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Complete Chloroplast Genomes of 14 Mangroves: Phylogenetic and Comparative Genomic Analyses
Shi,Chengcheng1,2; Han,Kai2; Li,Liangwei2; Seim,Inge3,4; Lee,Simon Ming Yuen5; Xu,Xun2,6,7; Yang,Huanming1,6; Fan,Guangyi2,5,6; Liu,Xin2,6,7,8
2020-05-06
Source PublicationBiomed Research International
ISSN2314-6133
Volume2020Pages:8731857
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, 25.8 kb), one large single-copy region (LSC, 89.0 kb), and one short single-copy region (SSC, 18.9 kb) as well as 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.

DOI10.1155/2020/8731857
URLView the original
Indexed BySCIE
Language英語English
WOS Research AreaBiotechnology & Applied Microbiology ; Research & Experimental Medicine
WOS SubjectBiotechnology & Applied Microbiology ; Medicine, Research & Experimental
WOS IDWOS:000536803200003
PublisherHINDAWI LTDADAM HOUSE, 3RD FLR, 1 FITZROY SQ, LONDON W1T 5HF, ENGLAND
Scopus ID2-s2.0-85085278840
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Citation statistics
Document TypeJournal article
CollectionInstitute of Chinese Medical Sciences
THE STATE KEY LABORATORY OF QUALITY RESEARCH IN CHINESE MEDICINE (UNIVERSITY OF MACAU)
Corresponding AuthorLiu,Xin
Affiliation1.School of Future Technology,University of Chinese Academy of Sciences,Beijing,101408,China
2.BGI-Qingdao,BGI-Shenzhen,Qingdao,266555,China
3.Integrative Biology Laboratory,Nanjing Normal University,Nanjing,210046,China
4.Comparative and Endocrine Biology Laboratory,Translational Research Institute-Institute of Health and Biomedical Innovation,School of Biomedical Sciences,Queensland University of Technology,Woolloongabba,4102,Australia
5.State Key Laboratory of Quality Research in Chinese Medicine,Institute of Chinese Medical Sciences,University of Macau,Macao
6.BGI-Shenzhen,Shenzhen,518083,China
7.China National GeneBank,BGI-Shenzhen,Shenzhen,518120,China
8.State Key Laboratory of Agricultural Genomics,BGI-Shenzhen,Shenzhen,518083,China
Recommended Citation
GB/T 7714
Shi,Chengcheng,Han,Kai,Li,Liangwei,et al. Complete Chloroplast Genomes of 14 Mangroves: Phylogenetic and Comparative Genomic Analyses[J]. Biomed Research International, 2020, 2020, 8731857.
APA Shi,Chengcheng., Han,Kai., Li,Liangwei., Seim,Inge., Lee,Simon Ming Yuen., Xu,Xun., Yang,Huanming., Fan,Guangyi., & Liu,Xin (2020). Complete Chloroplast Genomes of 14 Mangroves: Phylogenetic and Comparative Genomic Analyses. Biomed Research International, 2020, 8731857.
MLA Shi,Chengcheng,et al."Complete Chloroplast Genomes of 14 Mangroves: Phylogenetic and Comparative Genomic Analyses".Biomed Research International 2020(2020):8731857.
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