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The complete chloroplast genome sequence of Rubus hirsutus Thunb. and a comparative analysis within Rubus species

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Abstract

Rubus hirsutus is a type of tonifying kidney-essence herb that belongs to the Rosaceae family, and has been commonly used to treat multiple diseases, such as polyuria, impotence, and infertility. In this study, we determined the complete chloroplast sequence of R. hirsutus and conduced a comparative analysis within the genus Rubus. The assembled chloroplast (cp.) genome is 156,380 bp in length with a GC content of 37.0% and shares a conserved quadripartite structure within the other cp. genomes in this genus. A total of 132 unique genes were annotated in the cp. genome of R. hirsutus, which contained 87 protein-coding genes, 37 tRNAs, and eight rRNAs. Seventeen duplicated genes were identified in the inverted repeats region. Furthermore, 70 simple sequence repeats and 35 long repeats were detected in total in the R. hirsutus chloroplast genome. Eight mutational hotspots were identified in the cp. genome of this species with higher nucleotide variations in non-coding regions than those of coding regions. Furthermore, the gene order, codon usage, and repeat sequence distribution were highly consistent in Rubus according to the results of a comparative analysis. A phylogenetic analysis indicated that there was a sister relationship between R. hirsutus and R. chingii. Overall, the complete chloroplast genome of R. hirsutus and the comparative analysis will help to further the evolutionary study, conservation, phylogenetic reconstruction, and development of molecular barcodes for the genus Rubus.

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Acknowledgements

This work was financially supported by the Opening Project of Zhejiang Provincial Preponderant and Characteristic Subject of Key University (Traditional Chinese Pharmacology), Zhejiang Chinese Medical University (No. ZYAOX2018033), and Project of Quality Guarantee System of Chinese Herbal Medicines (Grant No. 201507002-4).

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  1. Qirui Wang and Ziru Huang have contributed equally to this work.

Authors and Affiliations

  1. School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, China

    Qirui Wang, Ziru Huang, Chenshu Gao & Rubin Cheng

  2. The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, Zhejiang Province, China

    Yuqing Ge

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  1. Qirui Wang
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Wang, Q., Huang, Z., Gao, C. et al. The complete chloroplast genome sequence of Rubus hirsutus Thunb. and a comparative analysis within Rubus species. Genetica 149, 299–311 (2021). https://doi.org/10.1007/s10709-021-00131-9

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