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Comparative analysis of the Oenococcus oeni pan genome reveals genetic diversity in industrially-relevant pathways.

Borneman AR, McCarthy JM, Chambers PJ, Bartowsky EJ - BMC Genomics (2012)

Bottom Line: These benefits are realised primarily through catalysing malolactic fermentation, but also through imparting other positive sensory properties.While any single strain of O. oeni was shown to contain around 1800 protein-coding genes, in-depth comparative annotation based on genomic synteny and protein orthology identified over 2800 orthologous open reading frames that comprise the pan genome of this species, and less than 1200 genes that make up the conserved genomic core present in all of the strains.This data is vital to understanding and harnessing the phenotypic variation present in this economically-important species.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Australian Wine Research Institute, Glen Osmond, South Australia 5064, Australia. anthony.borneman@awri.com.au

ABSTRACT

Background: Oenococcus oeni, a member of the lactic acid bacteria, is one of a limited number of microorganisms that not only survive, but actively proliferate in wine. It is also unusual as, unlike the majority of bacteria present in wine, it is beneficial to wine quality rather than causing spoilage. These benefits are realised primarily through catalysing malolactic fermentation, but also through imparting other positive sensory properties. However, many of these industrially-important secondary attributes have been shown to be strain-dependent and their genetic basis it yet to be determined.

Results: In order to investigate the scale and scope of genetic variation in O. oeni, we have performed whole-genome sequencing on eleven strains of this bacterium, bringing the total number of strains for which genome sequences are available to fourteen. While any single strain of O. oeni was shown to contain around 1800 protein-coding genes, in-depth comparative annotation based on genomic synteny and protein orthology identified over 2800 orthologous open reading frames that comprise the pan genome of this species, and less than 1200 genes that make up the conserved genomic core present in all of the strains. The expansion of the pan genome relative to the coding potential of individual strains was shown to be due to the varied presence and location of multiple distinct bacteriophage sequences and also in various metabolic functions with potential impacts on the industrial performance of this species, including cell wall exopolysaccharide biosynthesis, sugar transport and utilisation and amino acid biosynthesis.

Conclusions: By providing a large cohort of sequenced strains, this study provides a broad insight into the genetic variation present within O. oeni. This data is vital to understanding and harnessing the phenotypic variation present in this economically-important species.

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Phylogenetic divergence of O. oeni. A. Maximum-likelyhood phylogeny based on whole-genome alignment of fourteen O. oeni strains. Bootstrap proportions are indicated at each relevant position (total support from 100 replicates). B. Variation in exopolysaccharide (EPS) loci in O. oeni. Each of the three loci is composed of a variable number of individual ORFs. Each variant at a particular locus is represented by a separate color. C. Maximum-likelyhood phylogeny based on the concatenated predicted protein sequences of 872 conserved orthologs from fourteen strains of O. oeni in addition to its closest known relative, O. kitaharae[27].
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Figure 4: Phylogenetic divergence of O. oeni. A. Maximum-likelyhood phylogeny based on whole-genome alignment of fourteen O. oeni strains. Bootstrap proportions are indicated at each relevant position (total support from 100 replicates). B. Variation in exopolysaccharide (EPS) loci in O. oeni. Each of the three loci is composed of a variable number of individual ORFs. Each variant at a particular locus is represented by a separate color. C. Maximum-likelyhood phylogeny based on the concatenated predicted protein sequences of 872 conserved orthologs from fourteen strains of O. oeni in addition to its closest known relative, O. kitaharae[27].

Mentions: Independent of coding-region predictions, it was possible to determine the phylogenetic relationship of the various strains from the patterns of single-nucleotide polymorphisms deduced from whole-genome nucleotide alignments (Figure4A). The phylogeny produced from this alignment led to two major findings. First there was a large evolutionary distance between a basal clade formed by AWRIB418 and BAA-1163 and the other twelve strains of O. oeni, suggesting that these two strains form a distinct evolutionary group, a finding that is supported by the results of previous MLST typing of typing [26]. In order to investigate this apparent division, a second phylogeny was constructed using the predicted sequences of the core, conserved proteins present in the fourteen O. oeni strains, in addition to orthologous sequences from O. kitaharae DSM 17330 as an outgroup [27] (Figure4C). This phylogeny is consistent with BAA-1163 and AWRIB418 comprising a basal, divergent clade, however the genetic distance between these groups of strains is far less than observed between any strain of O. oeni and O. kitaharae. As such, BAA-1163 and AWRIB418 may together represent a divergent sub-species of O. oeni, a fact that is supported by the presence of a large number of ORFs that are found only in these two strains (See below).


Comparative analysis of the Oenococcus oeni pan genome reveals genetic diversity in industrially-relevant pathways.

Borneman AR, McCarthy JM, Chambers PJ, Bartowsky EJ - BMC Genomics (2012)

Phylogenetic divergence of O. oeni. A. Maximum-likelyhood phylogeny based on whole-genome alignment of fourteen O. oeni strains. Bootstrap proportions are indicated at each relevant position (total support from 100 replicates). B. Variation in exopolysaccharide (EPS) loci in O. oeni. Each of the three loci is composed of a variable number of individual ORFs. Each variant at a particular locus is represented by a separate color. C. Maximum-likelyhood phylogeny based on the concatenated predicted protein sequences of 872 conserved orthologs from fourteen strains of O. oeni in addition to its closest known relative, O. kitaharae[27].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472311&req=5

Figure 4: Phylogenetic divergence of O. oeni. A. Maximum-likelyhood phylogeny based on whole-genome alignment of fourteen O. oeni strains. Bootstrap proportions are indicated at each relevant position (total support from 100 replicates). B. Variation in exopolysaccharide (EPS) loci in O. oeni. Each of the three loci is composed of a variable number of individual ORFs. Each variant at a particular locus is represented by a separate color. C. Maximum-likelyhood phylogeny based on the concatenated predicted protein sequences of 872 conserved orthologs from fourteen strains of O. oeni in addition to its closest known relative, O. kitaharae[27].
Mentions: Independent of coding-region predictions, it was possible to determine the phylogenetic relationship of the various strains from the patterns of single-nucleotide polymorphisms deduced from whole-genome nucleotide alignments (Figure4A). The phylogeny produced from this alignment led to two major findings. First there was a large evolutionary distance between a basal clade formed by AWRIB418 and BAA-1163 and the other twelve strains of O. oeni, suggesting that these two strains form a distinct evolutionary group, a finding that is supported by the results of previous MLST typing of typing [26]. In order to investigate this apparent division, a second phylogeny was constructed using the predicted sequences of the core, conserved proteins present in the fourteen O. oeni strains, in addition to orthologous sequences from O. kitaharae DSM 17330 as an outgroup [27] (Figure4C). This phylogeny is consistent with BAA-1163 and AWRIB418 comprising a basal, divergent clade, however the genetic distance between these groups of strains is far less than observed between any strain of O. oeni and O. kitaharae. As such, BAA-1163 and AWRIB418 may together represent a divergent sub-species of O. oeni, a fact that is supported by the presence of a large number of ORFs that are found only in these two strains (See below).

Bottom Line: These benefits are realised primarily through catalysing malolactic fermentation, but also through imparting other positive sensory properties.While any single strain of O. oeni was shown to contain around 1800 protein-coding genes, in-depth comparative annotation based on genomic synteny and protein orthology identified over 2800 orthologous open reading frames that comprise the pan genome of this species, and less than 1200 genes that make up the conserved genomic core present in all of the strains.This data is vital to understanding and harnessing the phenotypic variation present in this economically-important species.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Australian Wine Research Institute, Glen Osmond, South Australia 5064, Australia. anthony.borneman@awri.com.au

ABSTRACT

Background: Oenococcus oeni, a member of the lactic acid bacteria, is one of a limited number of microorganisms that not only survive, but actively proliferate in wine. It is also unusual as, unlike the majority of bacteria present in wine, it is beneficial to wine quality rather than causing spoilage. These benefits are realised primarily through catalysing malolactic fermentation, but also through imparting other positive sensory properties. However, many of these industrially-important secondary attributes have been shown to be strain-dependent and their genetic basis it yet to be determined.

Results: In order to investigate the scale and scope of genetic variation in O. oeni, we have performed whole-genome sequencing on eleven strains of this bacterium, bringing the total number of strains for which genome sequences are available to fourteen. While any single strain of O. oeni was shown to contain around 1800 protein-coding genes, in-depth comparative annotation based on genomic synteny and protein orthology identified over 2800 orthologous open reading frames that comprise the pan genome of this species, and less than 1200 genes that make up the conserved genomic core present in all of the strains. The expansion of the pan genome relative to the coding potential of individual strains was shown to be due to the varied presence and location of multiple distinct bacteriophage sequences and also in various metabolic functions with potential impacts on the industrial performance of this species, including cell wall exopolysaccharide biosynthesis, sugar transport and utilisation and amino acid biosynthesis.

Conclusions: By providing a large cohort of sequenced strains, this study provides a broad insight into the genetic variation present within O. oeni. This data is vital to understanding and harnessing the phenotypic variation present in this economically-important species.

Show MeSH
Related in: MedlinePlus