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Consensus pan-genome assembly of the specialised wine bacterium Oenococcus oeni.
BMC Genomics. 2016 Apr 27; 17:308.BG

Abstract

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.

CONCLUSION

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.

Authors+Show Affiliations

The Australian Wine Research Institute, PO Box 197, Glen Osmond, South Australia, 5064, Australia.The Australian Wine Research Institute, PO Box 197, Glen Osmond, South Australia, 5064, Australia. anthony.borneman@awri.com.au.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

27118061

Citation

Sternes, Peter R., and Anthony R. Borneman. "Consensus Pan-genome Assembly of the Specialised Wine Bacterium Oenococcus Oeni." BMC Genomics, vol. 17, 2016, p. 308.
Sternes PR, Borneman AR. Consensus pan-genome assembly of the specialised wine bacterium Oenococcus oeni. BMC Genomics. 2016;17:308.
Sternes, P. R., & Borneman, A. R. (2016). Consensus pan-genome assembly of the specialised wine bacterium Oenococcus oeni. BMC Genomics, 17, 308. https://doi.org/10.1186/s12864-016-2604-7
Sternes PR, Borneman AR. Consensus Pan-genome Assembly of the Specialised Wine Bacterium Oenococcus Oeni. BMC Genomics. 2016 Apr 27;17:308. PubMed PMID: 27118061.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Consensus pan-genome assembly of the specialised wine bacterium Oenococcus oeni. AU - Sternes,Peter R, AU - Borneman,Anthony R, Y1 - 2016/04/27/ PY - 2016/02/10/received PY - 2016/03/28/accepted PY - 2016/4/28/entrez PY - 2016/4/28/pubmed PY - 2016/11/10/medline KW - Amino acid KW - Assembly KW - Comparative genomics KW - Competence KW - Industrial microbiology KW - Oenococcus KW - Ortholog KW - Pan-genome KW - Phosphotransferase SP - 308 EP - 308 JF - BMC genomics JO - BMC Genomics VL - 17 N2 - 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. CONCLUSION: 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. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/27118061/Consensus_pan_genome_assembly_of_the_specialised_wine_bacterium_Oenococcus_oeni_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2604-7 DB - PRIME DP - Unbound Medicine ER -