Analysis of the Genome of Oenococcus Oeni

The primary objective of this proposal is to fund gap closure of the Oenococcus oeni genome currently being sequenced at the Joint Genome Institute (JGI). Genome sequencing of O. oeni is part of a larger project undertaken at JGI to sequence the genomes of ten lactic acid bacteria. Of the ten LAB being sequenced, five are found in the wine environment (O. oeni, Pediococcus pentosaceus, Leuconostoc mesenteroides, Lactobacillus brevis, Lactobacillus casei). Two of these, P. pentosaceus and L. brevis, are prominent spoilage microorganisms in wine. The draft sequencing of the O. oeni and LAB genomes, is being done by the Joint Genome Institute at no cost to AVF/CCPRVE (a total of ~ $1.6 M in draft sequencing cost). Unfortunately, due to delays at JGI, mostly due to problems in finishing the human genome, sequencing of O. oeni and the other LAB was delayed until 2002 (actually it was first delayed from May 2001 to August, then again to Jan 2002). Currently ten LAB genomes, O. oeni included, are being sequenced and slated to be finished by summer 2002. The first completed genome of the group, Lactobacillus gasseri, is available from the JGI website (see As you might expect, a consequence of this delay is a correlating delay in my closing the O. oeni genome sequence. To date I have not hired a full time technician on the project but instead hired Lucy Joseph, our culture curator, at 25%time to work up the DNA and to generate and validate a cosmid library of O. oeni for eventual scaffolding of draft sequence. I have also purchased some computer equipment in preparation of the coming sequence analysis. To coordinate analysis of the ten LAB genomes we formed a group termed the Lactic Acid Bacterial Genome Consortium (LABGC) comprised of eleven researchers from seven universities in the US. With the expected completion of the O. oeni and other LAB sequences this summer, the LABGC is currently planning to hold a weeklong ?annotation-athon? at JGI in early October, 2002. At this meeting all of the genomes will be examined by a group of 30-40 LAB researchers from the US and assisted by bioinformatics staff at JGI. In the 2003-2003 report I expect to relay information learned at this meeting, especially as it pertains to wine-related LABs. Moreover I will report on the progress made to finish the O. oeni sequence (once the initial draft sequence is produced by JGI and we have something to work on).