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Conference Papers Year : 2008

The whole genome of Oenococcus strain IOEB 8413

Abstract

Taking advantage of recent technology developments of 454 pyrosequencing we have undertaken whole genome sequencing of O. oeni strain IOEB 8413. This strain performs malolactic fermentation, but has a relatively low level of adaptation to oenological environment. The genome draft was obtained with Genome Sequencer FLX System (Roche). The generated 111 Mb of raw data (406 255 individual reads) was processed with Newbler Assembler through two different modes. The assembly resulting from the "de novo" mode consisted of 39 major contigs attaining an average 50x coverage. Manual draft inspection revealed that, independently of the number of contigs, it contained only 19 real gaps. Cumulated size of missing fractions was estimated to be less than 10 kb, thus allowing us one-step finishing by Sanger sequencing. For the second assembly mode, particularly indicated for resequencing projects, we have used as a reference the recently achieved genome of strain ATCC BAA-1163 (LAB9, communication Bon et al.). The 1,8-Mb chromosome is covered by 90% of all mapped reads, whereas the fully covered 3,9-kb high-copy plasmid monopolizes the remaining 10%. More than 97% of all reads were fully mapped to the reference (chromosome or plasmid) and organized in 18 "mapping" contigs. Less than 2% of reads aligned partially at the oriC linearization site or corresponded to repeat regions (rRNA operons). Only 429 reads are unique meaning that both strains have very close nucleotide content. Preliminary evaluation of the two genomes indicates no significant large-scale rearrangements. Functional annotation as well as further comparative analyses between available strains (including PSU-1) will await completion of the strain IOEB 8413 genome.
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Dates and versions

inria-00340086 , version 1 (19-11-2008)

Identifiers

  • HAL Id : inria-00340086 , version 1
  • PRODINRA : 245878

Cite

Diliana Dimova, Elisabeth Bon, Patrick Lucas, R. Beugnot, Marcel de Leeuw, et al.. The whole genome of Oenococcus strain IOEB 8413. 9th Symposium on Lactic Acid Bacteria, Sep 2008, Egmond aan Zee, Netherlands. pp.A057. ⟨inria-00340086⟩
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