Mitochondrial genome of Artemisia argyi L. suggested conserved mitochondrial protein-coding genes among genera Artemisia, Tanacetum and Chrysanthemum

Haimei Chen; Linfang Huang; Jing Yu; Yujing Miao; Chang Liu

doi:10.1016/j.gene.2023.147427

Mitochondrial genome of Artemisia argyi L. suggested conserved mitochondrial protein-coding genes among genera Artemisia, Tanacetum and Chrysanthemum

Gene. 2023 Jun 30:871:147427. doi: 10.1016/j.gene.2023.147427. Epub 2023 Apr 10.

Authors

Haimei Chen¹, Linfang Huang², Jing Yu³, Yujing Miao⁴, Chang Liu⁵

Affiliations

¹ Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, PR China. Electronic address: hmchen@implad.ac.cn.
² Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, PR China. Electronic address: lfhuang@implad.ac.cn.
³ Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, PR China. Electronic address: jyu@implad.ac.cn.
⁴ Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, PR China.
⁵ Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, PR China. Electronic address: cliu6688@yahoo.com.

PMID: 37044183
DOI: 10.1016/j.gene.2023.147427

Abstract

Background: Artemisia argyi L., also known as mugwort, is a perennial herb whose leaves are commonly used as a source of traditional medicines. However, the evolution and structure of the mitochondrial genome (mitogenome) in A. argyi remain unclear. In this study, the mitogenome of A. argyi was assembled and characterized for the first time.

Results: The mitogenome of A. argyi was a circular molecule of 229,354 bp. It encodes 56 genes, including 33 protein-coding genes (PCGs), 20 tRNA genes, and three rRNA genes, and three pseudogenes. Five trans-spliced introns were observed in three PCGs namely, nad1, nad2 and nad5. Repeat analysis identified 65 SSRs, 14 tandem repeats, and 167 dispersed repeats. The A. argyi mitogenome contains 12 plastid transfer sequences from 79 bp to 2552 bp. Five conserved MTPTs were identified in all 18 Asteraceae species. Comparison of mitogenome between A. argyi and one Artemisia specie and two Chrysanthemum species showed 14 conserved gene clusters. Phylogenetic analysis with organelle genomes of A. argyi and 18 other Anthemideae plants showed inconsistent phylogenetic trees, which implied that the evolutionary rates of PCGs and rrna genes derived from mitochondrion and plastid were incongruent. The Ka/Ks ratio of the 27 shared protein-coding genes in the 18 Anthemideae species are all less than 1 indicating that these genes were under the effect of purifying selection. Lastly, a total of 568 RNA editing sites in PCGs were further identified. The average editing frequency of non-synonymous changes was significantly higher than that of synonymous changes (one-sample Student's t-test, p-values ≤ 0.05) in three tissues (root, leaf and stem).

Conclusions: In this study, the gene content, genome size, genome comparison, mitochondrial plastid sequences, dN/dS analysis of mitochondrial protein-coding genes, and RNA-editing events in A. argyi mitogenome were determined, providing insights into the phylogenetic relationships of Asteraceae plant.

Keywords: DNA transfer; De novo assembly; Organelle genomes; Phylogenetic analysis; Selective pressure analysis.

MeSH terms

Artemisia* / genetics
Chrysanthemum* / genetics
Genome, Mitochondrial*
Humans
Mitochondria / genetics
Mitochondrial Proteins / genetics
Phylogeny
Tanacetum* / genetics

Substances

Mitochondrial Proteins