Interspecific variation and phylogenetic relationship between mangrove and non-mangrove species of a same family (Meliaceae)-insights from comparative analysis of complete chloroplast genome.

The mahogany family, Meliaceae, contains 58 genera with only one mangrove genus: . Two of the three species of the genus are true mangroves ( and ), and one is a non-mangrove (). In order to resolve the phylogenetic relationship between the mangrove and non-mangrove species, we sequenced chloroplast genomes of these species along with two non-mangrove species of the Meliaceae family ( and ) and compared the genome features and variations across the five species. The five Meliaceae species shared 130 genes (85 protein-coding genes, 37 tRNA, and eight rRNA) with identical direction and order, with a few variations in genes and intergenic spacers. The repetitive sequences identified in gene region only occurred in , while the repetitive sequences in were found in and . The and gene regions and four non-coding gene regions showed high variabilities between and the two non-mangrove species ( and ). In addition, among the species, only two genes ( and ) showed positive selection. and owned unique RNA editing sites. The above genes played an important role in acclimation to different stress factors like heat, low temperature, high UV light, and high salinity. Phylogenetic analysis with 22 species in the order Sapindales supported previous studies, which revealed that the non-mangrove species is closer to than . Overall, our results provided important insights into the variation of genetic structure and adaptation mechanism at interspecific (three species) and intergeneric (mangrove and non-mangrove genera) levels.