Complete Chloroplast Genomes of 14 Mangroves: Phylogenetic and Comparative Genomic Analyses

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.

Figure 1

The Bayesian-inferred phylogenetic tree based on all chloroplast genes of 14 mangroves and 57 land plant species. Mangroves are indicated in red, and the background colors highlight the orders of mangroves and their sister species. Posterior probabilities are indicated near the branches.

Figure 2

Synteny between the chloroplast genomes. The species are shown in the phylogenetic tree with red fonts to indicate the mangrove species, and the synteny is shown by linking the homologous genes. Colors at the bottom indicate genes with different functions.

Figure 3

Pairwise comparisons of mangrove species and their most closely related species. Whole chloroplast genome comparisons are shown on the left, and the corresponding divergences are shown on the right.

Figure 4

Divergence within orders of Malpighiales, Myrtales, Malvales, Lamiales, and Sapindales. The IR regions are shown in grey background, and the average divergences of each region are indicated above the lines in the corresponding regions. Two bars at the bottom show the SNPs and InDels in both the gene regions (red) and the intergenic regions (blue).

Figure 5

Ka/Ks values of protein-coding genes in chloroplasts. Ka/Ks values (horizontal axis) of genes in the mangrove species and their related species in six orders (Lamiales, Fabales, Malpighiales, Malvales, Myrtales, and Sapindales) are indicated. Red dots indicate Ka/Ks values of genes in mangrove species, while blue dots indicate Ka/Ks values in terrestrial species.