Towards a streamlined approach to whole genome sequencing of Spongospora subterranea f. sp. subterranea (P-35)

Spongospora subterranea f. sp. subterranea (Sss), is a plasmodiophorid potato pathogen that causes powdery scab, resulting in tuber pustules and root galls. Sss vectors potato mop-top virus (PMTV), which causes necrotic rings, flecks, and arcs in tuber tissue. These pathogens cause substantial economic losses to potato production worldwide due to the lack of effective management strategies. Previous pathogen characterization studies have been hampered by the soilborne obligate biotrophic nature of Sss. The objective of this study was to increase whole genome sequencing efficiency by decreasing the time to generate pathogen biomass and reducing contaminants found in greenhouse potting mix or field soil. We optimized an existing protocol for hydroponics-based screening of Sss using a tomato-bait system. We tested inoculum from eight soils and tuber pustules at several sporosori quantities to establish infection in a susceptible tomato cv. Alaskan Fancy. Tomato seedlings were grown in a growth chamber in a standard hydroponic media and inoculated after two weeks. Fifteen days post-inoculation, the pathogen was successfully detected in root tissues by qPCR and histopathology. Whole genome sequencing was completed using Illumina Nextseq, and the reads were aligned to a reference genome. This is an important step toward the ongoing work on the whole genome-based characterization of pathogen samples collected across time and space. The present study may also contribute to a reliable and rapid screening of host genotypes for resistance against Sss and PMTV.