Pennellii Cheesmaniae genomes

Crop wild relatives represent valuable genetic resources for the improvement of cultivated crops. However, the precise introgression of wild genetic material into domesticated varieties is challenging and can not be fully characterized without high-quality genome assemblies. In this study, we employed PacBio HiFi, Oxford Nanopore ultra-long read, and Hi-C sequencing to generate chromosome-scale de novo genome assemblies for two wild relatives of cultivated tomato: the broadly stress-resistant Solanum pennellii (accession LA0716) and the salt-tolerant Solanum cheesmaniae (LA1039). In addition, to investigate recombination dynamics, we performed whole-genome sequencing of 709 recombinant plants derived from male and female backcrosses across three hybrid backgrounds. Together, these results provide high-quality genome assemblies for S. pennellii and S. cheesmaniae and demonstrate how repeat divergence and structural variation shape genome evolution and recombination landscapes within the Lycopersicon clade.