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Authors Shi, CC; Han, K; Li, LW; Seim, I; Lee, SMY; Xu, X; Yang, HM; Fan, GY; Liu, X
Author Full Name Shi, Chengcheng; Han, Kai; Li, Liangwei; Seim, Inge; Lee, Simon Ming-Yuen; Xu, Xun; Yang, Huanming; Fan, Guangyi; Liu, Xin
Title Complete Chloroplast Genomes of 14 Mangroves: Phylogenetic and Comparative Genomic Analyses
Source BIOMED RESEARCH INTERNATIONAL
Language English
Document Type Article
Keywords Plus SEQUENCE; EVOLUTION; DIVERSITY; DYNAMICS; GENES; DNA
Abstract Mangroves are a group of plant species that occupy the coastal intertidal zone and are major components of this ecologically important ecosystem. Mangroves belong to about twenty diverse families. Here, we sequenced and assembled chloroplast genomes of 14 mangrove species from eight families spanning five rosid orders and one asterid order: Fabales (Pongamia pinnata), Lamiales (Avicennia marina), Malpighiales (Excoecaria agallocha, Bruguiera sexangula, Kandelia obovata, Rhizophora stylosa, and Ceriops tagal), Malvales (Hibiscus tiliaceus, Heritiera littoralis, and Thespesia populnea), Myrtales (Laguncularia racemosa, Sonneratia ovata, and Pemphis acidula), and Sapindales (Xylocarpus moluccensis). These chloroplast genomes range from 149 kb to 168 kb in length. A conserved structure of two inverted repeats (IRa and IRb, similar to 25.8 kb), one large single-copy region (LSC, similar to 89.0 kb), and one short single-copy region (SSC, similar to 18.9 kb) as well as similar to 130 genes (85 protein-coding, 37 tRNAs, and 8 rRNAs) was observed. We found the lowest divergence in the IR regions among the four regions. We also identified simple sequence repeats (SSRs), which were found to be variable in numbers. Most chloroplast genes are highly conserved, with only four genes under positive selection or relaxed pressure. Combined with publicly available chloroplast genomes, we carried out phylogenetic analysis and confirmed the previously reported phylogeny within rosids, including the positioning of obscure families in Malpighiales. Our study reports 14 mangrove chloroplast genomes and illustrates their genome features and evolution.
Author Address [Shi, Chengcheng; Yang, Huanming] Univ Chinese Acad Sci, Sch Future Technol, Beijing 101408, Peoples R China; [Shi, Chengcheng; Han, Kai; Li, Liangwei; Xu, Xun; Fan, Guangyi; Liu, Xin] BGI Shenzhen, BGI Qingdao, Qingdao 266555, Peoples R China; [Seim, Inge] Nanjing Normal Univ, Integrat Biol Lab, Nanjing 210046, Peoples R China; [Seim, Inge] Queensland Univ Technol, Sch Biomed Sci, Inst Hlth & Biomed Innovat, Comparat & Endocrine Biol Lab,Translat Res Inst, Woolloongabba, Qld 4102, Australia; [Lee, Simon Ming-Yuen; Fan, Guangyi] Univ Macau, Inst Chinese Med Sci, State Key Lab Qual Res Chinese Med, Macau, Peoples R China; [Xu, Xun; Yang, Huanming; Fan, Guangyi; Liu, Xin] BGI Shenzhen, Shenzhen 518083, Peoples R China; [Liu, Xin] BGI Shenzhen, China Natl GeneBank, Shenzhen 518120, Peoples R China; [Liu, Xin] BGI Shenzhen, State Key Lab Agr Genom, Shenzhen 518083, Peoples R China
Reprint Address Fan, GY; Liu, X (corresponding author), BGI Shenzhen, BGI Qingdao, Qingdao 266555, Peoples R China.; Fan, GY (corresponding author), Univ Macau, Inst Chinese Med Sci, State Key Lab Qual Res Chinese Med, Macau, Peoples R China.; Fan, GY; Liu, X (corresponding author), BGI Shenzhen, Shenzhen 518083, Peoples R China.; Liu, X (corresponding author), BGI Shenzhen, China Natl GeneBank, Shenzhen 518120, Peoples R China.; Liu, X (corresponding author), BGI Shenzhen, State Key Lab Agr Genom, Shenzhen 518083, Peoples R China.
E-mail Address shichengcheng@genomics.cn; hankai@genomics.cn; liliangwei@genomics.cn; inge@seimlab.org; simonlee@um.edu.mo; xuxun@genomics.cn; yanghm@genomics.cn; fanguangyi@genomics.cn; liuxin@genomics.cn
ORCID Number Liu, Xin/0000-0003-3256-2940
Funding Agency and Grant Number National Key Research and Development Program of China [2016YFE0122000]
Funding Text This study was supported by the National Key Research and Development Program of China (No. 2016YFE0122000). We sincerely thank Professor Suhua Shi and Dr. Sen Li from Sun Yat-sen University for their help in providing samples.
Times Cited 1
Total Times Cited Count (WoS, BCI, and CSCD) 1
Publisher HINDAWI LTD
Publisher City LONDON
Publisher Address ADAM HOUSE, 3RD FLR, 1 FITZROY SQ, LONDON, W1T 5HF, ENGLAND
ISSN 2314-6133
29-Character Source Abbreviation BIOMED RES INT
ISO Source Abbreviation Biomed Res. Int.
Publication Date MAY 6
Year Published 2020
Volume 2020
Article Number 8731857
Digital Object Identifier (DOI) 10.1155/2020/8731857
Page Count 13
Web of Science Category Biotechnology & Applied Microbiology; Medicine, Research & Experimental
Subject Category Biotechnology & Applied Microbiology; Research & Experimental Medicine
Document Delivery Number LT0YV
Unique Article Identifier WOS:000536803200003
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