The Genome of Eggplant

Eggplant (Solanum melongena L.), exclusively native to the Old World, is one of the most important Solanaceae crops, which ranks third in total production and economic value in the genus Solanum. Here, we reported a high quality,chromosome-scale eggplant reference genome sequence of 1155.8 Mb with an N50 of 93.9 Mb, which is assembled by combining PacBio long reads and Hi-C sequencing data. Repetitivesequences occupied 70.1%oftheassembly size and 35,018 high-confidence protein-coding genes were annotated based on multiple evidence. Comparative analysis revealed 646 species-specific families as well as 364 positive selection genes in eggplant, conferring the distinguished traits in this plant. We performed genome-wide identification ofdisease resistance genes and discovered an expanded gene family of bacterial spot resistance in eggplant and pepper, compared to tomato and potato.The genes involved in chlorogenic acid synthesis were comprehensively characterized. A highly similar chromosomal distribution pattern of polyphenol oxidases was observed in the eggplant, tomato, and potato genomes. The eggplant reference genome sequence will not only promote the evolutionary studies in Solanaceae,but also facilitate theirbreeding and improvement.