Comparative analysis of complete Artemisia subgenus Seriphidium (Asteraceae: Anthemideae) chloroplast genomes: insights into structural divergence and phylogenetic relationships

Guangzhao Jin; Wenjun Li; Feng Song; Lei Yang; Zhibin Wen; Ying Feng

doi:10.1186/s12870-023-04113-1

Comparative analysis of complete Artemisia subgenus Seriphidium (Asteraceae: Anthemideae) chloroplast genomes: insights into structural divergence and phylogenetic relationships

BMC Plant Biol. 2023 Mar 10;23(1):136. doi: 10.1186/s12870-023-04113-1.

Authors

Guangzhao Jin^{1

2

3}, Wenjun Li^{1

2}, Feng Song⁴, Lei Yang^{1

2

3}, Zhibin Wen^{5

6}, Ying Feng^{7

8}

Affiliations

¹ State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
² The Herbarium of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
³ University of Chinese Academy of Sciences, Beijing, 100094, China.
⁴ Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
⁵ State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China. zhibinwen@ms.xjb.ac.cn.
⁶ The Herbarium of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China. zhibinwen@ms.xjb.ac.cn.
⁷ State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China. luckfy@ms.xjb.ac.cn.
⁸ The Herbarium of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China. luckfy@ms.xjb.ac.cn.

Abstract

Background: Artemisia subg. Seriphidium, one of the most species-diverse groups within Artemisia, grows mainly in arid or semi-arid regions in temperate climates. Some members have considerable medicinal, ecological, and economic value. Previous studies on this subgenus have been limited by a dearth of genetic information and inadequate sampling, hampering our understanding of their phylogenetics and evolutionary history. We therefore sequenced and compared the chloroplast genomes of this subgenus, and evaluated their phylogenetic relationships.

Results: We newly sequenced 18 chloroplast genomes of 16 subg. Seriphidium species and compared them with one previously published taxon. The chloroplast genomes, at 150,586-151,256 bp in length, comprised 133 genes, including 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and one pseudogene, with GC content of 37.40-37.46%. Comparative analysis showed that genomic structures and gene order were relatively conserved, with only some variation in IR borders. A total of 2203 repeats (1385 SSRs and 818 LDRs) and 8 highly variable loci (trnK - rps16, trnE - ropB, trnT, ndhC - trnV, ndhF, rpl32 - trnL, ndhG - ndhI and ycf1) were detected in subg. Seriphidium chloroplast genomes. Phylogenetic analysis of the whole chloroplast genomes based on maximum likelihood and Bayesian inference analyses resolved subg. Seriphidium as polyphyletic, and segregated into two main clades, with the monospecific sect. Minchunensa embedded within sect. Seriphidium, suggesting that the whole chloroplast genomes can be used as molecular markers to infer the interspecific relationship of subg. Seriphidium taxa.

Conclusion: Our findings reveal inconsistencies between the molecular phylogeny and traditional taxonomy of the subg. Seriphidium and provide new insights into the evolutionary development of this complex taxon. Meanwhile, the whole chloroplast genomes with sufficiently polymorphic can be used as superbarcodes to resolve interspecific relationships in subg. Seriphidium.

Keywords: Comparative genomics; Compositae; Molecular markers; Phylogenomics.

MeSH terms

Artemisia* / genetics
Bayes Theorem
Genome, Chloroplast*
Genomics
Phylogeny