Extreme phylogenomic diversity in non-pathogenic Xanthomonas strains associated with citrus

Abstract

Xanthomonas are primarily known as a group of phytopathogens infecting diverse plants. Recent molecular studies reveal existence of novel species and strains of Xanthomonas that follow non-pathogenic (NPX) lifestyle. Presently, we report whole genome sequence of four NPX reported from Citrus sp. (NPXc). Taxonogenomic analysis revealed surprising diversity as each of the three isolates were found to be novel genomospecies that together form a Citri associated non-pathogenic Xanthomonas species complex (NPXc complex). Interestingly, this NPXc complex is related to another non-pathogenic species, X. sontii from rice (NPXr). On the other hand, the fourth NPXc isolate was found to be related to NPX isolates from walnut (NPXw), altogether they form a potential taxonomic outlier of pathogenic X. arboricola species. Interestingly, their pathogenic counterparts, X. citri and X. arboricola are known to cause similar symptoms in diverse fruit plants. Further, genomic investigation of well-characterized pathogenicity clusters in NPXc isolates revealed lifestyle specific gene content dynamics. Majorly, genes essential for virulence (T3SS, effectors, T6SS, biofilm cluster etc.) and adaptation (gum, rpf, iron uptake and utilization, T2SS (xps) and variable repertoire of cell wall degrading enzymes) could be depicted by comparative genomics of Xanthomonas community comprising of diverse lifestyle isolates. Overall, present analysis confers that non-pathogenic isolates of diverse host phylogenomically converge and are evolving in parallel to their pathogenic counterparts. Hence, there is a need to understand the world of NPX isolates from diverse and economically important hosts. Genomic knowledge and resource will be invaluable in both basic and applied research of genus Xanthomonas.