Limits...
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.

Show MeSH
Aberrant tree. Tree inferred from the gene Asub on Chromosome I that is inconsistent with the trees inferred by other methods as described in this paper, including the trees for the individual gene phylogenies at other nearby genes. In this tree, the V. splendidus clade is found next to the V. fisheri clade, making it basal to its expected position. This tree is also referred to as "I" in Table 1, column 1. As shown, the tree is not fully resolved and branches with low support have been collapsed.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2875227&req=5

Figure 4: Aberrant tree. Tree inferred from the gene Asub on Chromosome I that is inconsistent with the trees inferred by other methods as described in this paper, including the trees for the individual gene phylogenies at other nearby genes. In this tree, the V. splendidus clade is found next to the V. fisheri clade, making it basal to its expected position. This tree is also referred to as "I" in Table 1, column 1. As shown, the tree is not fully resolved and branches with low support have been collapsed.

Mentions: The phylogenies estimated for each of the gene families near the origin support the estimations derived from the two chromosomes overall. This third method of analysis led thus to the same conclusion as the other two. Table 1 lists the genes studied at each origin, focusing on their gene phylogeny, while Table 2 specifies the longer annotation names for the genes used in Table 1 and the type of data (DNA or AA) used to create the trees. The genes within the Ori regions are naturally subject to horizontal gene transfer and mutational noise, like all other genes. Two of them are too conserved or too noisy to present a clear phylogenetic signal over the Vibrionales. In these cases, ALrT (approximate likelihood ratio test) and bootstrap support are lacking across the entire tree (2/28 genes on chromosome I, 0 on chromosome II). Many other trees have limited support for individual clades. Clades with less than 0.05 ALrT [35] support or less than 70% bootstrap support were reduced to polytomies. In addition, the long branch of V. cholerae sometimes distorts other elements in the tree. In 8/28 trees from chromosome I and 2/12 trees derived from chromosome II, removing the cholera clade from the tree also restored a topology consistent with the mean-field tree in the other portions of the tree where previously it had been inconsistent with the hypothesis (labeled B in the first column of the table). Finally, one clade (V. parahaemolyticus, V. alginolyticus, V. campbellii, V. harveyi) was reliably monophyletic but presented numerous permutations in its internal structure. At OriI 9/28 genes presented diverse variants in this clade; at OriII, 3/12 genes presented variability within this clade. Ignoring this variation, 16/28 genes from chromosome I and 10/12 genes from chromosome II confirm the chromosomal phylogenies inferred by the above methods (labeled A). Finally, the remaining two genes on chromosome I lead to inferences that conflict with the others by placing V. splendidus in the V. fischeri clade (basal to its expected position, see Figure 4). Genes in OriI show more variation in phylogeny but fewer genes are available for study in OriII.


Vibrio chromosomes share common history.

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

Aberrant tree. Tree inferred from the gene Asub on Chromosome I that is inconsistent with the trees inferred by other methods as described in this paper, including the trees for the individual gene phylogenies at other nearby genes. In this tree, the V. splendidus clade is found next to the V. fisheri clade, making it basal to its expected position. This tree is also referred to as "I" in Table 1, column 1. As shown, the tree is not fully resolved and branches with low support have been collapsed.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Aberrant tree. Tree inferred from the gene Asub on Chromosome I that is inconsistent with the trees inferred by other methods as described in this paper, including the trees for the individual gene phylogenies at other nearby genes. In this tree, the V. splendidus clade is found next to the V. fisheri clade, making it basal to its expected position. This tree is also referred to as "I" in Table 1, column 1. As shown, the tree is not fully resolved and branches with low support have been collapsed.
Mentions: The phylogenies estimated for each of the gene families near the origin support the estimations derived from the two chromosomes overall. This third method of analysis led thus to the same conclusion as the other two. Table 1 lists the genes studied at each origin, focusing on their gene phylogeny, while Table 2 specifies the longer annotation names for the genes used in Table 1 and the type of data (DNA or AA) used to create the trees. The genes within the Ori regions are naturally subject to horizontal gene transfer and mutational noise, like all other genes. Two of them are too conserved or too noisy to present a clear phylogenetic signal over the Vibrionales. In these cases, ALrT (approximate likelihood ratio test) and bootstrap support are lacking across the entire tree (2/28 genes on chromosome I, 0 on chromosome II). Many other trees have limited support for individual clades. Clades with less than 0.05 ALrT [35] support or less than 70% bootstrap support were reduced to polytomies. In addition, the long branch of V. cholerae sometimes distorts other elements in the tree. In 8/28 trees from chromosome I and 2/12 trees derived from chromosome II, removing the cholera clade from the tree also restored a topology consistent with the mean-field tree in the other portions of the tree where previously it had been inconsistent with the hypothesis (labeled B in the first column of the table). Finally, one clade (V. parahaemolyticus, V. alginolyticus, V. campbellii, V. harveyi) was reliably monophyletic but presented numerous permutations in its internal structure. At OriI 9/28 genes presented diverse variants in this clade; at OriII, 3/12 genes presented variability within this clade. Ignoring this variation, 16/28 genes from chromosome I and 10/12 genes from chromosome II confirm the chromosomal phylogenies inferred by the above methods (labeled A). Finally, the remaining two genes on chromosome I lead to inferences that conflict with the others by placing V. splendidus in the V. fischeri clade (basal to its expected position, see Figure 4). Genes in OriI show more variation in phylogeny but fewer genes are available for study in OriII.

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