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

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. We have used the mRNA-Seq used for de-novo annotation to assess the expression of selected PRRs in roots, stem, leaves, flowers and berries. We collected roots, stems, leaves, flowers and berries of Solanum dulcamara in liquid nitrogen. All tissues were sampled at the same time and stored at -80°C for further RNA extractions (Royal Botanic Gardens; Kew ID=39087). We extracted mRNA-Seq from these 5 tissues by grounding using liquid nitrogen and extracting total RNA using the E.Z.N.A. ® Plant RNA Kit, which included DNase treatment to remove residual DNA according to the manufacturer’s instructions. The quality of the RNA was assessed with Nanodrop and Qubit 4.0. using the Qubit™ RNA Broad Range kit and the Agilent Technology 2100 Bioanalyzer. We generated PromethION 9.4.1 cDNA libraries using total RNA from the 5 independently collected tissue samples which were kept separate.