The genomic gains on tip
nodes can be partly explained by the inclusion of non-chromosomal material in the draft genomes of X. vasicola, although this result was not found in other draft genomes in the study that have non-chromosomal material, such as XamC. An alternative explanation is that genomic gains have arisen by recent genetic Vadimezan exchange with other bacteria, as previously suggested for X. vasicola . However, the large ancestral losses cannot be explained by means of the incompleteness of the genomes, and may reflect an ancestral genomic AZD5582 price reduction in the species. The size of the regions involved in such events, and whether they affect restricted functional categories of genes or random regions, is still to be determined. We identified two clusters
buy Nutlin-3a of genes with paraphyletic distribution, suggesting lateral gene transfer. One of the clusters, present in X. campestris and the “”X. axonopodis”" clade, exhibits interesting functional relationships with the Type IV Secretion System (T4SS), while most of the genes are annotated as coding for either putative secreted or membrane proteins. Identification of LGT events based only on intrinsic features such as the G+C content and the CAI would fail to identify both clusters, showcasing the usefulness the phylogenetic distribution of orthologs as a complement for the prediction of putative LGT events. Conclusions Currently, phylogenomic methods are finding a privileged place in phylogenetic inference and evolutionary studies, yet common frameworks for the flexible automation of workflows are not widely available. Here we used Unus, a package developed to facilitate the execution of phylogenetic workflows, to explore the phylogenetic structure of the genus Xanthomonas. We recovered a strongly supported phylogeny in accordance with previous results and high resolution in the closely related genomes of X. oryzae. The results
also provide evidence for the reconsideration of the X. fuscans species, clarify relationships between X. citri, X. axonopodis and X. euvesicatoria, and show that the genus Xanthomonas is not a monophyletic clade. Thiamet G Our results allowed us to identify several interesting features in the evolution of Xanthomonas, including two large putative lateral gene transfer events, which would have been hard to detect by means of G+C content deviation or Codon Adaptation Index. We also detected evidence of an evolutionary tendency towards a reduction in genome size in at least two clades of the genus. Methods Xanthomonas genomes Seventeen Xanthomonas genomes were used in this study (Table 1). The names employed follow the list of prokaryotic names with standing nomenclature (LPSN) , although several additional names may exist in the scientific literature.