Exploring the chloroplast genomics, comparative analysis, evolution, and phylogenetic relationships of Phylica pubescens (Rhamnaceae) in the Cape Flora

被引：0

作者：

Shi, Wenbo ^{[1
]}

Huang, Yahui ^{[1
]}

Hu, Siqi ^{[1
]}

Wang, Huan ^{[1
]}

Lin, Qianhui ^{[1
]}

Zhang, Zirui ^{[1
]}

Shi, Chao ^{[1
,2
]}

Wang, Shuo ^{[1
]}

机构：

[1] Qingdao Univ Sci & Technol, Coll Marine Sci & Biol Engn, Qingdao 266042, Peoples R China

[2] Chinese Acad Sci, Plant Germplasm & Genom Ctr, Germplasm Bank Wild Species Southwest China, Kunming Inst Bot, Kunming 650204, Peoples R China

来源：

SOUTH AFRICAN JOURNAL OF BOTANY | 2024年 / 164卷

基金：

中国国家自然科学基金;

关键词：

Phylica pubescens; Chloroplast genome; Comparative analysis; Evolution; Phylogenetic analysis; TRNL-F; SEQUENCE; DNA; TOOLS; ORGANIZATION; ANNOTATION; ALIGNMENT; HISTORY; NUCLEAR; PLANTS;

D O I：

10.1016/j.sajb.2023.11.051

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

Phylica (Rhamnaceae) plants are mainly distributed in southern Africa and nearby islands. They play a crucial role in studying diversification rates, climate change, and vegetation evolution in the Cape Flora. However, there have been no reports on the complete chloroplast genome of Phylica species, which is essential for investigating evolution and phylogenetic relationships. Herein, we sequenced the complete chloroplast genome of Phylica pubescens and conducted a comparative analysis with 12 Rhamnaceae species. The chloro-plast genome size of Phylica pubescens was 161,187 bp, similar to that of other Rhamnaceae species. The absence of infA and psbL genes in certain Rhamnaceae species, compared to Phylica pubescens, has no appar-ent impact on these species. Positive selection has been observed in the rpl32, psbK, and psbH genes of Rham-naceae species. Some highly variable regions (trnH-GUG-psbA, trnK-UUU-rps16, rps16-trnQ-UUG, trnS- GCU-trnG-UCC, trnR-UCU-atpA, atpH-atpI, trnC-GCA-petN, trnT-GGU-psbD, psbZ-trnG-GCC, trnT- UGU-trnL-UAA, ndhC-trnV-UAC, accD-psaI, petA-psbJ, ndhF-rpl32, and rpl32-trnL-UAG) were identified, which might be useful for phylogenetic analysis. Based on complete chloroplast genomes for the greatest number of species, the phylogenetic tree of the Rhamnaceae was reconstructed. Phylica pubescens displayed a close phylogenetic relationship with Spyridium species. This study provides valuable information regarding the complete chloroplast genome of Phylica pubescens and its comparative analysis with other Rhamnaceae species. These findings enhance our knowledge of the evolution within the Rhamnaceae family and shed light on the relationships between Phylica pubescens and closely related taxa.(c) 2023 SAAB. Published by Elsevier B.V. All rights reserved.

引用

页码：374 / 385

页数：12