Comparative Analysis and Phylogenetic Relationships of Ceriops Species (Rhizophoraceae) and Avicennia lanata (Acanthaceae): Insight into the Chloroplast Genome Evolution between Middle and Seaward Zones of Mangrove Forests

Simple Summary We sequenced the complete chloroplast genomes of three Ceriops species (C. decandra, C. zippeliana, and C. tagal) and Avicennia lanata and performed comparative analyses among them. All chloroplast genomes have a circular quadripartite structure containing LSC, SSC, and two IR regions. The rpl32 gene was lost in C. zippeliana, and the infA gene was present in only A. lanata. Comparative genome analysis showed that the IR contraction or expansion events resulted in the differentiation of three genes and pseudogenes. Additionally, repeats and SSRs were identified and compared among them and other relative mangrove species. The phylogenetic analysis strongly supports that C. decandra is evolutionarily closer to C. zippeliana and A. lanata is closer to A. marina. In addition, two primer pairs were developed for species identification unique to the three Ceriops species. Ceriops and Avicennia are true mangroves in the middle and seaward zones of mangrove forests, respectively. The chloroplast genomes of Ceriops decandra, Ceriops zippeliana, and Ceriops tagal were assembled into lengths of 166,650, 166,083 and 164,432 bp, respectively, whereas Avicennia lanata was 148,264 bp in length. The gene content and gene order are highly conserved among these species. The chloroplast genome contains 125 genes in A. lanata and 129 genes in Ceriops species. Three duplicate genes (rpl2, rpl23, and trnM-CAU) were found in the IR regions of the three Ceriops species, resulting in expansion of the IR regions. The rpl32 gene was lost in C. zippeliana, whereas the infA gene was present in A. lanata. Short repeats (<40 bp) and a lower number of SSRs were found in A. lanata but not in Ceriops species. The phylogenetic analysis supports that all Ceriops species are clustered in Rhizophoraceae and A. lanata is in Acanthaceae. In a search for genes under selective pressures of coastal environments, the rps7 gene was under positive selection compared with non-mangrove species. Finally, two specific primer sets were developed for species identification of the three Ceriops species. Thus, this finding provides insightful genetic information for evolutionary relationships and molecular markers in Ceriops and Avicennia species.