Genomic characterizations of Xanthomonas cucurbitae and using comparative genomics to predict novel microbe-associated molecular patterns in Xanthomonas

Bacterial spot is a major plant disease caused by many plant-pathogenic members of the genus Xanthomonas. While each species is narrow in host range, bacterial spot Xanthomonads infect a large variety of plant hosts, leading to large economic losses for farmers around the world. Although Xanthomonas utilizes a wide array of virulence and pathogenicity factors to infect their hosts, plants have a range of methods to recognize invaders and prevent infection. Understanding the genomic and molecular interactions between Xanthomonas and their hosts are an important part of developing effective crop protection strategies and breeding plants for resistance. While X. cucurbitae has been identified as the causal agent of bacterial spot on cucurbits, no genomic-level analyses have been carried out regarding the pathogen. Using the first reference quality X. cucurbitae genome assembly, an RNA-seq analysis was carried out to assess virulence characteristics of the pathogen. By analyzing the X. cucurbitae transcriptome, we observed behavioral changes between nutrient-sufficient and host-mimicking conditions, as well as the upregulation of genes related to virulence and pathogenicity. We also identified virulence genes likely to be essential in successful bacterial spot infection. In addition, a RAD-seq analysis was performed to characterize populations clusters of X. cucurbitae isolated throughout the Midwestern United States. We revealed multiple populations of X. cucurbitae present throughout the region and demonstrated clear genetic differences between these populations using population genetics analyses. These studies demonstrate clear value in future genomic studies regarding X. cucurbitae. X. euvesicatoria and X. perforans are two bacterial spot Xanthomonads affecting tomatoes and peppers. We conducted a comparative genomics study in X. euvesicatoria and X. perforans populations to identify genes under selection pressure, and to characterize potential genes involved in plant-pathogen interactions. By calculating the test statistic Tajima’s D, we found evidence of purifying selection throughout the genomes of both bacterial spot Xanthomonads. In addition, Tajima’s D was successfully able to detect known microbe-associated molecular patterns (MAMPs), and we were able to characterize the recognition of these MAMPs between species in luminol-based reactive oxygen species (ROS) assays. While this study was not yet able to identify novel MAMPs, we show that Tajima’s D is a powerful tool in detecting genes that are important to plant-pathogen interactions