Comparative genomics on chloroplasts of Chinese Rubus: genetic structure and phylogenetic relationships with other species of Rosaceae

As a large genus in Rosaceae, Rubus contains approximately 863 species worldwide, which distributed in the temperate regions of the Northern Hemisphere. The number of species in China accounts for approximately one quarter of the total, so China is the diversity distribution center of Rubus in the world. Given this, in this study, the chloroplast genomes and their characteristics of Chinese Rubus species were sequenced, assembled, and analyzed to provide molecular evidence for the Rubus systematic classification. The results indicated that the chloroplast genomes of Rubus exhibited a typical circular quadripartite structure, which consists of a large single-copy region (LSC), a small single-copy region (SSC), and a pair of inverted repeat regions (IR). Its size ranged from 155,472 to 156,886 base pairs (bp). It contained 131 genes, including 88 protein-coding genes (PCGs), 35 tRNA genes, and 8 rRNA genes. The Rubus chloroplast genome showed a high degree of conservation in gene arrangement, in the occurrence frequencies of different types of long repeat sequences, in simple sequence repeats (SSRs), in codon usage patterns, and in selection pressures on PCG s. Differences were mainly manifested in subtle expansion and contraction changes in the inverted repeat (IR) regions, as well as variations in the number of SSRs and long repeat sequences. In some branches, certain genes underwent enhanced or relaxed purifying selection. Phylogenetic analysis revealed that Chinese endemic Rubus species could be divided into eight evolutionary branches, which corresponding to the eight subgenera of Rubus . These data not only clarify the phylogenetic relationships among the Chinese Rubus species, but also provide the basic data for the taxonomic revision under the level of Chinese Rubus subgenera.