Genomic Characterization of Xanthomonas cucurbitae, the Causal Agent of Bacterial Spot Disease of Cucurbits

Plants in the Cucurbitaceae family comprise several economically-important vegetable and fruit crops including pumpkin, squash, zucchini, cucumber, melon, and watermelon. In 2017, world production of pumpkins, squash, and gourds exceeded 24 million tons worth more than $4 billion, and U.S. production of pumpkins, squash, and gourds was worth $370 million. Illinois farmers are responsible for 40% of total pumpkin production and 85% of the processing pumpkins grown in the U.S., making it a top vegetable commodity in Illinois. Economically important diseases, including bacterial spot on cucurbits, are a problem globally and particularly in Illinois where pumpkin fields can have both high disease incidence and extensive (up to 90%) yield losses. Bacterial species in the genus Xanthomonas can cause bacterial spot disease on a variety of plants. In recent years, bacterial spot disease caused by X. cucurbitae has spread throughout the U.S. and globally, and has become an important bacterial diseases of cucurbit plants. Large-scale genomic studies of other Xanthomonas species has increased our general understanding of virulence mechanisms, evolution, and host specificity factors of these phytopathogens. However, as bacterial species in this genus have many host-specific factors essential to their virulence functions, and as our current genetic and genomic knowledge of X. cucurbitae is limited, a high-quality reference genome would significantly aid in characterizing this particular bacterial species. Since the X. cucurbitae strain ATCC 23378 has been utilized in many previous studies, we used this strain to create a X. cucurbitae reference genome. We employed Oxford Nanopore long-read sequencing technology along with Illumina paired-end short-read sequences to generate a high-quality hybrid genome assembly. The assembly consists of a single, circular, 4.6 Mbp chromosome and one 14 kb plasmid. Initial gene prediction using Prokka estimated approximately 4,000 genes, and characterization of several genes of interest, include one TAL (transcription activator-like) effector, are currently in progress. Additionally, we are using RAD-seq to evaluate population genomics of field isolates from the Midwest region, and we plan to expand our analysis to include strains from different regions of the U.S. isolated from different cucurbit host plants.