%0 Journal Article
%@ 0031-949X 
%A Kaur, Amandeep
%A Rana, Rekha
%A Bansal, Kanika
%A Patel, Hitendra K.
%A Sonti, Ramesh V.
%A Patil, Prabhu B
%D 2023
%F open:3179
%I The American Phytopathology
%J Phytopathology
%K Oxford Nanopore; Xanthomonas oryzae pv. oryzae; pathotype; resistance (R) genes; transcription activator-like effectors
%N 6
%P 953-959
%T Insights into the Diversity of Transcription Activator-Like Effectors in Indian Pathotype Strains of Xanthomonas oryzae pv. oryzae 
%U http://crdd.osdd.net/open/3179/
%V 113
%X Xanthomonas oryzae pv. oryzae (Xoo) is a major rice pathogen, and its genome harbors extensive inter-strain and inter-lineage variations. The emergence of highly virulent pathotypes of Xoo that can overcome major resistance (R) genes deployed in rice breeding programs is a grave threat to rice cultivation. The present study reports on a long-read Oxford nanopore-based complete genomic investigation of Xoo isolates from 11 pathotypes that are reported based on their reaction toward 10 R genes. The investigation revealed remarkable variation in the genome structure in the strains belonging to different pathotypes. Furthermore, transcription activator-like effector (TALE) proteins secreted by the type III secretion system 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. Furthermore, in silico analysis of the genome-wide rice targets of TALEs allowed us to understand the emergence of pathotypes compatible with major R genes. Long-read, cost-effective sequencing technologies such as 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 R genes in rice breeding programs.    
%Z The copyright of this article belongs to The American Phytopathology