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Chloroplast Genome Analysis of Two Medicinal Coelogyne spp. (Orchidaceae) Shed Light on the Genetic Information, Comparative Genomics, and Species Identification
Plants ( IF 4.658 ) Pub Date : 2020-10-09 , DOI: 10.3390/plants9101332
Kai Jiang , Li-Yuan Miao , Zheng-Wei Wang , Zi-Yi Ni , Chao Hu , Xin-Hua Zeng , Wei-Chang Huang

Although the medicinal properties of Coelogyne spp. have been previously studied, there is little genomic information providing a valuable tool for the plant taxonomy, conservation, and utilization of this genus. This study used the next-generation MiSeq sequencing platform to characterize the chloroplast (cp) genomes of Coelogyne fimbriata and Coelogyne ovalis. The Maximum Likelihood (ML) and Bayesian (BI) methods were employed to confirm the phylogenetic position of two Coelogyne species based on the whole chloroplast genome sequences. Additionally, we developed eight new primers based on the two cp genomes’ medium variable regions and evaluated the transferability to another 16 Coelogyne species. We constructed phylogenetic trees including 18 Coelogyne species and four outgroup species using the chloroplast fragments with the ML method. Our results showed that the cp genomes of C. fimbriata and C. ovalis contained a small single-copy region (18,839 and 18,851 bp, respectively) and a large single-copy region (87,606 and 87,759 bp, respectively), separated by two same-length inverted-repeat regions (26,675 bp in C. fimbriata and 26,715 bp C. ovalis, respectively). They all contained 86 protein-coding genes, 38 tRNA genes, and eight rRNA genes, revealing strong structure and gene content similarities. The phylogenetic analysis indicated a close relationship between the genera Coelogyne and Pleione. The newly developed primers revealed good transferability among the Coelogyne taxa and provided enough variable sites to distinguish C. fimbriata and C. ovalis. The two complete cp genomes and the eight new primers of Coelogyne provide new genomic data for further studies on phylogenomics, population genetics, and evolutionary history of Coelogyne taxa.

中文翻译:

两种药用Coelogyne spp的叶绿体基因组分析。(兰科)揭示遗传信息,比较基因组学和物种鉴定

虽然Coelogyne spp的药用特性。以前已经研究过,几乎没有基因组信息可为该属的植物分类学,保存和利用提供有价值的工具。本研究采用 新一代MiSeq测序平台表征的叶绿体(CP)的基因组贝母兰属贝母兰属卵圆。基于整个叶绿体基因组序列,采用最大似然法(ML)和贝叶斯(BI)方法来确定两个Coelogyne物种的系统发生位置。此外,我们基于两个cp基因组的中等可变区开发了八种新引物,并评估了向其他16种的转移性 Coelogyne物种。我们使用叶绿体片段和ML方法构建了包括18个Coelogyne物种和4个外群物种的系统发育树。我们的结果表明的CP基因组C.黑斑病C.卵圆包含一个小的单拷贝区(18839和18851碱基对,分别地)和大的单拷贝区(87606和87759碱基对,分别地),由两个相同的分离长度的反向重复区(C. fimbriata中为26,675 bp,卵圆中为26,715 bp, 分别)。它们都包含86个蛋白质编码基因,38个tRNA基因和8个rRNA基因,显示出很强的结构和基因含量相似性。系统发育分析表明,Coelogyne属和Pleione属之间有密切的关系。新开发的引物揭示了Coelogyne类群之间的良好转移能力,并提供了足够的可变位点来区分C. fimbriataC.卵形Coelogyne的两个完整的cp基因组和八种新引物为 进一步研究Coelogyne类群的系统遗传学,种群遗传学和进化史提供了新的基因组数据。
更新日期:2020-10-11
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