-PGF to JGI-HAGSC.  We have concentrated our assembly development work on large plant genomes and complex fungal and algal genomes. 

This work is supported by the Office of Biological and Environmental Research of the US Department of Energy under Cooperative Agreement No. DE-FC02-09ER64726