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Structural and Comparative Analysis of the Complete Chloroplast Genome of a Mangrove Plant: Scyphiphora hydrophyllacea Gaertn. f. and Related Rubiaceae Species

机译:红树林植物完全叶绿体基因组的结构与对比分析:Scyphiphora hydrophylaclea Gaertn。 F。和相关的Rubiaceae物种

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摘要

Scyphiphora hydrophyllacea Gaertn. f. (Rubiaceae) is an endangered mangrove species found in China, and its only known location is in Hainan Island. Previous studies conducted on S. hydrophyllaceae have mainly focused on its location, biological characteristics, and medical effects. However, to date, there has been no published report regarding the genetics or genome of this endangered mangrove species. In this study, we developed valuable chloroplast genome-related molecular resources of S. hydrophyllaceae by comparing with it related Rubiaceae species. The chloroplast genome of S. hydrophyllaceae was found to be a circular molecule with a total size of 155,132 bp, and it is observed to have a quadripartite structure. The whole chloroplast genome contains 132 genes, of which 88 and 36 are protein-coding and transfer RNA genes, respectively; it also contains four ribosomal RNA genes with an overall GC content of 37.60%. A total of 52 microsatellites were detected in the S. hydrophyllacea chloroplast genome, and microsatellite marker detection identified A/T mononucleotides as majority simple sequence repeats in all nine Rubiaceae chloroplast genomes. Comparative analyses of these nine chloroplast genomes revealed variable regions, including matK, rps16, and atpF. All nine species shared 13 RNA-editing sites distributed across eight coding genes. Phylogenetic analyses based on the complete sequences of the chloroplast genomes revealed that the position of S. hydrophyllaceae is closer to the Coffeeae genus than to Cinchoneae, Naucleeae, Morindeae, and Rubieae in the Rubiaceae family. The genome information reported in this study could find further application in the evolution and population genetic studies, and it helps improve our understanding of the endangered mechanism and the development of conservation strategies of this endangered mangrove plant.
机译:瓶花木冰草。 F。 (茜草科)是中国发现的濒临灭绝的红树林品种,它的唯一已知的位置是海南岛。 S上hydrophyllaceae进行以往的研究主要集中在它的位置,生物学特性,以及医疗效果。然而,迄今为止,一直没有发表关于这一濒危种红树植物的遗传或基因组报告。在这项研究中,我们通过与它相关的茜草科的物种比较发达S. hydrophyllaceae宝贵的叶绿体基因组相关分子的资源。 S. hydrophyllaceae的叶绿体基因组被发现是与155132 bp的总大小的圆形分子,并且可以观察到具有四方结构。整个叶绿体基因组含有132个基因,其中88和36分别是蛋白质编码和转移RNA基因;它也包含了37.60%的总GC 4个内容与核糖体RNA基因。总共52个微卫星在S. hydrophyllacea叶绿体基因组进行检测,和微卫星标记检测鉴定A / T的单核苷酸在所有九个茜草科叶绿体基因组大多数简单序列重复。这九个叶绿体基因组的比较分析显示可变区,包括matK序列,rps16和ATPF。所有九种共享在八个编码基因分布13 RNA编辑位点。基于所述叶绿体基因组的完整序列的系统发育分析表明S. hydrophyllaceae的位置是在茜草科更靠近Coffeeae属比Cinchoneae,Naucleeae,巴戟,和Rubieae。基因组信息,与本研究报告能找到在进化和群体遗传学研究进一步应用程序,它可以帮助我们提高对濒危机制的理解和这一濒危红树植物的保护策略的发展。

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