title: Ecological and Evolutionary Insights into Xanthomonas citri Pathovar Diversity.
abstract: Citrus canker, caused byXanthomonas citripv. citri, is a serious disease of citrus plants worldwide. Earlier phylogenetic studies using housekeeping genes revealed thatX. citripv. citri is related to many other pathovars, which can be collectively referred asXanthomonas citripathovars (XCPs). From the present study, we report the genome sequences of 18 XCPs and compared them with four XCPs available in the public domain. In a tree based on phylogenomic marker genes, all the XCPs form a monophyletic cluster, suggesting their origin from a common ancestor. Phylogenomic analysis using the type strain further established that all the XCPs belong to one species. Clonal analysis of the core genome revealed the presence of two major lineages within this monophyletic cluster consisting of some clonal variants. Incidentally, the majority of these XCPs were first noticed in India, corroborating their clonal relationship and their common origin. Comparative analysis revealed an open pan-genome and the role of interstrain genomic flux of these XCPs since their diversification from a common ancestor. Even though there are wide variations in type III gene effectomes, we identified three core effectors which can be valuable in resistance-breeding programs. Overall, genomic examination of ecological relatives allowed us to dissect the tremendous genomic potential ofX. citrispecies to rapidly evolve into specialized strains infecting diverse crop plants.IMPORTANCEHost specialization is one of the characteristic features of highly evolved pathogens such as theXanthomonasgroup of phytopathogenic bacteria. Since the hosts involve staple crops and economically important fruits such as citrus, detailed understanding of the diversity and evolution of such strains infecting diverse plants is important for quarantine purposes. In the present study, we carried out genomic investigation of members of a phylogenetically and ecologically defined group ofXanthomonasstrains pathogenic to diverse plants, including citrus. This group includes the oldestXanthomonaspathovars and also recently emerged pathovars in a particular country where they are endemic. Our high-throughput genomic study has provided novel insights into the evolution of a unique lineage consisting of serious pathogens and their ecological relatives, suggesting the nature, scope, and pattern of rapid and recent diversification. Further, from the level of species to that of clonal variants, the study revealed interesting genomic patterns in diversification of aXanthomonaslineage and perhaps will inspire careful study of the host range of the included pathovars.
authors.affiliation: CSIR-Institute of Microbial Technology, Chandigarh, India.
authors.forename: Kanika
authors.initials: K
authors.lastname: Bansal
authors.affiliation: CSIR-Institute of Microbial Technology, Chandigarh, India.
authors.forename: Samriti
authors.initials: S
authors.lastname: Midha
authors.affiliation: CSIR-Institute of Microbial Technology, Chandigarh, India.
authors.forename: Sanjeet
authors.initials: S
authors.lastname: Kumar
authors.affiliation: CSIR-Institute of Microbial Technology, Chandigarh, India pbpatil@imtech.res.in.
authors.forename: Prabhu B
authors.initials: PB
authors.lastname: Patil
mesh_terms: D002957:Citrus / Q000382:microbiology*; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D014644:Genetic Variation; D016680:Genome, Bacterial; D005838:Genotype; D007194:India; D010802:Phylogeny; D010935:Plant Diseases / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D014974:Xanthomonas / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification
chemical_list: D004269:DNA, Bacterial
keywords: India; Xanthomonas; ecology; evolution; hypervariation; pathovar