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

Abstract

Background: Artemisia in East Asia includes a number of economically important taxa that are widely used for food, medicinal, and ornamental purposes. The identification of taxa, however, has been hampered by insufficient diagnostic morphological characteristics and frequent natural hybridization. Development of novel DNA markers or barcodes with sufficient resolution to resolve taxonomic issues of Artemisia in East Asia is significant challenge. Results: To establish a molecular basis for taxonomic identification and comparative phylogenomic analysis of Artemisia, we newly determined 19 chloroplast genome (plastome) sequences of 18 Artemisia taxa in East Asia, de novo-assembled and annotated the plastomes of two taxa using publicly available Illumina reads, and compared them with 11 Artemisia plastomes reported previously. The plastomes of Artemisia were 150,858-151,318 base pairs (bp) in length and harbored 87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNA genes in conserved order and orientation. Evolutionary analyses of whole plastomes and 80 non-redundant protein-coding genes revealed that the noncoding trnH-psbA spacer was highly variable in size and nucleotide sequence both between and within taxa, whereas the coding sequences of accD and ycf1 were under weak positive selection and relaxed selective constraints, respectively. Phylogenetic analysis of the whole plastomes based on maximum likelihood and Bayesian inference analyses yielded five groups of Artemisia plastomes clustered in the monophyletic subgenus Dracunculus and paraphyletic subgenus Artemisia, suggesting that the whole plastomes can be used as molecular markers to infer the chloroplast haplotypes of Artemisia taxa. Additionally, analysis of accD and ycf1 hotspots enabled the development of novel markers potentially applicable across the family Asteraceae with high discriminatory power. Conclusions: The complete sequences of the Artemisia plastomes are sufficiently polymorphic to be used as superbarcodes for this genus. It will facilitate the development of new molecular markers and study of the phylogenomic relationships of Artemisia species in the family Asteraceae.

Intraspecific variations among the chloroplast genomes of Artemisia scoparia (asteraceae) from Pakistan and China

“…This genome consists of a large single copy (LSC) region, a small single copy (SSC) region, and a pair of inverted repeat (IRs) regions, with lengths of 82,778 bp, 18,306 bp, and 24,962 bp, respectively. The overall GC content of the total genome, LSC, SSC, and IR regions are 37.47%, 35.56%, 30.75%, and 43.08%, respectively, which is similar to other taxa in Artemisia (Kim et al 2020). Besides, the genome encodes a total of 132 genes, including 87 protein-coding genes, 37 tRNA genes and 8 rRNA genes, respectively.…”

Development of Genomic Resources From Crossostephium Chinense (Asteraceae) Based on Genome Skimming Data

“…For instance, 20 mutational hotspots were respectively recognized for Artemisia scoparia [28], A. maritima and A. absinthium [29]. Meanwhile, Kim et al [30] compared 21 Artemisia (32 accessions) and suggested the markers accD and ycf1 may represent the potential markers to be tested for the whole Asteraceae. Recognition of these two markers seem to be line with several other studies on the genera in Asteraceae, where either one of both markers were observed in the suggestion list [31,32].…”

Chloroplast phylogenomics and the dynamic evolution of Santalum (Santalaceae)

“…2). The number of SSR in the Santalum chloroplast genome was low compared to photoautotrophic plant lineages [31][32][33][34].…”