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.
Highlights
Mangroves grow on the intertidal zone of the ocean, the transition zone connecting the land and ocean
The true mangroves exclusively live in mangrove ecosystems and usually have distinct marine environment adaptations, including the ability to grow in seawater, complex root structures, and viviparous reproduction [4]
Using a reference genomebased strategy, a total of 483 Mb chloroplast data were generated for 14 mangrove species in six orders: 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)
Summary
Mangroves grow on the intertidal zone of the ocean, the transition zone connecting the land and ocean. Mangrove ecosystems provide essential habitats for marine creatures and benthic organisms and play important roles in regulating energy cycle and maintaining biodiversity [1, 2]. According to their habitats, root morphology, and salt metabolism patterns, mangroves are generally categorized into true mangroves and mangrove associates (or semi-mangroves) [3]. Semi-mangroves are amphibious, and many can inhabit both terrestrial and aquatic environments (for instance, Pongamia pinnata (L.) Pierre) In mangrove ecosystems, they may grow at the edge of the true mangroves and are often dominant species on degraded beaches
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