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On the origins of a Vibrio species.

Vesth T, Wassenaar TM, Hallin PF, Snipen L, Lagesen K, Ussery DW - Microb. Ecol. (2010)

Bottom Line: By comparing gene family content of the analysed genomes, the relatedness to a particular species is identified for two unspeciated genomes.Conversely, two genomes presumably belonging to the same species have suspiciously dissimilar gene family content.Some of these genes may be crucial to the niche adaptation of this species.

View Article: PubMed Central - PubMed

Affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Kgs. Lyngby, Denmark.

ABSTRACT
Thirty-two genome sequences of various Vibrionaceae members are compared, with emphasis on what makes V. cholerae unique. As few as 1,000 gene families are conserved across all the Vibrionaceae genomes analysed; this fraction roughly doubles for gene families conserved within the species V. cholerae. Of these, approximately 200 gene families that cluster on various locations of the genome are not found in other sequenced Vibrionaceae; these are possibly unique to the V. cholerae species. By comparing gene family content of the analysed genomes, the relatedness to a particular species is identified for two unspeciated genomes. Conversely, two genomes presumably belonging to the same species have suspiciously dissimilar gene family content. We are able to identify a number of genes that are conserved in, and unique to, V. cholerae. Some of these genes may be crucial to the niche adaptation of this species.

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Related in: MedlinePlus

Pan- and core genome plot of the 32 Vibrionaceae genomes. The colours highlighting species are the same as in Fig. 1
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Fig3: Pan- and core genome plot of the 32 Vibrionaceae genomes. The colours highlighting species are the same as in Fig. 1

Mentions: BLAST results were analysed to construct a pan-genome, which is a hypothetical collection of all the gene families that are found in the investigated genomes [28]. The core genome was constructed from all gene families that were represented at least once in every genome. Thus, the gene families conserved in all genomes represent their core genome; adding the remaining gene families produces the pan-genome. The resulting pan- and core genome plot is shown in Fig. 3. The genomes start with the documented clinical isolates of V. cholerae and then follow the order suggested by the pan-genome family clustering (Fig. 2), although genomes from the same species were kept together (the two V. parahaemolyticus genomes were split in the trees). As more genomes are added in the plot, the number of gene families in the pan-genome (blue line) increases, and the number of conserved gene families (red line) in the core genome decreases, albeit at a lower rate. This is because every genome can add many novel (and frequently different) genes to the pan-genome but only decreases the core genome with a few genes that are absent in that particular strain but that were conserved in the previously analysed genomes. The pan-genome curve increases with a relative steep slope when a novel species is added, as is obvious when a V. parahaemolyticus genome is added after the last V. cholerae. A stable plateau can be seen for the pan-genome of V. cholerae around 6,500 genes. Nevertheless, a small increase occurs when adding V. cholerae 11587; this is caused by the difference between the two subclusters of V. cholerae seen in Fig. 2. V. cholerae strain 2740-80 behaves atypical in all the figures shown; although documented as an environmental isolate, it appears closer to the clinical isolates, in terms of overall genomic properties.Figure 3


On the origins of a Vibrio species.

Vesth T, Wassenaar TM, Hallin PF, Snipen L, Lagesen K, Ussery DW - Microb. Ecol. (2010)

Pan- and core genome plot of the 32 Vibrionaceae genomes. The colours highlighting species are the same as in Fig. 1
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2807590&req=5

Fig3: Pan- and core genome plot of the 32 Vibrionaceae genomes. The colours highlighting species are the same as in Fig. 1
Mentions: BLAST results were analysed to construct a pan-genome, which is a hypothetical collection of all the gene families that are found in the investigated genomes [28]. The core genome was constructed from all gene families that were represented at least once in every genome. Thus, the gene families conserved in all genomes represent their core genome; adding the remaining gene families produces the pan-genome. The resulting pan- and core genome plot is shown in Fig. 3. The genomes start with the documented clinical isolates of V. cholerae and then follow the order suggested by the pan-genome family clustering (Fig. 2), although genomes from the same species were kept together (the two V. parahaemolyticus genomes were split in the trees). As more genomes are added in the plot, the number of gene families in the pan-genome (blue line) increases, and the number of conserved gene families (red line) in the core genome decreases, albeit at a lower rate. This is because every genome can add many novel (and frequently different) genes to the pan-genome but only decreases the core genome with a few genes that are absent in that particular strain but that were conserved in the previously analysed genomes. The pan-genome curve increases with a relative steep slope when a novel species is added, as is obvious when a V. parahaemolyticus genome is added after the last V. cholerae. A stable plateau can be seen for the pan-genome of V. cholerae around 6,500 genes. Nevertheless, a small increase occurs when adding V. cholerae 11587; this is caused by the difference between the two subclusters of V. cholerae seen in Fig. 2. V. cholerae strain 2740-80 behaves atypical in all the figures shown; although documented as an environmental isolate, it appears closer to the clinical isolates, in terms of overall genomic properties.Figure 3

Bottom Line: By comparing gene family content of the analysed genomes, the relatedness to a particular species is identified for two unspeciated genomes.Conversely, two genomes presumably belonging to the same species have suspiciously dissimilar gene family content.Some of these genes may be crucial to the niche adaptation of this species.

View Article: PubMed Central - PubMed

Affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Kgs. Lyngby, Denmark.

ABSTRACT
Thirty-two genome sequences of various Vibrionaceae members are compared, with emphasis on what makes V. cholerae unique. As few as 1,000 gene families are conserved across all the Vibrionaceae genomes analysed; this fraction roughly doubles for gene families conserved within the species V. cholerae. Of these, approximately 200 gene families that cluster on various locations of the genome are not found in other sequenced Vibrionaceae; these are possibly unique to the V. cholerae species. By comparing gene family content of the analysed genomes, the relatedness to a particular species is identified for two unspeciated genomes. Conversely, two genomes presumably belonging to the same species have suspiciously dissimilar gene family content. We are able to identify a number of genes that are conserved in, and unique to, V. cholerae. Some of these genes may be crucial to the niche adaptation of this species.

Show MeSH
Related in: MedlinePlus