Yang Mingliu, Han Nanyu, Li Heng, Meng Lihua
Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals-Plants in Southwest Mountain Ecosystem of University in Yunnan Province, School of Life Sciences Yunnan Normal University, Kunming, P. R. China.
Economic and Management, Luoyang Institute of Science and Technology, Luoyang, P. R. China.
Evol Bioinform Online. 2018 Jul 25;14:1176934318790263. doi: 10.1177/1176934318790263. eCollection 2018.
is a popular Chinese medicinal herb that is used to treat jaundice disease and virus hepatitis, and its wild populations have been reduced significantly due to overharvesting recently. However, effective conservation could not be implemented because of the lack of genomic information and genetic markers. In this study, a de novo transcriptome of was sequenced using the NGS Illumina, and 132 695 unigenes with the length >200 bp (base pairs) were obtained. Among them, a total of 32 109 unigenes were scanned to develop simple sequence repeats (SSRs). Based on NCBI (National Center for Biotechnology Information) nonredundant database (Nr), these SSR sequences were annotated and assigned into gene ontology categories. In addition, we designed 126 pairs of SSR primers for polymerase chain reaction amplification, of which 12 pairs were identified to be polymorphic among 40 individuals from 8 populations. We then used the 12 polymorphic SSRs to construct a UPGMA dendrogram of the 40 individuals. In addition, a significant correlation between the genetic relationship and the geographic distance was found, suggesting a phylogeographic structure in . Moreover, 2 of these SSRs were also successfully amplified in a related species , suggesting their cross-species transferability. Generally, the SSR markers with high polymorphisms identified in this study provide valuable genetic resources and represent an initial step for exploring the genetic diversity and population histories of and its related species.
是一种常用的中草药，用于治疗黄疸病和病毒性肝炎，由于近期过度采收，其野生种群数量已大幅减少。然而，由于缺乏基因组信息和遗传标记，无法实施有效的保护措施。在本研究中，使用Illumina二代测序技术对的转录组进行了从头测序，共获得132695条长度大于200bp（碱基对）的单基因。其中，共筛选出32109条单基因用于开发简单序列重复序列（SSR）。基于美国国立生物技术信息中心（NCBI）的非冗余数据库（Nr），对这些SSR序列进行注释并归类到基因本体论类别中。此外，我们设计了126对用于聚合酶链反应扩增的SSR引物，其中12对在来自8个种群的40个个体中被鉴定为具有多态性。然后，我们使用这12个多态性SSR构建了40个个体的UPGMA聚类图。此外，发现遗传关系与地理距离之间存在显著相关性，表明中存在系统发育地理结构。此外，其中2个SSR在一个近缘物种中也成功扩增，表明它们具有跨物种转移性。总体而言，本研究中鉴定出的具有高度多态性的SSR标记提供了有价值的遗传资源，是探索及其近缘物种遗传多样性和种群历史的第一步。
