LAUSR

Xanthomonas oryzae pv. oryzae (Xoo) is a major rice pathogen, and its genome harbours extensive inter-strain and inter-lineage variations. The emergence of highly virulent pathotypes of Xoo that can overcome major resistance genes deployed in rice breeding programs is a grave threat to rice cultivation. The present study reports long-read Oxford nanopore-based complete genomic investigation of Xoo isolates from eleven pathotypes that are reported based on their reaction toward ten resistance (R) genes. The investigation revealed remarkable variation in the genome structure in the strains belonging to different pathotypes. Further, transcription activator-like effector (TALE) proteins secreted by the type III secretion system (T3SS) display marked variation in content, genomic location, classes, and DNA binding domain. We also found the association of tal genes in the vicinity of regions with genome structural variations. Further, in silico analysis of their genome-wide rice targets of TALEs allowed us to understand the emergence of pathotypes compatible with major resistance genes. Long-read, cost-effective sequencing technologies like nanopore can be a game changer in the surveillance of major and emerging pathotypes. The resource and findings will be invaluable in the management of Xoo and in appropriate deployment of resistance genes in rice breeding programs.