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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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Related in: MedlinePlus

Core and pan genomes of O. oeni . A. Proportions of core (conserved) ORFs, strain-specific ORFs and putative pseudogenes in fourteen strains of O. oeni. The overall number of each type of ORF is also indicated based upon syntenic assignment of orthologs across all fourteen strains. B. The estimated average size of the O. oeni core (pink solid line) and pan (light blue solid line) genomes as a function of the number of individual strains compared. For each point, the size of core and pan genome was calculated for all combinations of x strains from the fourteen strains analysed with the results presented as filled circles.
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Figure 1: Core and pan genomes of O. oeni . A. Proportions of core (conserved) ORFs, strain-specific ORFs and putative pseudogenes in fourteen strains of O. oeni. The overall number of each type of ORF is also indicated based upon syntenic assignment of orthologs across all fourteen strains. B. The estimated average size of the O. oeni core (pink solid line) and pan (light blue solid line) genomes as a function of the number of individual strains compared. For each point, the size of core and pan genome was calculated for all combinations of x strains from the fourteen strains analysed with the results presented as filled circles.

Mentions: On average, each strain was predicted to contain 1800 ± 52 full length ORFs and 104 ± 27 potential pseudogenes associated with the chromosomal replicon (Figure1), with some strains also containing ORFs (n<50) associated with the plasmid replicon. However, despite the relatively tight distribution in the number of protein-coding genes in each strain, there is considerable variation in the subset of ortholgous genes present in each strain. In order to quantify this variation in coding potential, the extent of the core and pan genomes of this collection of O. oeni strains were calculated. There were 2846 non-degenerate ORFs that were shown to comprise the chromosomal pan genome of this group of O. oeni strains, with 1165 of these representing core ORFs conserved across all fourteen strains (Figure1). As observed for other bacterial species, the size of the conserved core of protein from O. oeni decreases as a function of the number of strains compared, while size of the pan genome increases [15-17] (Figure1B). Also, given that the rate of expansion of the pan genome showed no signs of significant decrease as additional numbers of strains were added to the analysis, it appears that the genetic diversity present within this strain has not yet been exhaustively recorded.


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)

Core and pan genomes of O. oeni . A. Proportions of core (conserved) ORFs, strain-specific ORFs and putative pseudogenes in fourteen strains of O. oeni. The overall number of each type of ORF is also indicated based upon syntenic assignment of orthologs across all fourteen strains. B. The estimated average size of the O. oeni core (pink solid line) and pan (light blue solid line) genomes as a function of the number of individual strains compared. For each point, the size of core and pan genome was calculated for all combinations of x strains from the fourteen strains analysed with the results presented as filled circles.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Core and pan genomes of O. oeni . A. Proportions of core (conserved) ORFs, strain-specific ORFs and putative pseudogenes in fourteen strains of O. oeni. The overall number of each type of ORF is also indicated based upon syntenic assignment of orthologs across all fourteen strains. B. The estimated average size of the O. oeni core (pink solid line) and pan (light blue solid line) genomes as a function of the number of individual strains compared. For each point, the size of core and pan genome was calculated for all combinations of x strains from the fourteen strains analysed with the results presented as filled circles.
Mentions: On average, each strain was predicted to contain 1800 ± 52 full length ORFs and 104 ± 27 potential pseudogenes associated with the chromosomal replicon (Figure1), with some strains also containing ORFs (n<50) associated with the plasmid replicon. However, despite the relatively tight distribution in the number of protein-coding genes in each strain, there is considerable variation in the subset of ortholgous genes present in each strain. In order to quantify this variation in coding potential, the extent of the core and pan genomes of this collection of O. oeni strains were calculated. There were 2846 non-degenerate ORFs that were shown to comprise the chromosomal pan genome of this group of O. oeni strains, with 1165 of these representing core ORFs conserved across all fourteen strains (Figure1). As observed for other bacterial species, the size of the conserved core of protein from O. oeni decreases as a function of the number of strains compared, while size of the pan genome increases [15-17] (Figure1B). Also, given that the rate of expansion of the pan genome showed no signs of significant decrease as additional numbers of strains were added to the analysis, it appears that the genetic diversity present within this strain has not yet been exhaustively recorded.

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