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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

BLAST atlas with V. cholerae strain N16961 as a reference strain, showing chromosomes 1 (top) and 2 (bottom). The best BLAST hits identified with genes from N16961 in the other V. cholerae genomes are represented in dark red, for the location as it appears in N16961. Blast hits in the other genomes are shown in various colours as indicated to the right. Major areas conserved in V. cholerae but not in other Vibrionaceae are identified as gap B, gap C, gap D and gap F in green; areas that are found in toxigenic V. cholerae only are marked black as gap A, gap E and gap G. The superintegron on chromosome 2 of V. cholerae is also indicated
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Fig5: BLAST atlas with V. cholerae strain N16961 as a reference strain, showing chromosomes 1 (top) and 2 (bottom). The best BLAST hits identified with genes from N16961 in the other V. cholerae genomes are represented in dark red, for the location as it appears in N16961. Blast hits in the other genomes are shown in various colours as indicated to the right. Major areas conserved in V. cholerae but not in other Vibrionaceae are identified as gap B, gap C, gap D and gap F in green; areas that are found in toxigenic V. cholerae only are marked black as gap A, gap E and gap G. The superintegron on chromosome 2 of V. cholerae is also indicated

Mentions: A BLAST atlas was constructed using V. cholerae N16961 (O1, El Tor) as the reference genome, shown in Fig. 5. The best blast hits identified in the query genomes are plotted in the lanes around the reference genome, with different colours for different species. In general, chromosome 1 is more strongly conserved than chromosome 2. A large part of chromosome 2 of N16961 displays very little conservation in the other genomes; this area represents a super integron [40] that contains the V. cholerae-specific repeat (VCR) sequences, as well as a high number of gene cassettes. The repeat sequences are visible as black boxes in the repeat lane of the reference genome (second inner lane). Although all V. cholerae genomes contain a superintegron, its genes are very diverse between isolates [34] which explains the lack of blast hits in this region.Figure 5


On the origins of a Vibrio species.

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

BLAST atlas with V. cholerae strain N16961 as a reference strain, showing chromosomes 1 (top) and 2 (bottom). The best BLAST hits identified with genes from N16961 in the other V. cholerae genomes are represented in dark red, for the location as it appears in N16961. Blast hits in the other genomes are shown in various colours as indicated to the right. Major areas conserved in V. cholerae but not in other Vibrionaceae are identified as gap B, gap C, gap D and gap F in green; areas that are found in toxigenic V. cholerae only are marked black as gap A, gap E and gap G. The superintegron on chromosome 2 of V. cholerae is also indicated
© Copyright Policy
Related In: Results  -  Collection

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

Fig5: BLAST atlas with V. cholerae strain N16961 as a reference strain, showing chromosomes 1 (top) and 2 (bottom). The best BLAST hits identified with genes from N16961 in the other V. cholerae genomes are represented in dark red, for the location as it appears in N16961. Blast hits in the other genomes are shown in various colours as indicated to the right. Major areas conserved in V. cholerae but not in other Vibrionaceae are identified as gap B, gap C, gap D and gap F in green; areas that are found in toxigenic V. cholerae only are marked black as gap A, gap E and gap G. The superintegron on chromosome 2 of V. cholerae is also indicated
Mentions: A BLAST atlas was constructed using V. cholerae N16961 (O1, El Tor) as the reference genome, shown in Fig. 5. The best blast hits identified in the query genomes are plotted in the lanes around the reference genome, with different colours for different species. In general, chromosome 1 is more strongly conserved than chromosome 2. A large part of chromosome 2 of N16961 displays very little conservation in the other genomes; this area represents a super integron [40] that contains the V. cholerae-specific repeat (VCR) sequences, as well as a high number of gene cassettes. The repeat sequences are visible as black boxes in the repeat lane of the reference genome (second inner lane). Although all V. cholerae genomes contain a superintegron, its genes are very diverse between isolates [34] which explains the lack of blast hits in this region.Figure 5

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