Detecting useful genetic markers and reconstructing the phylogeny of an important medicinal resource plant, Artemisia selengensis, based on chloroplast genomics

Abstract

Artemisia selengenesis is not only a health food, but also a well-known traditional Chinese medicine. Only a fraction of the chloroplast (cp) genome data of Artemisia has been reported and chloroplast genomic materials have been widely used in genomic evolution studies, molecular marker development, and phylogenetic analysis of the genus Artemisia, which makes evolutionary studies, genetic improvement, and phylogenetic identification very difficult. In this study, the complete chloroplast genome of A. selengensis was compared with that of other species within Artemisia and phylogenetic analyses was conducted with other genera in the Asteraceae family. The results showed that A. selengensis is an AT-rich species and has a typical quadripartite structure that is 151,215 bp in length. Comparative genome analyses demonstrated that the available chloroplast genomes of species of Artemisia were well conserved in terms of genomic length, GC contents, and gene organization and order. However, some differences, which may indicate evolutionary events, were found, such as a re-inversion event within the Artemisia genus, an unequal duplicate phenomenon of the ycf1 gene because of the expansion and contraction of the IR region, and the fast-evolving regions. Repeated sequences analysis showed that Artemisia chloroplast genomes presented a highly similar pattern of SSR or LDR distribution. A total of 257 SSRs and 42 LDRs were identified in the A. selengensis chloroplast genome. The phylogenetic analysis showed that A. selengensis was sister to A. gmelinii. The findings of this study will be valuable in further studies to understand the genetic diversity and evolutionary history of Asteraceae.

Comparative chloroplast genome analysis of Artemisia (Asteraceae) in East Asia: insights into evolutionary divergence and phylogenomic implications

“…In contrast, the ω for ycf1 and accD was 0.67 and 1.06, respectively, suggesting that these genes are under relaxed selective constraints and weak positive selection, respectively. These results are consistent with reports that most genes in the Artemisia plastome evolve under negative selection; however, accD is under positive selection [38,44]. The likelihood ratio test of the site-specific model in CodeML program validated the evolutionary selection patterns of accD and ycf1.…”

“…The IR border structure was conserved in Artemisia, except A. selengensis in which three independent plastomes have seven bp expansion in rps19 at the LSC/IR and SSC/IR junctions. In addition, unlike the reports of Meng et al [38] and Shen et al [33], ψrps19 was located at the IRb/LSC junction in all Artemisia plastomes. Seven protein-coding genes (ndhB, rpl2, rpl23, rps7, rps12, ycf2, and ycf15), four rRNA genes, and seven tRNA genes were duplicated in the two IRs.…”

“…These genes contained nucleotide diversity hotspots in exon (accD and ycf1) or intron (rps16) regions that were under weak positive selection or relaxed selective constraints. accD was reported to be under positive selection (ω > 1) in A. selengensis [38] whereas the 5′-region of the ycf1-coding sequence was suggested to be a plastid barcode for land plants [30]. These two genes play important roles in flowering plants.…”

ycf1-ndhF genes, the most promising plastid genomic barcode, sheds light on phylogeny at low taxonomic levels in Prunus persica

“…Our data infer a similar feature with obvious differences was observed ranged from 109 to 124 bp, especially between cultivated and wild types. This concept has gained much acceptance and support through recently plastid genome studies [9,17,29,30]. With more direct interest in our results, a positive association in the IGS region was observed within the two genes, owing to sequence divergence in the cpDNA.…”

The complete chloroplast genome sequence of medicinal plant, Artemisia lavandulaefolia YC

“…Artemisia lavandulaefolia YC, referred to as 'Ye Aihao' in China, has been used for the treatment of dispelling cold, dampness and stopping bleeding. Despite its useful applications, there has been little report of molecular and genomic resources (Meng et al 2019). In this article, the chloroplast genome sequence of medicinal plant, A. lavandulaefolia YC, was completely characterized.…”