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The complete chloroplast genome of the rare species Epimedium tianmenshanensis and comparative analysis with related species

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Abstract

Epimedium tianmenshanensis is a rare perennial herb distributed in China, and it is also an important medicinal plant. Here, we used illumina paired-end sequencing technology to obtain the complete chloroplast genome of E. tianmenshanensis, and compared analysis with related species. The length of the complete chloroplast genome of E. tianmenshanensis is 156,956 bp, which is a relatively conserved quadripartite structure including a large single copy (LSC) region of 88,409 bp, a small single copy (SSC) region of 17,448 bp, and a pair of inverted repeat (IRa/IRb) regions of 25,550 bp. The whole genome contains 132 unique genes, including 85 protein-coding genes, 38 tRNA genes, eight rRNA genes and one pseudogene. 87 simple sequence repeats (SSRs) were identified, and most of them were found to be composed of A/T. In addition, 22,923 codons were detected in 78 protein-coding genes of E. tianmenshanensis, and the overall codon bias pattern in the genome tended to use A/U ending codons. Phylogenetic analysis demonstrated that all the Epimedium species formed a monophyletic clade, and E. tianmenshanensis had the closest relationship to E. dolichostemon. The results of this study provided useful molecular information about the evolution and molecular biology of E. tianmenshanensis.

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Availability of data

The DNA sequences was submitted to GenBank under the accession number MT028488.

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Acknowledgements

This work was supported by Special project of “National Chinese materia medica (CMM) resources survey” ([2017] 66), Key project at central government level: The ability establishment of sustainable use for valuable Chinese medicine resources (2060302), “Double First-Class” University project (CPU2018GY11) and National Natural Science Foundation of China (81660639).

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Authors and Affiliations

  1. Institute of Chinese Materia Medica, Hunan Academy of Chinese Medicine, Changsha, 410013, China

    Hao Liu, Shuihan Zhang, Jian Jin & Xuejuan Liang

  2. School of Traditional Chinese Medicine, China Pharmaceutical University, Nanjing, 211198, China

    Bing Huang & Long Wang

  3. School of Pharmacy, Gannan Medical University, Ganzhou, 341000, China

    Haibo Hu

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  1. Hao Liu
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  2. Haibo Hu
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  3. Shuihan Zhang
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  4. Jian Jin
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  5. Xuejuan Liang
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  6. Bing Huang
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  7. Long Wang
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Contributions

HL conceived and designed the study; HH reviewed draft of the manuscript; JJ and SZ analyzed the data; BH and XL performed the experiments; LW performed the experiments, analyzed the data and wrote the manuscript.

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Correspondence to Long Wang.

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Liu, H., Hu, H., Zhang, S. et al. The complete chloroplast genome of the rare species Epimedium tianmenshanensis and comparative analysis with related species. Physiol Mol Biol Plants 26, 2075–2083 (2020). https://doi.org/10.1007/s12298-020-00882-3

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  • DOI: https://doi.org/10.1007/s12298-020-00882-3

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