We explored these genomes to construct phylogenies for each of the two Selleck Elafibranor chromosomes using three approaches. First, single copy genes from each chromosome were assembled en suite and a phylogeny for each chromosome was inferred from these concatenated sequences. Second, the organization and gene content at the origins of replication of each chromosome (OriI and OriII for chromosomes I and II, respectively) were studied. Third, the genes from near the two chromosomal origins of replication were studied and their phylogenies estimated individually. Results and Discussion Chromosome Phylogenies 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 Ivacaftor 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 Loperamide strains; that clade is effectively unresolved because the internal BTSA1 manufacturer 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. 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.