Complete chloroplast genome sequences of five species (Rhizophoraceae): comparative analysis and phylogenetic relationships.

is a genus of true mangroves that are mostly distributed in the Indo-West Pacific region. However, the number of published whole chloroplast genome sequences of species are limited. Here, the complete chloroplast sequences of five species were sequenced and assembled using Illumina data. The chloroplast genomes of , , and were assembled into 161,195, 164,295, 164,297, 163,228 and 164,170 bp, respectively. All chloroplast genomes contain 37 tRNA and eight rRNA genes, with either 84 or 85 protein-coding genes. A comparative analysis of these genomes revealed high similarity in gene structure, gene order and boundary position of the LSC, SSC and two IR regions. Interestingly, lost a gene in the SSC region. In addition, a gene in straddles both the SSC and IRB boundary regions. These genes reveal differences in chloroplast evolution among species. Repeats and SSRs in the chloroplast genome sequences were found to be highly conserved between and as well as and indicating close genetic relationships based on maternal inheritance. Notably, , which is considered a hybrid between and , appears to have inherited the chloroplast from . Investigating the effects of selection events on shared protein-coding genes showed a positive selection in and genes in all species compared to land-plant species. A phylogenetic analysis, based on 59 conserved chloroplast protein-coding genes, showed strong support that all species are in the clade Rhizophoraceae. This study provides valuable genetic information for the study of evolutionary relationships and population genetics in and other mangrove species.