Advancing understanding of : a comprehensive genomic analysis reveals evolutionary patterns and metabolic pathway insights.

L. (dioecious), the most significant commercial species in the genus , which has been cultivated for more than 11,000 years and was one of the first species to be domesticated. Herein, we reported the most comprehensive genome currently. The contig N50 of the Orphan was 9.78 Mb, and genome size was 366.34 Mb with 13 chromosomes. Based on the high-quality genome, we discovered that diverged from ~34 MYA, and a WGD event took place about 2─3 MYA. Throughout the evolutionary history of , chromosomes 2, 8, and 10 had experienced chromosome recombination, while chromosome 3 saw a fusion and fission. It is worth proposing that the chromosome 9 experienced both inversion and translocation, which facilitated the emergence of the as a new species. And the selections of for the genes of recombination chromosomal fragment are compatible with their goal of domestication. In addition, we found that the has the gene, but there are structural deletions and positional jumps. This gene is thought to replace the one needed for female common type to be pollinated. Subsequently, we conducted genomic, transcriptomic, and metabolomic analysis to demonstrate significant differences in the expression of among different varieties of . The playing an important role in the anthocyanin metabolism pathway of . Moreover, the gene of has a different evolutionary trend compared to other species. These high-quality genome assembly, transcriptomic, and metabolomic resources further enrich genomics and provide insights for studying the chromosomes evolution, sexual system, and color characteristics of .