Assembly and annotation ofSolanum dulcamaraandSolanum nigrumplant genomes, two nightshades with different susceptibilities toRalstonia solanacearum

To understand why close wild plant relatives of crops, such asSolanum dulcamara, are resistant toRalstonia solanacearumwe need genetic resources to perform comparative studies and identify key genes and pathways. Wede-novoassembled and annotated the genome of resistantS. dulcamaraand susceptibleSolanum nigrumplants using a hybrid approach including Oxford Nanopore Technologies and Illumina sequencing. Comparative genomic analysis was then performed to find differences between the genome ofS. dulcamaraand other susceptible Solanaceous species including potato, tomato, aubergine, andS. nigrumand one susceptible and one resistantS. americanumaccession. We identified genes associated with auxin-transport only inS. dulcamaraand a collection of pattern recognition receptors (PRRs) was identified in orthogroups only found in plant species with resistant/tolerant phenotype, suggesting novel plant receptors in these accessions that may improve recognition of pathogen-associated molecular patterns (PAMPs) associated withR. solanacearum. We also 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 during bacterial wilt development to determine if they could offer potential novel targets for breeding improved wilt resistance.