Pan genome of Rubus

Rubus (raspberries and blackberries), one of the largest genera within Rosaceae, is well-known for its taxonomical identification challenges. Some raspberry species hold significant economic value as important edible and medicinal plants. In this study, we present near complete chromosome-scale reference genomes for four wild raspberry species located in China, including high heterozygous diploid red raspberry (R. idaeus) and its closely related species R. sachalinensis, as well as two wild edible diploid species, R. ellipticus and R. niveus. By analyzing these four genomes along with other available related genomes, we inferred the phylogenetic relationships within the Rubus and investigated the possible origin patterns of sub-genomes of R. idaeus . Moreover, we conducted genome re-sequencing of 123 accessions, representing 98 raspberry species, to explore the evolutionary history and dynamics of Rubus.