Core genome MLST for epidemiological and evolutionary analyses of phytopathogenic Xanthomonas citri

Xanthomonas citri subspecies citri (XCC) is the cause of bacterial citrus canker, responsible for major economic losses to the citrus industry that includes sweet orange, lime and grapefruit production in regions including South America, United States, China and Japan. Other X. citri subsp. and pathovars are responsible for diseases in crops such as soy bean, common bean, mango, pomegranate and cashew. Tracing the spread of X. citri disease has been performed using several different typing methods over the years but recent studies using genomic sequencing have been key to understanding evolutionary relationships within the species including fundamental differences between XCC pathotypes. In this study we developed a core genome multilocus typing scheme (cgMLST) for X. citri based upon 250 genomes comprising multiple examples of X. citri subsp. citri pathotypes A, A* and Aw, X. citri subsp. malvacearum and X. citri pathovars aurantifolii, fuscans, glycines, malvacearum, mangiferaeindicae, viticola, vignicola and single isolates of X. citri pathovars dieffenbachiae and punicae. This dataset included genomic sequencing of 100 novel XCC isolates. The cgMLST scheme, based upon 1618 core genes across 250 genomes, has been implemented at PubMLST (https://pubmlst.org/organisms/xanthomonas-citri/). Grapetree minimum-spanning, and iTOL Neighbour-joining phylogenies generated from cgMLST data resolved almost identical groupings of isolates to a core genome SNP - based neighbour joining phylogeny taking 4 min, 15 min and 36 h respectively. These resolved identical groupings of XCC pathotypes and X. citri subsp. and pathovars. X. citri cgMLST should prove to be an increasingly valuable resource for the study of this key species of plant pathogenic bacteria. Users can submit genomic and associated metadata to compare with previously characterised isolates at PubMLST.org to allow rapid characterization of local, national and global epidemiology of these pathogens and examine evolutionary relationships.