Abstract: Rubus (raspberries and blackberries) is a large genus of over 700 species well known for its taxonomic challenges. Many of its species hold significant economic value as important edible and medicinal plants. Here, near-complete genomes for four wild diploid raspberry species were assembled, including R. ellipticus, R. niveus, as well as the highly heterozygous diploid red raspberry (R. idaeus), and its closely related species R. sachalinensis. Pan-genome analysis of Rubus identified 10,243 core gene families (64% of total), and highlights expansions of flavonoid/terpenoid pathways in Rubus, correlating with fruit bioactive compound diversity. Our discovery of shared ancestral components between R. idaeus and R. sachalinensis subgenomes provides evidence for their homoploid hybrid origin. The centromere sequence characteristics could serve as markers for subgenome assignment in R. idaeus and R. sachalinensis. Moreover, population genomic studies of 125 accessions from ca. 80 species uncovered widespread genetic introgression, particularly in red raspberries, with centromeric haplotype signatures tracing ancestral contributions to cultivated varieties. By integrating metabolome and transcriptome data, we explore the fruit quality regulatory network of Chinese raspberries. We identified a glutathione S-transferase gene that may inhibit the successful transport of anthocyanins into the vacuole and appears to be a limiting factor for the anthocyanin pigmentation in R. ellipticus fruits. In summary, this research sheds new light on the genetic intricacies of raspberry species and their cultivars, and provides a robust foundation for horticultural improvement and genomic selection in raspberry breeding.

Key words: entromere, edible and medicinal plant, evolutionary dynamics, fruit quality, raspberry (Rubus)