Genomics-Enabled Novel Insight Into the Pathovar-Specific Population Structure of the Bacterial Leaf Streak Pathogen Xanthomonas translucens in Small Grain Cereals

Abstract

The Gram-negative bacterium <i>Xanthomonas translucens</i> infects a wide range of gramineous plants with a notable impact on small grain cereals. However, genomics-informed intra-species population structure and virulence repertories of the pathogen have rarely been investigated. In this study, the complete genome sequences of seven <i>X. translucens</i> strains representing an entire set of genetic diversity of two pathovars <i>X. translucens</i> pv. <i>undulosa</i> and <i>X. translucens</i> pv. <i>translucens</i> is provided and compared with those of seven publicly available complete genomes of the pathogen. Organization of the 25 type III secretion system genes in all the 14 <i>X. translucens</i> strains was exactly the same, while TAL effector genes localized singly or in clusters across four loci in <i>X. translucens</i> pv. <i>translucens</i> and five to six loci in <i>X. translucens</i> pv. <i>undulosa</i>. Beside two previously unreported endogenous plasmids in <i>X. translucens</i> pv. <i>undulosa</i>, and variations in repeat variable diresidue (RVD) of the 14 strains, <i>tal1a</i> of <i>X. translucens</i> pv. <i>translucens</i> strain XtKm8 encode the new RVDs HE and YI which have not previously been reported in xanthomonads. Further, a number of truncated <i>tal</i> genes were predicted among the 14 genomes lacking conserved <i>Bam</i>HI site at N-terminus and <i>Sph</i>I site at C-terminus. Our data have doubled the number of complete genomes of <i>X. translucens</i> clarifying the population structure and genomics of the pathogen to pave the way in the small grain cereals industry for disease resistance breeding in the 21st century's agriculture.