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. Origin of Replication Organization The second method of analysis, studying the gene organization at the origins of replication (Ori), VX-689 supported the finding that the two chromosomes share a single phylogeny at the species level. This method of analysis was more advantageously applied to chromosome II than chromosome I: Gene order in the region immediately surrounding the chromosome I origin appears too highly conserved between species to provide robust data on its phylogeny (Figure 3; expanded in Additional files 3 and 4). However, gene content is informative in that region
suggesting that the species largely conform to the expected clustering even though the tree is not well supported (Figure 3). The difficulties are caused by a paucity of organizational changes that differentiate species at OriI – such as the inversion of three genes that sets apart the V. fisheri. Frequently, a change is unique to a sequenced strain and not shared by other members of its species. Niclosamide This can be extraordinarily disruptive of a distance estimate learn more if the number of unique differences is large. In particular, at least three obvious saltations in the gene content introduce spikes of noise. In V. cholerae B33, an apparently mobile genetic
region has imposed itself very close to the origin of replication. These 18 genes, almost as large as the region to be compared, interrupt an otherwise absolutely conserved region shared by the other selleck chemicals llc Vibrio cholerae. A 9 gene region in Photobacterium sp. SKA34 contains several transposon and transposase genes. Similarly, 16 gene region in Vibrio splendidus MED222 interrupts an otherwise conserved region with a number of secretory system genes; it lacks apparent mobility elements which would explain its origin. Among the photobacteria, the flanking regions sometimes differ dramatically, as well, which disturbs the phylogeny with a very long branch, and the Vibrio cholerae appear to have inverted the entire region – but this would not impact a gene content 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.