Chromosome-scale Solanum pennellii and Solanum cheesmaniae genome assemblies reveal structural variants, repeat content and recombination barriers of the tomato clade

Crop wild relatives are important resources for improving cultivated crops, yet the precise introgression of wild genetic material into cultivated crops is often difficult and cannot be fully defined without high-quality genome assemblies. Here we used PacBio HiFi, ONT ultra-long and Hi-C sequencing approaches to generate chromosome-scale de novo genome assemblies of two wild species related to the domesticated tomato (Solanum lycopersicum) -- the broadly stress-resistant Solanum pennellii (accession LA0716) and the salt-resistant Solanum cheesmaniae (accession LA1039). K-mer and BUSCO analysis of both assemblies demonstrated above 99% completeness and the improved S. pennellii genome adds 146 Mbp to the 12 chromosomes compared with the original reference. We aligned the new assemblies with seven gold-standard assemblies from the Lycopersicon clade, using Solanum tuberosum as an outgroup, and identified shared and species-specific structural variants. The repeat content of all nine assemblies was characterized, providing evidence for independent explosions of Tekay (gypsy superfamily) retrotransposons in S. pennellii and S. peruvianum. Whole genome sequencing of 709 recombinant plants derived from male and female backcrosses of three different hybrids (S.pennellii, S. cheesemaniae and Solanum lycopersicum cv. Micro-Tom crossed with Solanum lycopersicum cv. Moneyberg-TMV) revealed higher crossover rate in female meiosis. Recombination landscape analysis identified conserved female-enhanced recombination regions, and coldspots that were completely devoid of meiotic crossovers including megabase-scale inversions and insertion-deletion polymorphisms between S. lycopersicum and S. pennellii. In summary, we harnessed our high-quality S. pennellii and S. cheesmaniae genome assemblies to reveal how repeat content diverged in nature and during breeding, and uncovered how reproductive gender interacts with structural variants to dictate the recombination landscape in tomato hybrids.