Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea.
Genes (Basel). 2019 Jan 3;10(1):23. doi: 10.3390/genes10010023.
Species belonging to section (Rosaceae) are mainly distributed in East Asia, and represent recently diverged lineages within the genus. Over decades, inferring phylogenetic relationships within section have been exceptional challenges, due to short branch lengths and low support values. Of approximately 36 species in the section , , and are widely distributed in the Sino-Japanese floristic region. In this study, we assembled chloroplast genomes of these three species to compare the genomic features within section , and to compare with other infrageneric groups. We found that three sect. species had lost genes with pseudogenization, and they were almost identical to each other. Two protein-coding gene regions ( and ) and five non-coding regions (5'-, --, -, - and -) were identified as being highly informative markers. Within three section chloroplast genomes, 85 simple sequence repeat (SSR) motifs were detected, of which at least 13 motifs were identified to be effective markers. The phylogenetic relationships of , and could not be resolved, even with chloroplast genome-wide data. This study reveals the chloroplast genomic data of sect. , and it provides valuable markers for DNA barcoding and phylogenetic analyses for further studies.
隶属于（蔷薇科）的物种主要分布在东亚，是该属中最近分化的谱系。几十年来，由于分支长度短和支持值低，推断（蔷薇科）内的系统发育关系一直是一个特殊的挑战。在该属中约有 36 个种，、和在中日植物区系中广泛分布。在这项研究中，我们组装了这三个物种的叶绿体基因组，以比较（蔷薇科）内的基因组特征，并与其他亚属群体进行比较。我们发现三个种失去了基因的功能并发生了假基因化，它们彼此之间几乎完全相同。两个蛋白编码基因区域（和）和五个非编码区域（5'-, --, -, - 和 -）被鉴定为高度信息性标记。在三个（蔷薇科）叶绿体基因组中，检测到 85 个简单重复序列（SSR）基序，其中至少有 13 个基序被鉴定为有效标记。即使使用叶绿体全基因组数据，也无法解决、和的系统发育关系。本研究揭示了（蔷薇科）的叶绿体基因组数据，并为进一步研究的 DNA 条形码和系统发育分析提供了有价值的标记。
