Bioinformatics can change phylogenetic relations of bacterial strains: a case study on pathovars of Xanthomonas campestris

Background and Aim : Xanthomonas campestris pathovars are phytopathogenic bacteria which are classified into numerous categories based on their selective and specific hosts. Complete genome sequences of different bacteria are increasingly available due to the advent of high-throughput sequencing technologies and the development of bioinformatics tools. This provides new opportunities for investigating phylogenetic relations of Xanthomonas campestris pathovars at the genome level.Methods : Available genome sequences of sixty Xanthomonas campestris strains from different pathovars were retrieved from GenBank and were submitted to RAST to use a uniform methodology for genome annotation. Taking Xanthomonas campestris pv. campestris ATCC ۳۳۹۱۳ as a reference, ANI was calculated by JSpecies and dDDH was determined using Web tool GGDC for intergenomic distance analysis. For phylogenomic analysis, sequences of ۲۰ universal housekeeping genes were extracted from Xanthomonas campestris genomes and then were aligned and concatenated by CLUSTALW and SeaView, respectively. A maximum likelihood phylogenomic tree was constructed using IQ-TREE. The phylogenomic tree was displayed by TreeGraph ۲.Results : ANI and dDDH are the similarity indices for genome comparison which are used to confirm the taxonomic hierarchy at the species level. ANI and dDDH values for ۴۵ strains of Xanthomonas campestris were above the species cutoff values (۹۵% and ۷۰%, respectively). The G+C content of each genome was also determined and was compared with Xanthomonas campestris pv. campestris ATCC ۳۳۹۱۳. A genome was considered to belong to species campestris if it showed less than ۱% difference in G+C content with the reference strain. Relatedness of these ۴۵ strains to reference, Xanthomonas campestris pv. campestris ATCC ۳۳۹۱۳ in the phylogenomic tree was confirmed the species status of them as Xanthomonas campestris and they were restricted to three pathovars including campestris, incanae and raphani.Conclusion : According to the results of present study, it is suggested that comparison of related genomes using bioinformatics tools can be considered as a new approach for biosystematics study of different bacteria as well as Xanthomonas campestris pathovars and may be avoided ecological and evolutionary misinterpretation in subsequent studies of these industrially and agriculturally important bacteria.

کلیدواژه ها:

Xanthomonas campestris ، bioinformatics ، phylogenetic ، phylogenomic tree ، genome ، pathovar