The High-Quality Genome Sequence of Solanum etuberosum provides Insights into Genome and Trait Evolution of the Solanum Genus

Genomic rearrangements may involve different mechanisms such as translocations, inversions, deletions, duplications and/or chromosome fusions and lead to genetic novelty and variability. In this study we focused on the Solanum genus which comprises over a thousand species, most notably the crops tomato and potato. To elucidate the evolutionary history and basis of chromosomal, molecular and phenotypic differences between tomato and potato, we used Solanum etuberosum, a tuberless species from Chile, as an outgroup species. Here we used the high quality Solanum etuberosum genome assembly we produced from Illumina and BioNano optical mapping data to investigate genome and trait evolution. Whole-genome synteny analyses revealed that the genome of S. etuberosum is more similar to the genome of potato than tomato. In addition, phylogenetic analysis based on both nuclear genomes and chloroplast sequences confirmed its place as a sister-species to tomato and potato. We also identified eight new genomic events to the already known seven events that differentiate these three species. The molecular characterization of the breakpoints surrounding these events will allow us to decipher if common mechanisms are found, such as the presence of specific transposable elements. Moreover, analysis revealed an accelerated structural evolution in the tomato lineage mediated by transposable elements. It also illuminated the molecular mechanism and the role of the SP6A protein in tuber formation.