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The rice bacterial blight pathogen  Xanthomonas oryzae  pv. oryzae ( Xoo ) constrains production in major rice growing countries of Asia.  Xoo  injects transcription activator-like effectors (TALEs) that bind to and activate host “susceptibility” ( S ) genes that are important for disease. The bacterial blight resistance gene  xa 5, which reduces TALE activity generally, has been widely deployed. However, strains defeating  xa 5 have been reported in India and recently also in Thailand. We completely sequenced and compared the genomes of one such strain from each country and examined the encoded TALEs. The two genomes are nearly identical, including the TALE genes, and belong to a previously identified, highly clonal lineage. Each strain harbors a TALE known to activate the major  S  gene  SWEET11  strongly enough to be effective even when diminished by  xa 5. The findings suggest international migration of the  xa5 -compatible pathotype and highlight the utility of whole genome sequencing and TALE analysis for understanding and responding to breakdown of resistance.

An xa5 Resistance Gene-Breaking Indian Strain of the Rice Bacterial Blight Pathogen Xanthomonas oryzae pv. oryzae Is Nearly Identical to a Thai Strain