Comparative and phylogenetic analysis of complete chloroplast genomes from five Artemisia species

Abstract

Artemisia Linn. is a large genus within the family Asteraceae that includes several important medicinal plants. Because of their similar morphology and chemical composition, traditional identification methods often fail to distinguish them. Therefore, developing an effective identification method for Artemisia species is an urgent requirement. In this study, we analyzed 15 chloroplast (cp) genomes, including 12 newly sequenced genomes, from 5 Artemisia species. The cp genomes from the five Artemisia species had a typical quadripartite structure and were highly conserved across species. They had varying lengths of 151,132–151,178 bp, and their gene content and codon preferences were similar. Mutation hotspot analysis identified four highly variable regions, which can potentially be used as molecular markers to identify Artemisia species. Phylogenetic analysis showed that the five Artemisia species investigated in this study were sister branches to each other, and individuals of each species formed a monophyletic clade. This study shows that the cp genome can provide distinguishing features to help identify closely related Artemisia species and has the potential to serve as a universal super barcode for plant identification.

Complete chloroplast genomes of eight Artemisia species: Comparative analysis, molecular identification, and phylogenetic analysis

“…In this study, we find similar codon usage and amino acid frequencies among the nine species of Artemisia. The amino acids with the highest coding rates were leucine (Leu), and except for one codon, all higher RSCU (>1) codons ended with either A or U, indicating codon usage bias similar to previous findings (Lan et al 2022).…”

“…The amino acids with the highest coding rates were leucine (Leu), and except for one codon, all higher RSCU (>1) codons ended with either A or U, indicating codon usage bias similar to previous findings (Lan et al . 2022).…”

Analysis of genetic variation inMacadamiashows evidence of extensive reticulate evolution

“…Phylogenetics helps to unravel evolutionary histories and provides valuable insights into the factors driving the growth and adaptation of important plant groups worldwide (Lan et al ., 2022). The current study, using whole genome of sequencing, has resolved the phylogeny of the four Macadamia species and confirmed that all the wild accessions belonged to 4 distinct species.…”

Comparative study on chloroplast genomes of three Hansenia forbesii varieties (Apiaceae)

“…Fu et al obtained 48 cp genome from 16 Taxus species and Pseudotaxus chienii and constructed the ML evolutionary tree, which showed that the cp genome can successfully distinguish all Taxus species and can be used as a super barcode to identify species [ 46 ]. Lan et al analyzed five cp genomes from Artemisia species, and showed that the cp genome can provide distinguishing features to help identify closely related Artemisia species and had the potential to serve as a universal super barcode for plant identification [ 20 ]. Most studies on the application of the cp genome have pointed out that a complete cp genome can be used as super barcodes for species identification.…”

“…It is widely used in the study of plant molecular evolution and phylogeny, as well as in genetic transformation, genetic engineering, and molecular breeding [ 13 – 15 ]. Recently, with the gradual popularization and low cost of high-throughput sequencing technology, some scientists have proposed that cp genome data can be used for species identification and interspecific differentiation research [ 16 – 20 ]. There is no significant difference in some appearance indicators among the three H .…”