Molecular evolution and SSRs analysis based on the chloroplast genome of .

Chloroplast genome sequences have been used to understand evolutionary events and to infer efficiently phylogenetic relationships. (Cupressaceae) is an endemic species in China. Its phylogenetic position is controversial due to morphological characters similar to those of , and . This study used next-generation sequencing technology to sequence the complete chloroplast genome of and then constructed the phylogenetic relationship between and its related species based on a variety of data sets and methods. Simple sequence repeats (SSRs) and adaptive evolution analysis were also conducted. Our results showed that the monophyletic branch consisting of and is a sister to while is not monophyletic; and are nested in turn at the base of the monophyletic group . The statistical results of SSRs supported the closest relationship between and . By performing adaptive evolution analysis under the phylogenetic background of Cupressales, the Branch model detected three genes and the Site model detected 10 genes under positive selection; and the Branch-Site model uncovered that A has experienced positive selection in the branch. Molecular analysis from the chloroplast genome highly supported that is at the base of . Of note, SSR features were found to be able to shed some light on phylogenetic relationships. In short, this chloroplast genomic study has provided new insights into the phylogeny of and revealed multiple chloroplast genes possibly undergoing adaptive evolution.