Fifteen years of vegetable crop genome sequencing: achievements, challenges, and prospects

Vegetables are a crucial component of the global diet, providing essential vitamins, minerals, dietary fiber, and medicinal value to humans while also holding a key position in agricultural economies. Since the first vegetable genome sequencing was completed for cucumber in 2009, a total of 108 vegetable species had their genomes sequenced by April 2025. To better understand and utilize these genomics data resources of vegetable crops, we have carried out detailed data collation and discussion. This review provides an overview of the current status of vegetable crop sequencing, construction of a genomic database platform for vegetable crops, the identification of functional genes, the revolutionary changes in sequencing technology for vegetable crops, and research progress in important agronomic traits. It also examines the development directions and challenges faced by vegetable genomics, comparative genomics, and breeding, offering valuable insights for modern vegetable biology research and agricultural intelligent breeding.