Comparative genomics of Xanthomonas cucurbitae isolates collected from Midwestern United States pumpkin fields

Abstract

Bacterial spot disease of cucurbits, caused by Xanthomonas cucurbitae, is a major problem in cucurbit-growing areas worldwide. In the Midwestern region of the United States, pumpkin and squash fields can have greater than 90% infected fruits, leading to high yield losses. While reference genomes are available for this bacterial species, the genetic diversity between different strains and populations is unknown. After performing restriction-site associated DNA sequencing (RAD-seq) analysis of X. cucurbitae isolates collected from the Midwestern region, we selected five representative isolates for further characterization, which included whole-genome sequencing and in vitro enzyme and in planta virulence assays. Our results suggest that minimal genetic diversity exists between these isolates, and that the isolates have differential virulence on different cucurbit host plants. This study contributes to our understanding of X. cucurbitae population dynamics in the Midwestern region and may assist with developing additional management strategies for controlling bacterial spot disease of cucurbits.