Panax plastid genome matrix

Full plastid alignment of 61 Araliaceae plastid genomes. <br><br>Plastome phylogenomics resolves relationships in Panax and identifies markers for molecular identification<br><br>Manzanilla V.1, Kool A. 1, Nguyen Nhat L. 2, Nong Van H. 2, Le Thi Thu H.2§, de Boer H.J.1§<br><br>1. The Natural History Museum, University of Oslo, Oslo, Norway<br>2. Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam<br>§ These authors are co-last authors.<br><br>Abstract<br>The economic value of ginseng in the global medicinal plant trade is estimated to be in excess of US$2.1 billion. At the same time the evolutionary placement of ginseng (Panax ginseng) and the complex evolutionary history of the genus is poorly understood despite several molecular phylogenetic studies. In this study we use a full plastome phylogenomic framework to resolve relationships among Panax genus and to identify molecular markers for species discrimination. We used high-throughput sequencing of MBD2-Fc fractionated Panax DNA to supplement publicly available plastid genomes to create a phylogeny based on fully assembled and annotated plastid genomes from 60 accessions of 8 species. The plastome phylogeny is based on a 163 kbp matrix and resolves the sister relationship of Panax ginseng with P. quinquefolius. The closely related species, P. vietnamensis, described in 1985, is supported as the sister of P. japonicus. The plastome matrix also shows that the markers trnC-rps16, trnS-trnG, and trnE-trnM could be used for unambiguous molecular identification of all the represented species in the genus. MBD2 depletion reduces the cost of plastome sequencing, which makes it a cost-effective alternative to Sanger sequencing based DNA barcoding for molecular identification. The plastome phylogeny provides a robust framework that can be used to study the evolution of morphological characters and biosynthesis pathways of ginsengosides for phylogenetic bioprospecting. Molecular identification of ginseng species is essential for authenticating ginseng in international trade and provides an incentive for manufacturers to create authentic products with verified ingredients.<br>

61份五加科（Araliaceae）质体基因组的完整质体比对序列。

质体基因组（plastome）系统发育组学解析人参属（Panax）系统演化关系并鉴定分子鉴定标记

曼萨尼利亚·V.¹、库尔·A.¹、阮日良²、农文怀²、黎氏秋河²§、德博尔·H.J.¹§

1. 挪威奥斯陆大学自然历史博物馆，奥斯陆，挪威
2. 越南科学技术研究院基因组研究所，越南河内市纸桥郡黄国越路18号

§ 上述作者为共同最后作者。

摘要
全球药用植物贸易中，人参的经济价值据估算超过21亿美元。尽管已有多项分子系统发育研究，但人参（Panax ginseng）的演化位置及其所在属的复杂演化历史仍未得到充分阐明。本研究采用完整质体基因组系统发育组学框架，解析人参属的系统演化关系并鉴定用于物种鉴定的分子标记。我们对经MBD2-Fc分级分离的人参属DNA开展高通量测序，并结合公开获取的质体基因组数据，基于8个物种共60份种质材料的完整组装与注释质体基因组构建系统发育树。该系统发育分析基于长度为163 kbp的矩阵，解析出人参（Panax ginseng）与西洋参（Panax quinquefolius）互为姊妹群的演化关系。1985年定名的近缘种越南人参（Panax vietnamensis）被支持为日本人参（Panax japonicus）的姊妹群。该质体基因组矩阵还显示，trnC-rps16、trnS-trnG及trnE-trnM这3个分子标记可无歧义地鉴定该属所有受试物种。MBD2分级分离技术可降低质体基因组测序成本，使其成为基于Sanger测序（Sanger sequencing）的DNA条形码（DNA barcoding）分子鉴定方法的经济高效替代方案。该质体基因组系统发育框架可为研究人参属形态性状演化及人参皂苷生物合成通路提供可靠支撑，助力系统发育生物勘探。人参属物种的分子鉴定对于国际贸易中的人参真伪核验至关重要，同时也可激励厂商生产成分可溯源的正品人参产品。