Vibrio chromosomes share common history

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.

Figure 1

Tree (Chromosome I). Inferred mean-field phylogeny of Chromosome I derived from a sampled concatenated gene sequence of single-copy orthologs distributed around the entire Chromosome I. The species tree is fully resolved and has 100% bootstrap support on all nodes outside of V. cholerae (1000 replicates). The list of genes and included locus tags is found in Additional file 1, supplementary materials.

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.

Figure 3

OriI and OriII synteny figures. The two origin regions of (A) Chromosome I and (B) Chromosome II. Open reading frames called in the annotated genomes are polygons pointing in the direction of their orientation. Colors label the open reading frames analyzed individually in estimating the phylogeny of the origin. The expanded figures with all labels are found in Additional files 3 and 4, supplementary materials.

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.