Genome sequencing and comparative analysis of the carrot bacterial blight pathogen, Xanthomonas hortorum pv. carotae M081, for insights into pathogenicity and applications in molecular diagnostics.

Xanthomonas hortorum pv. carotae (Xhc) is an economically important pathogen of carrots. Its ability to epiphytically colonize foliar surfaces and infect seeds can result in bacterial blight of carrots when grown in warm and humid regions. We used high-throughput sequencing to determine the genome sequence of isolate M081 of Xhc. The short reads were de novo assembled and the resulting contigs were ordered using a syntenic reference genome sequence from X. campestris pv. campestris ATCC 33913. The improved, high-quality draft genome sequence of Xhc M081 is the first for its species. Despite its distance from other sequenced xanthomonads, Xhc M081 still shared a large inventory of orthologous genes, including many clusters of virulence genes common to other foliar pathogenic species of Xanthomonas. We also mined the genome sequence and identified at least 21 candidate type III effector genes. Two were members of the avrBs2 and xopQ families that demonstrably elicit effector-triggered immunity. We showed that expression in planta of these two type III effectors from Xhc M081 was sufficient to elicit resistance gene-mediated hypersensitive responses in heterologous plants, indicating a possibility for resistance gene-mediated control of Xhc. Finally, we identified regions unique to the Xhc M081 genome sequence, and demonstrated their potential in the design of molecular diagnostics for this pathogen.