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Comparative Analysis of Complete Chloroplast Genomes of Rubus in China: Hypervariable Regions and Phylogenetic Relationships

文献类型： 外文期刊

作者： Xu, Yufen 1 ; Li, Yongquan 1 ; Chen, Yanzhao 1 ; Wang, Longyuan 1 ; Xue, Bine 1 ; Zhang, Xianzhi 1 ; Song, Wenpei 1 ; Guo, Wei 1 ; Wu, Wei 1 ;

作者机构： 1.Zhongkai Univ Agr & Engn, Dept Hort & Landscape Architecture, Guangzhou 510225, Peoples R China

2.Chinese Acad Trop Agr Sci, Coconut Res Inst, Wenchang 571339, Peoples R China

关键词： Rubus; chloroplast genome; phylogeny; mutation hotspot; infrageneric relationship

期刊名称：GENES （ 影响因子：2.8； 五年影响因子：3.3 ）

ISSN：

年卷期： 2024 年 15 卷 6 期

页码：

收录情况： SCI

摘要： 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.

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