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Volume 11
Issue 10
10.3390/horticulturae11101209
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

Comparative Chloroplast Genomes to Gain Insights into the Phylogenetic Relationships and Evolution of Opisthopappus Species

by
Liqin Liang
1,†,
Bingui Ma
1,
Mian Han
1,†,
Xiaolong Feng
1,†,
Haoyuan Dan
1,
Tingyu Wang
1,
Jinghui Han
1,
Minghui Yang
1,
Li Liu
1,
Genlou Sun
2,* and
Yiling Wang
1,*
1
School of Life Science, Shanxi Normal University, Taiyuan 030031, China
2
Department of Botany, Saint Mary’s University, Halifax, NS B3H 3C3, Canada
*
Authors to whom correspondence should be addressed.
†
These authors have contributed equally to this work.
Horticulturae 2025, 11(10), 1209; https://doi.org/10.3390/horticulturae11101209
Submission received: 3 September 2025 / Revised: 1 October 2025 / Accepted: 6 October 2025 / Published: 7 October 2025
(This article belongs to the Special Issue Omics Era in Medicinal and Aromatic Plants: Towards a New Age of Agriculture and Sustainability)
Versions Notes

Abstract

The investigation and comparison of chloroplast genomes facilitate our deeper elucidation of the evolutionary dynamics and phylogenetics of plant species, particularly non-model plants. Opisthopappus is a genus of Asteraceae that is endemic to the Taihang Mountains in China, which includes Opisthopappus taihangensis and Opisthopappus longilobus. Although certain chloroplast genomic data are available, the comprehensive evolutionary relationships of chloroplast genomes in this genus are not yet fully understood. In this study, the assembled O. taihangensis chloroplast genomes exhibited a quadripartite structure with 131 genes, encompassing 86 protein-coding, 37 tRNA, and eight rRNA genes. The basic phylogenetic relationships of 275 Asteraceae species were consistent with preceding studies. Opisthopappus with Ajania and Chrysanthemum were gathered together in Trib. Anthemideae. However, O. taihangensis and O. longilobus were not clustered into a group. Six and eight variable hotspots were detected in Opisthopappus and Asteraceae respectively. A total of 18 optimal codons were identified in two species. Differentiation in codon usage patterns was primarily influenced by natural selection between O. taihangensis and O. longilobus. Thereinto, GCU (Ala) was specific to O. taihangensis, while ACU (Thr) was to O. longilobus. Most of the codons preferentially ended with A/U, with only two genes (rpl16 and matK) being subjected to positive selection in Opisthopappus. Under salt stress, 25 editing sites were detected in O. longilobus, and 34 editing sites were found in O. taihangensis. All editing sites were C to U transitions. Distinct editing events occurred in the two species. During the evolution of chloroplast genomes, the genes that undergo positive selection may help two Opisthopappus species to adapt the harsh cliff environment of the Taihang Mountains and ensure their normal growth and development. In response to stress, O. taihangensis and O. longilobus tended to utilize different codons and initiate unique RNA editing events. These will facilitate further work on taxonomy, phylogenetics, and adaptive evolution of Opisthopappus, even Anthemideae or Asteraceae.
Keywords: chloroplast genome; Opisthopappus; evolution; phylogenetic relationship chloroplast genome; Opisthopappus; evolution; phylogenetic relationship

Share and Cite

MDPI and ACS Style

Liang, L.; Ma, B.; Han, M.; Feng, X.; Dan, H.; Wang, T.; Han, J.; Yang, M.; Liu, L.; Sun, G.; et al. Comparative Chloroplast Genomes to Gain Insights into the Phylogenetic Relationships and Evolution of Opisthopappus Species. Horticulturae 2025, 11, 1209. https://doi.org/10.3390/horticulturae11101209

AMA Style

Liang L, Ma B, Han M, Feng X, Dan H, Wang T, Han J, Yang M, Liu L, Sun G, et al. Comparative Chloroplast Genomes to Gain Insights into the Phylogenetic Relationships and Evolution of Opisthopappus Species. Horticulturae. 2025; 11(10):1209. https://doi.org/10.3390/horticulturae11101209

Chicago/Turabian Style

Liang, Liqin, Bingui Ma, Mian Han, Xiaolong Feng, Haoyuan Dan, Tingyu Wang, Jinghui Han, Minghui Yang, Li Liu, Genlou Sun, and et al. 2025. "Comparative Chloroplast Genomes to Gain Insights into the Phylogenetic Relationships and Evolution of Opisthopappus Species" Horticulturae 11, no. 10: 1209. https://doi.org/10.3390/horticulturae11101209

APA Style

Liang, L., Ma, B., Han, M., Feng, X., Dan, H., Wang, T., Han, J., Yang, M., Liu, L., Sun, G., & Wang, Y. (2025). Comparative Chloroplast Genomes to Gain Insights into the Phylogenetic Relationships and Evolution of Opisthopappus Species. Horticulturae, 11(10), 1209. https://doi.org/10.3390/horticulturae11101209

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