Rubus chingii chloroplast genome sequences: a comparative analysis with other Rubus L.chloroplast genomes

Rubus belong to the Rosaceae family, and they are commonly used as nutritious foods and medicinal plants in China. The fruits of Rubus plants are rich in nutrients and are renowned for their excellent antioxidant properties. Many Rubus plants can be processed into Chinese medicinal materials, with the fruits of Rubus chingii being a typical example. However, due to the similar appearance of Rubus fruits, they cannot be well distinguished after processing. Therefore, this study seeks to characterize the chloroplast genomes of 28 Rubus species and examine variations in their sequences, so as to provide valid data support for the identification of closely related species and the analysis of their genetic evolutionary relationships.

Our research found that the chloroplast genomes of the 28 Rubus species possess a canonical quadripartite organization, comprising one Large Single Copy (LSC) region, a pair of inverted repeat (IR) regions(IRa and IRb), and one Small Single Copy (SSC) region. Their overall size varied between 155,470 and 156,429 bp, showing only slight fluctuations, and the GC contents ranged from 36.91% to 37.28%. The RSCU analysis revealed that UUA was the most frequently used synonymous codon, whereas its synonymous counterparts CUC and CUG exhibited the lowest RSCU values. Shrinkage and expansion phenomena were primarily observed at the junctions between the SSC region and IR region in the chloroplast genomes. Repeat sequences demonstrated that A/T base pairs were most prevalent in simple sequence repeats (SSRs). Nucleotide polymorphism analysis indicated that there were multiple regions with high PI values in the chloroplast genes of the 28 Rubus species, namely trnH-psbA, rps16-trnQ 1, rps16-trnQ 2, trnS-trnG, petN-psbM, petA-psbJ, psbE-petL and rpl32-trnL. Codon usage analysis showed that most genes had Ka/Ks values less than one. Phylogenetic analysis showed that these 28 genomes were mainly divided into two major clades: Rubus chingii was placed in Clade B and was most closely related to Rubus corchorifolius. We further validated the molecular markers rpl32-trnL and rps16-trnQ2, which showed efficiency in species identification.

These findings enrich our knowledge of Rubus chloroplast genomes, and offer valuable molecular data for its taxonomic classification, evolutionary exploration and species discrimination.