The complete chloroplast genome of the rare species Epimedium tianmenshanensis and comparative analysis with related spe
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RESEARCH ARTICLE
The complete chloroplast genome of the rare species Epimedium tianmenshanensis and comparative analysis with related species Hao Liu1 • Haibo Hu3 • Shuihan Zhang1 • Jian Jin1 • Xuejuan Liang1 Bing Huang2 • Long Wang2
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Received: 1 March 2020 / Revised: 30 August 2020 / Accepted: 7 September 2020 Ó Prof. H.S. Srivastava Foundation for Science and Society 2020
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
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12298-020-00882-3) contains supplementary material, which is available to authorized users. & Long Wang [email protected] 1
Institute of Chinese Materia Medica, Hunan Academy of Chinese Medicine, Changsha 410013, China
2
School of Traditional Chinese Medicine, China Pharmaceutical University, Nanjing 211198, China
3
School of Pharmacy, Gannan Medical University, Ganzhou 341000, China
about the evolution and molecular biology of E. tianmenshanensis. Keywords Chloroplast genome Epimedium Phylogenetic analysis RSCU SSRs
Introduction Epimedii Folium (EF) is one of the most popular Traditional Chinese Medicine (TCM), with a history of more than 2000 years (Zhang et al. 2016). The dried leaves of Epimedium brevicomu, E. sagittatum, E. pubescens and E. koreanum are recorded as the source plants of EF in the 2020 edition of Chinese Pharmacopoeia (Chinese Pharmacopoeia 2020), however, a total of 15 species of Epimedium are common sources of EF in the market (Ma et al. 2011). The aboveground portion of Epimedium can be used for nourishing kidney, reinforcing yang and regulating bone remodeling (Ma et al. 2011; Jiang et al. 2015). As one of the most important genera in Berberidaceae, the Epimedium comprises more than 50 species (Ying et al. 2011). China is the modern geographical distribution center of Epimedium, in which alm
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