Chloroplast genome sequencing is becoming a valuable process for developing several DNA barcodes. At present, plastid DNA barcode for systematics and evolution in flowering plant rely heavily on the use of non-coding genes. The present study was performed to verify the novelty and suitability of the two hotspot barcode plastid coding gene ycf1 and ndhF, to estimate the rate of molecular evolution in the Prunus genus at low taxonomic levels. Here, 25 chloroplast genomes of Prunus genus were selected for sequences annotation to search for the highly variable coding DNA barcode regions. Among them, 5 genera were of our own data, including the ornamental, cultivated, and wild haplotype, while 20 genera have been downloaded from the GenBank database. The results indicated that the two hotspot plastid gene ycf1 and ndhF were the most variable regions within the coding genes in Prunus with an average of 3268 to 3416 bp in length, which have been predicted to have the highest nucleotide diversity, with the overall transition/transversion bias (R = 1.06). The ycf1-ndhF structural domains showed a positive trend evident in structure variation among the 25 specimens tested, due to the variant overlap’s gene annotation and insertion or deletion with a broad trend of the full form of IGS sequence. As a result, the principal component analysis (PCA) and the ML tree data drew an accurate monophyletic annotations cluster in Prunus species, offering unambiguous identification without overlapping groups between peach, almond, and cherry. To this end, we put forward the domain of the two-locus ycf1-ndhF genes as the most promising coding plastid DNA barcode in P. persica at low taxonomic levels. We believe that the discovering of further variable loci with high evolutionary rates is extremely useful and potential uses as a DNA barcode in P. persica for further phylogeny study and species identification.

中文翻译：

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ycf1-ndhF基因是最有前途的质体基因组条形码，它在桃李的低分类学水平上揭示了系统发育。

叶绿体基因组测序正在成为开发几种DNA条形码的有价值的过程。目前，用于开花植物系统化和进化的质体DNA条形码在很大程度上依赖于非编码基因的使用。进行本研究是为了验证两个热点条形码质体编码基因ycf1和ndhF的新颖性和适用性，以估计低分类学水平下李属中的分子进化速率。在这里，选择李属的25个叶绿体基因组进行序列注释，以搜索高度可变的编码DNA条码区域。其中有5个属属于我们自己的数据，包括观赏，栽培和野生单倍体，而20个属已从GenBank数据库中下载。结果表明，两个质体质点基因ycf1和ndhF是李属编码基因内变化最大的区域，平均长度为3268至3416 bp，据预测它们具有最高的核苷酸多样性，且总体过渡/颠倒偏差（R = 1.06）。ycf1-ndhF结构域在测试的25个样本中显示出结构变异中的明显正趋势，这是由于变异重叠的基因注释以及具有完整IGS序列形式的广泛趋势的插入或缺失。结果，主成分分析（PCA）和ML树数据在李属物种中绘制了准确的单系统注释簇，从而提供了明确的标识，而桃，杏仁和樱桃之间没有重叠的组。为此，我们提出了两基因座ycf1-ndhF基因的结构域，作为低分类学水平下桃蚜的最有希望的编码质体DNA条码。我们认为，发现具有高进化速率的进一步可变位点是非常有用的，并且可以作为多年生斑潜蝇中的DNA条码用于进一步的系统发育研究和物种鉴定。