Avicennia marina Genome sequencing and assembly. Avicennia marina

Avicenna marina is a pioneer mangrove tree which thrives in intertidal environment. It has great ecological significance in maintaining coastal ecosystem, but its unique potential for genetic diversity and phylogenetic relationships underlying ecological adaptation remains investigation. In this study, we characterized the chloroplast genome of A. marina from chloroplast DNA through Illumina sequencing and de novo assembling, which showed a size of 147,909 bp with 112 genes, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The sequence differentiation analysis between A. marina and its related non-mangrove species highlighted that the partly lost ycf2 might account for the IR boundary shift, and gene relocation in A. marina. Besides, 15 most divergent sequences and regions containing accD, ycf2, ndhB, ycf1, atpI-atpH, trnT-psbD, rbcL-accD, accD-ycf4, ycf4-cemA, clpP-rps12, psbH-petB, petB-petD, rps3-rpl16, rpl32-trnL, ndhB-trnL were detected and a total of 158 specific simple sequence repeats (SSRs) were established. These identified SSRs coupled with the hotspot regions can be used as specific molecular markers for future analyzing the maternal lineage distributions and population genetic structures of A. marina. A phylogenetic analysis based on all protein-coding genes confirmed the placement of A. marina within Verbenaceae. Molecular evolution analysis showed that rps7, rps15, psbK, and ycf2 were under selective pressure, implying these genes might play critical roles in the adaptation of A. marina to the harsh intertidal habitat. Taken together, the results provide important resources for further chloroplast derived investigations of A. marina populations, such as its phylogenetics, conservation, photosynthesis, and stress tolerance to environment.