CRISPR/Cas9 mediates precise and efficient gene editing in Xanthomonas oryzae pv. oryzae

Xanthomonas oryzae pv. oryzae (Xoo), a non-obligate phytopathogen that causes bacterial leaf blight, poses a severe threat to rice production. Although the clustered regularly interspaced short palindromic repeats (CRISPR) system represents a versatile genome-editing tool derived from prokaryotic adaptive immunity, its application in Xoo remains largely underdeveloped. To address this, we engineered an all-in-one plasmid for the constitutive expression of CRISPR-associated protein 9 (Cas9) and single-guide RNA (sgRNA) in the model strain Xoo PXO99^A, and electroporation with this construct led to over 99% cell death. Among the surviving colonies, the majority retained the wild-type (WT) genotype, and only one rare mutant carrying a small insertion or deletion (indel) was obtained, indicating extremely low endogenous non-homologous end joining (NHEJ)-like activity. Furthermore, we successfully achieved homologous recombination (HR)-mediated gene fragment deletion and point mutation using plasmid-borne double-stranded DNA (dsDNA) and phosphonothioate-modified single-stranded DNA (ssDNA) oligos as donor templates, with efficiencies reaching up to 29% and 57%, respectively. Compared with the traditional two-step homologous double-crossover (HDC) method, this novel one-step strategy combining transformation and PCR-based screening accelerates functional genomic research in Xanthomonas species and facilitates the dissection of plant-pathogen interaction mechanisms.