Consensus pan-genome assembly of the specialised wine bacterium Oenococcus oeni.
BACKGROUND
Oenococcus oeni is a lactic acid bacterium that is specialised for growth in the ecological niche of wine, where it is noted for its ability to perform the secondary, malolactic fermentation that is often required for many types of wine. Expanding the understanding of strain-dependent genetic variations in its small and streamlined genome is important for realising its full potential in industrial fermentation processes.


RESULTS
Whole genome comparison was performed on 191 strains of O. oeni; from this rich source of genomic information consensus pan-genome assemblies of the invariant (core) and variable (flexible) regions of this organism were established. Genetic variation in amino acid biosynthesis and sugar transport and utilisation was found to be common between strains. Furthermore, we characterised previously-unreported intra-specific genetic variations in the natural competence of this microbe.


CONCLUSIONS
By assembling a consensus pan-genome from a large number of strains, this study provides a tool for researchers to readily compare protein-coding genes across strains and infer functional relationships between genes in conserved syntenic regions. This establishes a foundation for further genetic, and thus phenotypic, research of this industrially-important species.
The Australian Wine Research Institute, PO Box 197, Glen Osmond, South Australia, 5064, Australia.
Peter R
PR
Sternes
The Australian Wine Research Institute, PO Box 197, Glen Osmond, South Australia, 5064, Australia. anthony.borneman@awri.com.au.
Anthony R
AR
Borneman
D000595:Amino Acid Sequence; D000596:Amino Acids / Q000096:biosynthesis; D050260:Carbohydrate Metabolism; D005285:Fermentation; D005516:Food Microbiology; D014644:Genetic Variation; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D019344:Lactic Acid / Q000378:metabolism; D008969:Molecular Sequence Data; D056585:Oenococcus / Q000235:genetics*; D014920:Wine / Q000382:microbiology*
D000596:Amino Acids; D019344:Lactic Acid
Amino acid; Assembly; Comparative genomics; Competence; Industrial microbiology; Oenococcus; Ortholog; Pan-genome; Phosphotransferase