College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
Molecules. 2018 Nov 8;23(11):2917. doi: 10.3390/molecules23112917.
belongs to the genus (Rosaceae) and is an indigenous wild crabapple of China. This species has received more and more attention, due to its important medicinal, and excellent ornamental and economical, values. In this study, the whole chloroplast (cp) genome of , using a Hiseq X Ten sequencing platform, is reported. The cp genome is 160,065 bp in size, containing a large single copy region (LSC) of 88,166 bp and a small single copy region (SSC) of 19,193 bp, separated by a pair of inverted repeats (IRs) of 26,353 bp. It contains 112 genes, including 78 protein-coding genes (PCGs), 30 transfer RNA genes (tRNAs), and four ribosomal RNA genes (rRNAs). The overall nucleotide composition is 36.6% CG. A total of 96 simple sequence repeats (SSRs) were identified, most of them were found to be mononucleotide repeats composed of A/T. In addition, a total of 49 long repeats were identified, including 24 forward repeats, 21 palindromic repeats, and four reverse repeats. Comparisons of the IR boundaries of nine complete chloroplast genomes presented slight variations at IR/SC boundaries regions. A phylogenetic analysis, based on 26 chloroplast genomes using the maximum likelihood (ML) method, indicates that clustered closer ties with , , and than with . The availability of the complete chloroplast genome using genomics methods is reported here and provides reliable genetic information for future exploration on the taxonomy and phylogenetic evolution of the and related species.
属于蔷薇科苹果属，是中国本土的野生海棠。由于其重要的药用、极佳的观赏和经济价值，该物种受到了越来越多的关注。本研究利用 Hiseq X Ten 测序平台报道了 的全叶绿体（cp）基因组。该 cp 基因组大小为 160065bp，包含一个长的单一拷贝区（LSC）为 88166bp 和一个小的单一拷贝区（SSC）为 19193bp，由一对 26353bp 的反向重复（IR）隔开。它包含 112 个基因，包括 78 个蛋白质编码基因（PCGs）、30 个转移 RNA 基因（tRNAs）和 4 个核糖体 RNA 基因（rRNAs）。总的核苷酸组成是 36.6%的 CG。总共鉴定出 96 个简单重复序列（SSRs），其中大多数是由 A/T 组成的单核苷酸重复。此外，共鉴定出 49 个长重复序列，包括 24 个正向重复序列、21 个回文重复序列和 4 个反向重复序列。对 9 个苹果属完整叶绿体基因组的 IR 边界比较表明，IR/SC 边界区域的边界略有变化。基于 26 个叶绿体基因组，采用最大似然（ML）法的系统发育分析表明， 与 、 、 聚类关系较近，而与 聚类关系较远。本研究采用基因组学方法获得了完整的叶绿体基因组，为今后对 属及相关物种的分类学和系统发育进化的研究提供了可靠的遗传信息。
