Comparative and Phylogenetic Analysis of Six New Complete Chloroplast Genomes of Rubus (Rosaceae)

Rubus includes a group of important plants with medicinal and culinary significance, as well as ornamental value. However, due to its status as one of the largest genera in the Rosaceae family and frequent occurrences of apomixis, hybridization, and polyploidy among its species, the morphological identification of this genus is highly challenging. The plastid genome serves as a valuable tool for studying the evolutionary relationships among plants. Therefore, based on the raw data of the whole genomes from six popular Rubus taxa, the complete Cp genomes were assembled, annotated, and subjected to comparative and phylogenetic analyses. In this research, six newly complete Cp genomes were reported, which all had a representative quadripartite formation, with a similar GC content (37.06%&ndash:37.26%), and their size ranged from 155,493 bp to 156,882 bp. They all encode 111 unique genes, containing 79 PCGs, 28 tRNA, and 4 rRNA. The analysis of gene structure of different groups showed that the sequence and content of genes were relatively conservative, and there was no gene rearrangement. Most of their PCGs had a high frequency codon usage bias and all genes were in purifying selection states. A nucleotide variable analysis revealed that the IR areas had less variation than the SC areas, and there was the greatest diversity in the SSC area. Eleven hypervariable areas were identified, containing rpl32-trnL, rpl32, rps16-trnQ, trnT-trnL, trnQ-psbK, trnK-rps16, and rps15-ycf1, which could be used as labels for genetic diversity and taxa identification. The phylogenetic trees of 72 Rosaceae plants were constructed based on ML and BI methods. The results strongly support the theory that the Rubus genus was a monophyletic group and sampled species could be arranged into seven subgenera. Overall, this study sheds its new light into the phylogeny of the Rubus genus, providing valuable insights for future studies of the Cp genomes from the expanded taxa of the Rosaceae family.