Assembly and annotation of Solanum dulcamara and Solanum nigrum plant genomes, two nightshades with contrasting susceptibilities to Ralstonia solanacearum

Ralstonia solanacearum causes disease in more than 200 plant species including bacterial wilt of tomatoes and brown rot of potatoes. This bacterium is a soilborne and waterborne pathogen, with a worldwide distribution and is on the EPPO A2 list of quarantine pathogens. ln the UK, the bacterium is present in the rivers, but its prevalence depends on the season; it is highly abundant in the summer and undetectable during winter. To survive the cold winter temperatures, R. solanacearum overwinters inside plants growing alongside the rivers such as Solanum dulcamara. Interestingly, this plant species doesn’t show bacterial wilt symptoms. To understand genomic differences with susceptible hosts, we assembled the genome using Oxford Nanopore Technologies and Illumina sequencing. Solanum dulcamara (Royal Botanic Gardens, Kew ID=39087) leaves were collected from 3-month old adult plant. DNA was extacted following the High molecular weight gDNA extraction from plant leaves protocol, Oxford Nanopore Technologies [ONT]), which utilised Carlson buffer and further purification using QIAGEN genomic-tip, see preprint Vaillancourt and Buell (2019) for details.The libraries were prepared using the SQK-LSK109 ligation sequencing kit and run with PromethION R9.4.1 (FLO-PRO002) flow cells. Base calling was obtained onboard with Guppy. f5c v1.2 was used to identify the methylated regions as well as the frequency of methylation in the whole genome.