Identification and Genome Sequencing of Novel Virulent Strains of Xanthomonas oryzae pv. oryzae Causing Rice Bacterial Blight in Zhejiang, China.

Xanthomonas oryzae pv. oryzae (Xoo) is the causative agent of rice bacterial blight (RBB), resulting in substantial harvest losses and posing a challenge to maintaining a stable global supply. In this study, Xoo strains isolated from Shaoxing, Quzhou, and Taizhou, where RBB occurred most frequently in Zhejiang Province in 2019, were selected as the subjects of research. Three isolated pathogenic bacteria of ZXooS (from Shaoxing), ZXooQ (from Quzhou), and ZXooT (from Taizhou) were all identified as novel Xoo strains. These novel strains demonstrate greater virulence compared to Zhe173, the previous epidemic Xoo strain from Zhejiang Province. Subsequent genomic sequencing and analysis revealed that there existed significant differences in the genome sequence, especially in effector genes corresponding to some known rice resistance (R) genes between the novel strains and Zhe173. The sequence alignment of avirulent genes (effector genes) indicated that nucleic and amino acid sequences of AvrXa5, AvrXa7, AvrXa10, and AvrXa23 in the novel strains varied prominently from those in Zhe173. Interestingly, it seemed that only the genome of ZXooQ might contain the AvrXa3 gene. In addition, the phylogenetic analysis of 61 Xoo strains revealed that the novel strains were situated in a distinct evolutionary clade separate from Zhe173. These results here suggest that the emergence of novel Xoo strains may lead to resistance loss of some R genes used in commercial rice varieties, potentially serving as one of the factors leading to RBB resurgence in Zhejiang Province, China.