PDF(Pubmed)
Abstract：
With more than 200 species of native Rubus, China is considered a center of diversity for this genus. Due to a paucity of molecular markers, the phylogenetic relationships for this genus are poorly understood. In this study, we sequenced and assembled the plastomes of 22 out of 204 Chinese Rubus species (including varieties) from three of the eight sections reported in China, i.e., the sections Chamaebatus, Idaeobatus, and Malachobatus. Plastomes were annotated and comparatively analyzed with the inclusion of two published plastomes. The plastomes of all 24 Rubus species were composed of a large single-copy region (LSC), a small single-copy region (SSC), and a pair of inverted repeat regions (IRs), and ranged in length from 155,464 to 156,506 bp. We identified 112 unique genes, including 79 protein-coding genes, 29 transfer RNAs, and four ribosomal RNAs. With highly consistent gene order, these Rubus plastomes showed strong collinearity, and no significant changes in IR boundaries were noted. Nine divergent hotspots were identified based on nucleotide polymorphism analysis: trnH-psbA, trnK-rps16, rps16-trnQ-psbK, petN-psbM, trnT-trnL, petA-psbJ, rpl16 intron, ndhF-trnL, and ycf1. Based on whole plastome sequences, we obtained a clearer phylogenetic understanding of these Rubus species. All sampled Rubus species formed a monophyletic group; however, sections Idaeobatus and Malachobatus were polyphyletic. These data and analyses demonstrate the phylogenetic utility of plastomes for systematic research within Rubus.
摘要：
有200多种原生的Rubus，中国被认为是该属的多样性中心。由于缺乏分子标记,该属的系统发育关系知之甚少。在这项研究中,我们从中国报告的八个部分中的三个部分中，对204个中国悬钩子物种（包括品种）中的22个进行了测序和组装，即，Chamaebatus部分,Idaeobatus,还有Malachobatus.对浆体进行注释并进行比较分析，其中包括两个已发表的浆体。所有24种Rubus物种的质体都由一个大的单拷贝区域（LSC）组成，一个小的单拷贝区域(SSC)，和一对反向重复区(IRs)，长度从155,464到156,506bp不等。我们确定了112个独特的基因,包括79个蛋白质编码基因，29个转移RNA，和四个核糖体RNA。基因顺序高度一致，这些Rubus质体表现出强烈的共线性，并且没有注意到IR边界的显著变化。根据核苷酸多态性分析确定了九个不同的热点：trnH-psbA，trnK-rps16,rps16-trnQ-psbK,petN-psbM,trnT-trnL,peta-psbJ,rpl16内含子,ndhF-trnL,和ycf1。基于整个质体序列，我们对这些Rubus物种有了更清晰的系统发育理解。所有采样的Rubus物种都形成了单系群；然而，枝叶和枝叶为多系。这些数据和分析证明了质体在Rubus系统研究中的系统发育效用。
