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Vibrio chromosomes share common history.

Kirkup BC, Chang L, Chang S, Gevers D, Polz MF - BMC Microbiol. (2010)

Bottom Line: Single copy genes from each chromosome (142 genes from chromosome I and 42 genes from chromosome II) were identified from 19 sequenced Vibrionales genomes and their phylogenetic comparison suggests consistent phylogenies for each chromosome.Additionally, study of the gene organization and phylogeny of the respective origins of replication confirmed the shared history.Thus, while elements within the chromosomes may have experienced significant genetic mobility, the backbones share a common history.

View Article: PubMed Central - HTML - PubMed

Affiliation: Dept, of Civil and Environmental Engineering, 15 Vassar Street, Cambridge, MA 02139, USA. bckirkup@post.harvard.edu

ABSTRACT

Background: While most gamma proteobacteria have a single circular chromosome, Vibrionales have two circular chromosomes. Horizontal gene transfer is common among Vibrios, and in light of this genetic mobility, it is an open question to what extent the two chromosomes themselves share a common history since their formation.

Results: Single copy genes from each chromosome (142 genes from chromosome I and 42 genes from chromosome II) were identified from 19 sequenced Vibrionales genomes and their phylogenetic comparison suggests consistent phylogenies for each chromosome. Additionally, study of the gene organization and phylogeny of the respective origins of replication confirmed the shared history.

Conclusions: Thus, while elements within the chromosomes may have experienced significant genetic mobility, the backbones share a common history. This allows conclusions based on multilocus sequence analysis (MLSA) for one chromosome to be applied equally to both chromosomes.

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Related in: MedlinePlus

Tree (Chromosome II). Inferred mean-field phylogeny of Chromosome II derived from a sampled concatenated gene sequence of single-copy orthologs distributed around the entire Chromosome II. The species tree is fully resolved and has 100% bootstrap support on all nodes (10000 replicates). The list of genes and included locus tags is found in Additional file 2, supplementary materials. Only closed genomes were included in this analysis.
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Figure 2: Tree (Chromosome II). Inferred mean-field phylogeny of Chromosome II derived from a sampled concatenated gene sequence of single-copy orthologs distributed around the entire Chromosome II. The species tree is fully resolved and has 100% bootstrap support on all nodes (10000 replicates). The list of genes and included locus tags is found in Additional file 2, supplementary materials. Only closed genomes were included in this analysis.

Mentions: The inferred phylogenies for the two chromosomes are congruent (Figures 1 and 2) and contain the expected major features, such as Photobacterium being basal to the Vibrionaceae and V. fisheri forming the next most basal clade. There are no unexpected sister taxa. The results of this analysis are compatible with published multi-locus analyses. However, instead of using 6 or 8 genes commonly used in MLSA, this analysis included 142 genes from chromosome I and 42 from chromosome II. These single copy genes include a range of functions including metabolism, information processing, flagellar structure and cytoskeletal components; as such, they represent sampling points from various pathways and genomic sections from around the entire genome. The concatenation of these well conserved genes provides a shared signal for the chromosomes as a whole, despite only composing a small fraction of the entire genome. The genes included in the analysis are listed under Additional files 1 and 2. The chromosome I tree is easily rooted by the various other genomes included in the analysis. All of these other clades fell together along accepted taxonomic lines. The most closely related strains in the tree are the V. cholerae strains; that clade is effectively unresolved because the internal distances are too short. The chromosome II tree cannot be rooted in the same manner as chromosome I because there is no obviously available outgroup: the chromosome II of P. atlantica is not homologous to the chromosome II of the Vibrionaceae being analyzed. However, rooting it identically by using the information from the chromosome I tree preserves the branching order of each tree. Thus, the 'mean field' approximation for the phylogeny of the two chromosomes is congruent at the species level. There is insufficient resolution among V. cholerae strains and too few members of other species to make inferences at a finer phylogenetic scale.


Vibrio chromosomes share common history.

Kirkup BC, Chang L, Chang S, Gevers D, Polz MF - BMC Microbiol. (2010)

Tree (Chromosome II). Inferred mean-field phylogeny of Chromosome II derived from a sampled concatenated gene sequence of single-copy orthologs distributed around the entire Chromosome II. The species tree is fully resolved and has 100% bootstrap support on all nodes (10000 replicates). The list of genes and included locus tags is found in Additional file 2, supplementary materials. Only closed genomes were included in this analysis.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2875227&req=5

Figure 2: Tree (Chromosome II). Inferred mean-field phylogeny of Chromosome II derived from a sampled concatenated gene sequence of single-copy orthologs distributed around the entire Chromosome II. The species tree is fully resolved and has 100% bootstrap support on all nodes (10000 replicates). The list of genes and included locus tags is found in Additional file 2, supplementary materials. Only closed genomes were included in this analysis.
Mentions: The inferred phylogenies for the two chromosomes are congruent (Figures 1 and 2) and contain the expected major features, such as Photobacterium being basal to the Vibrionaceae and V. fisheri forming the next most basal clade. There are no unexpected sister taxa. The results of this analysis are compatible with published multi-locus analyses. However, instead of using 6 or 8 genes commonly used in MLSA, this analysis included 142 genes from chromosome I and 42 from chromosome II. These single copy genes include a range of functions including metabolism, information processing, flagellar structure and cytoskeletal components; as such, they represent sampling points from various pathways and genomic sections from around the entire genome. The concatenation of these well conserved genes provides a shared signal for the chromosomes as a whole, despite only composing a small fraction of the entire genome. The genes included in the analysis are listed under Additional files 1 and 2. The chromosome I tree is easily rooted by the various other genomes included in the analysis. All of these other clades fell together along accepted taxonomic lines. The most closely related strains in the tree are the V. cholerae strains; that clade is effectively unresolved because the internal distances are too short. The chromosome II tree cannot be rooted in the same manner as chromosome I because there is no obviously available outgroup: the chromosome II of P. atlantica is not homologous to the chromosome II of the Vibrionaceae being analyzed. However, rooting it identically by using the information from the chromosome I tree preserves the branching order of each tree. Thus, the 'mean field' approximation for the phylogeny of the two chromosomes is congruent at the species level. There is insufficient resolution among V. cholerae strains and too few members of other species to make inferences at a finer phylogenetic scale.

Bottom Line: Single copy genes from each chromosome (142 genes from chromosome I and 42 genes from chromosome II) were identified from 19 sequenced Vibrionales genomes and their phylogenetic comparison suggests consistent phylogenies for each chromosome.Additionally, study of the gene organization and phylogeny of the respective origins of replication confirmed the shared history.Thus, while elements within the chromosomes may have experienced significant genetic mobility, the backbones share a common history.

View Article: PubMed Central - HTML - PubMed

Affiliation: Dept, of Civil and Environmental Engineering, 15 Vassar Street, Cambridge, MA 02139, USA. bckirkup@post.harvard.edu

ABSTRACT

Background: While most gamma proteobacteria have a single circular chromosome, Vibrionales have two circular chromosomes. Horizontal gene transfer is common among Vibrios, and in light of this genetic mobility, it is an open question to what extent the two chromosomes themselves share a common history since their formation.

Results: Single copy genes from each chromosome (142 genes from chromosome I and 42 genes from chromosome II) were identified from 19 sequenced Vibrionales genomes and their phylogenetic comparison suggests consistent phylogenies for each chromosome. Additionally, study of the gene organization and phylogeny of the respective origins of replication confirmed the shared history.

Conclusions: Thus, while elements within the chromosomes may have experienced significant genetic mobility, the backbones share a common history. This allows conclusions based on multilocus sequence analysis (MLSA) for one chromosome to be applied equally to both chromosomes.

Show MeSH
Related in: MedlinePlus