Molecular evolution and SSRs analysis based on the chloroplast genome of<i>Callitropsis funebris</i>

Abstract

Chloroplast genome sequences have been used to understand evolutionary events and to infer efficiently phylogenetic relationships. <i>Callitropsis funebris</i> (Cupressaceae) is an endemic species in China. Its phylogenetic position is controversial due to morphological characters similar to those of <i>Cupressus</i>, <i>Callitropsis,</i> and <i>Chamaecyparis</i>. This study used next-generation sequencing technology to sequence the complete chloroplast genome of <i>Ca. funebris</i> and then constructed the phylogenetic relationship between <i>Ca. funebris</i> 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 <i>Ca. funebris</i> and <i>Cupressus tonkinensis</i> is a sister to <i>Cupressus,</i> while <i>Callitropsis</i> is not monophyletic; <i>Ca. nootkatensis</i> and <i>Ca. vietnamensis</i> are nested in turn at the base of the monophyletic group <i>Hesperocyparis</i>. The statistical results of SSRs supported the closest relationship between <i>Ca. funebris</i> and <i>Cupressus</i>. 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 <i>rpo</i>A has experienced positive selection in the <i>Ca. funebries</i> branch. Molecular analysis from the chloroplast genome highly supported that <i>Ca. funebris</i> is at the base of <i>Cupressus</i>. 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 <i>Ca. funebris</i> and revealed multiple chloroplast genes possibly undergoing adaptive evolution.