Comparative and phylogenetic analysis of the complete chloroplast genomes of 10 Artemisia selengensis resources based on high- throughput sequencing

Abstract

Abstract Background: Artemisia selengensis, a perennial herb of the genus Artemisiain the family Asteraceae, has both edible and medicinal values. There are few studies on the chloroplast genome of Artemisia selengensis, and the phylogeographic classification is vague, which makes phylogenetic analysis and evolutionary studies very difficult. Results: The chloroplast genomes of 10 Artemisia selengensisin this study were highly conserved in terms of gene content, gene order, and gene intron number. The genome lengths ranged from 151,148 to 151,257 bp and were typical of a quadripartite structure with a total GC content of approximately 37.5%. The chloroplast genomes of all species encode 133 genes, including 88 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Due to the contraction and expansion of the inverted repeats (IR), the overlap of ycf1and ndhF genes occurred at the inverted repeats B (IRB) and short single copy sequence (SSC) boundaries. According to a codon use study, the frequent base in the chloroplast genome of Artemisia selengensis' third codon position was A/T. The number of SSR repeats was 42-44, most of which were single nucleotide A/T repeats. Sequence alignment analysis of the chloroplast genome showed that variable regions were mainly distributed in single copy regions, nucleotide diversity values of 0 to 0.009 were calculated by sliding window analysis, eight mutation hotspot regions were detected, and coding regions were more conserved than non-coding regions. Analysis of non-synonymous substitution (Ka) and synonymous substitution (Ks) revealed that accD, rps12, petB, and atpF genes were affected by positive selection and no genes were affected by neutral selection. Based on the findings of the phylogenetic analysis, Artemisia selengensis was sister to the genus Chrysanthemumand formed a monophyletic group with other Artemisia genera. Conclusions: In this research, the present study systematically compared the chloroplast genomic features of Artemisia selengensis and provided important information for the study of the chloroplast genome of Artemisia selengensis and the evolutionary relationships among Asteraceae species.