The complete chloroplast genome of the C. tangutica (Maxim.) Korsh. and an adaptive evolutionary analysis of the ycf2 gene

Abstract

Clematis. tangutica (Maxim.) Korsh. is widely cultivated in Northwest China. The whole plant was called “Ye-Mang-Na-Bao” in traditional Tibetan medicine. In this study, Illumina sequencing technology was utilized to assemble and annotate the complete chloroplast genome sequences of it. The total length was 159, 584 bp, including four conserved regions: A pair of reverse repeat regions (IRa 31,042 bp and IRb 31,042 bp), a large single-copy region (79,515 bp), and a small single-copy region (17,985 bp). The genome had a total of 136 genes, with 16 presented in the reverse direction in the IR region. A total of 23 simple sequence repeats (SSRs) were identified in the coding and non-coding regions, most of which were biased toward A/T bases. A total of 15 SSRs were distributed in the non-coding regions. A comparative analysis of the chloroplast genome sequence of the C. tangutica (Maxim.) Krosh. and other species of the Ranunculaceae revealed that the chloroplast genome sequences of plants of the Ranunculaceae were highly conserved. Differences were observed in 13 gene loci in the coding region, with the degree of differentiation of the ycf2 gene being the most obvious. A phylogenetic analysis showed that Clematis glauca had the closest relationship with C. tangutica (Maxim.) Krosh., both members of the Clematis genus. Selective locus detection of the ycf2 gene in nine species of the Ranunculaceae was performed to explore adaptive evolution traits of the ycf2 gene in it. The results show that there are significant and extremely significant positive selection sites at the 103L, 352L, 356S, 362S, 363D, 366P, 368C, 369L, 374R, 376F, 377T and 382Q loci, respectively, indicating that the ycf2 gene has been subject to adaptive evolution.Insights from our assessment of the complete chloroplast genome sequences of C. tangutica (Maxim.) Krosh. will aid in the in-depth study of the evolutionary relationship of the Ranunculaceae and provide significant sequencing information for the genetic improvement of it.