Characteristics and phylogenetic analysis of the complete chloroplast genome of Rubus chingii Hu 1925 from the family Rosaceae

Abstract

Rubus chingii Hu 1925 is an important medicinal vine shrub in the Rosaceae family, widely distributed in China and Japan. In this study, the complete chloroplast genome of R. chingii was sequenced and identified. The chloroplast genome was 155,563 bp in size with a total GC content of 37.06%. Two 25,749-bp inverted repeat (IRA and IRB) regions divided the genome as four sections, with the remainder forming a large single-copy (LSC, 85,322 bp) and a small single-copy (SSC, 18,743 bp) regions. This genome contained a total of 131 genes, of which 86 were protein-coding genes, 37 tRNA genes, and eight rRNA genes. The phylogenetic analysis showed that R. chingii, along with several other R. longisepalus, R. tsangii, R. hirsutus, R. taiwanicola, R. rubroangustifolius, and R. glandulosopunctatus, formed the monophylic group. Interestingly, the chloroplast genome structure we reported was different from the previously reported structure and provided richer phylogenetic analysis information in the Rubus genus compared to previous studies. The genome information reported in this paper will provide some useful information for further investigation on the evolution of the family Rosaceae.

Keywords:

• Rubus chingii
• complete chloroplast genome
• phylogenetic analysis
• Rosaceae

Ethics statement

This study strictly follows the wild plant protection regulations of China, which was first promulgated by Decree No. 204 of the state council of China on 30 September 1996 and amended on 7 October 2017 under Decision of The State Council on Revising Some Administrative Regulations.

Author contributions

Conceptualization, methodology: Zhang Y; data acquisition, analysis, and interpretation: Li Y, Qiu Y, Yang M, and Li M; the plant material collecting and identifying: Yin Y; manuscript writing and revising: Li Y, Zhang Y, and Li M; all authors have read and approved the final manuscript and agree to be accountable for all aspects of the work.

Disclosure statement

The authors report no conflict of interest.

Data availability statement

The genome sequence data of R. chingii that support the findings of this study are openly available in GenBank of NCBI under the accession no. OL449946. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA782849, SRR17013867, and SAMN23401999, respectively.

Additional information

Funding

This work was supported by the Key Technology Research and Demonstration Base Construction for Ecological Planting of 30 Authentic Medicinal Materials [Grant No. 2021YFD1600902].