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

To understand why close wild plant relatives of crops, such as Solanum dulcamara, are resistant to Ralstonia solanacearum we need genome resources to perform comparative studies and identify key genes and pathways. We de-novo assembled and annotated the genome of a resistant/tolerant S. dulcamara and susceptible Solanum nigrum plant using a hybrid approach including Oxford Nanopore Technologies and Illumina sequencing. Comparative genomic analysis was then performed to find differences between the genome of S. dulcamara and other susceptible Solanaceous species including potato, tomato, aubergine, and S. nigrum and one susceptible and one resistant S. americanum accession. We identified genes associated with auxin-transport only in S. dulcamara and a collection of pattern recognition receptors (PRRs) in orthogroups only found in resistant/tolerant plant species, which we hypothesise may improve recognition of pathogen-associated molecular patterns (PAMPs) associated with R. solanacearum. We also identified an arsenal of nucleotide-binding leucine-rich repeat receptors (NLRs) in the S. nigrum genome that are shared with the other susceptible species and could be acting as susceptibility factors. Finally, we identified differences in methylation frequency across the gene bodies in both species, which may be associated with epigenetic regulation of resistance. Future work should assess the functional role of these PRRs and NLRs during bacterial wilt development to determine if they could offer potential novel targets for breeding to improve bacterial wilt resistance.