The complete chloroplast genome sequence of Vincetoxicum mongolicum (Apocynaceae), a perennial medicinal herb

Abstract Vincetoxicum mongolicum Maxim. (1876), is a perennial medicinal herb, widely distributed in the Loess Plateau of China. Here, we sequenced, assembled, and annotated the complete chloroplast (cp) genome of V. mongolicum, and compared the highly variable gene regions and phylogenetic positions between V. mongolicum and other related species. Results showed that the complete cp genome of V. mongolicum was 160,157 bp in length, containing a large single copy (LSC) region of 91,263 bp, a pair of inverted repeats (IR) region of 23,892 bp, and a small single copy (SSC) region of 21,110 bp. The GC content accounts for 37.8%, and we annotated 131 single genes, which include 86 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. By comparing and analyzing the variable region of the cp gene of V. mongolicum and other Vincetoxicum, we found that the variable sequences of rpoC1-rpoB, ycf4-cemA, ndhF, ndhF-rpl32, and rpl32-ccsA fragments were highly significant, which could be targeted as the DNA barcodes for evidence of V. mongolicum and its relatives in Apocynaceae. Maximum-likelihood (ML) phylogenetic tree analysis elucidated that V. mongolicum was sister to V. pycnostelma with strong support. Our results provide useful information for future phylogenetic studies and plastid super-barcodes of the family Apocynaceae.

摘要：蒙古鹅绒藤（Vincetoxicum mongolicum Maxim.，1876）为多年生药用草本植物，广泛分布于中国黄土高原。本研究对该物种的完整叶绿体基因组（chloroplast genome，简称cp基因组）进行了测序、组装与注释，并比较了其与其他近缘物种的高变基因区域及系统发育位置。
结果显示，蒙古鹅绒藤的完整cp基因组全长160157 bp，包含91263 bp的大单拷贝区（large single copy, LSC）、23892 bp的一对反向重复区（inverted repeats, IR）以及21110 bp的小单拷贝区（small single copy, SSC）。其GC含量为37.8%，共注释得到131个单基因，其中包括86个蛋白编码基因、8个核糖体RNA（rRNA）基因以及37个转运RNA（tRNA）基因。
通过对蒙古鹅绒藤与其他鹅绒藤属植物的cp基因可变区域进行比较分析，本研究发现rpoC1-rpoB、ycf4-cemA、ndhF、ndhF-rpl32及rpl32-ccsA片段的可变序列具有高度显著性，可作为DNA条形码（DNA barcodes）用于鉴定蒙古鹅绒藤及其在夹竹桃科（Apocynaceae）中的近缘类群。
最大似然（maximum-likelihood, ML）系统发育树分析表明，蒙古鹅绒藤与V. pycnostelma呈姊妹群，且支持度极高。本研究结果可为未来夹竹桃科的系统发育研究及质体超级条形码研究提供宝贵的参考资料。