Complete Chloroplast Genomes of 14 Mangroves: Phylogenetic and Comparative Genomic Analyses
| Autor: | Xun Xu, Kai Han, Guangyi Fan, Liangwei Li, Huanming Yang, Xin Liu, Chengcheng Shi, Inge Seim, Simon Ming-Yuen Lee |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
0301 basic medicine Article Subject ved/biology.organism_classification_rank.species Lamiales Excoecaria agallocha 010603 evolutionary biology 01 natural sciences Genome General Biochemistry Genetics and Molecular Biology Evolution Molecular Magnoliopsida 03 medical and health sciences Malvales Phylogenetics Botany Genome Chloroplast Phylogeny General Immunology and Microbiology biology ved/biology Genomics General Medicine biology.organism_classification Pemphis acidula Malpighiales 030104 developmental biology Sonneratia ovata Medicine Research Article |
| Zdroj: | BioMed Research International BioMed Research International, Vol 2020 (2020) |
| ISSN: | 2314-6141 2314-6133 |
| DOI: | 10.1155/2020/8731857 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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