Organization, Phylogenetic Marker Exploitation, and Gene Evolution in the Plastome of Thalictrum (Ranunculaceae)

Abstract

<i>Thalictrum</i> is a phylogenetically and economically important genus in the family Ranunculaceae, but is also regarded as one of the most challengingly difficult in plants for resolving the taxonomical and phylogenetical relationships of constituent taxa within this genus. Here, we sequenced the complete plastid genomes of two <i>Thalictrum</i> species using Illumina sequencing technology <i>via de novo</i> assembly. The two <i>Thalictrum</i> plastomes exhibited circular and typical quadripartite structure that was rather conserved in overall structure and the synteny of gene order. By updating the previously reported plastome annotation of other nine <i>Thalictrum</i> species, we found that the expansion or contraction of the inverted repeat region affect the boundary of the single-copy regions in <i>Thalictrum</i> plastome. We identified eight highly variable noncoding regions-<i>infA-rps8</i>, <i>ccsA-ndhD</i>, <i>trnS^UGA-psbZ</i>, <i>trnH^GUG-psbA</i>, <i>rpl16-rps3</i>, <i>ndhG-ndhI</i>, <i>ndhD-psaC</i>, and <i>ndhJ-ndhK</i>-that can be further used for molecular identification, phylogenetic, and phylogeographic in different species. Selective pressure and codon usage bias of all the plastid coding genes were also analyzed for the 11 species. Phylogenetic relationships showed <i>Thalictrum</i> is monophyly and divided into two major clades based on 11 <i>Thalictrum</i> plastomes. The availability of these plastomes offers valuable genetic information for accurate identification of species and taxonomy, phylogenetic resolution, and evolutionary studies of <i>Thalictrum</i>, and should assist with exploration and utilization of <i>Thalictrum</i> plants.