ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Systematics and Evolution
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1670568
This article is part of the Research TopicEvolutionary Dynamics, Functional Variation and Application of Plant Organellar GenomeView all 28 articles
Molecular phylogenetic relationships based on chloroplast genomes of Zingiberaceae species: Insights into evolution and adaptation to extreme environments
Provisionally accepted
- 1Wuhan University, Wuhan, China
- 2Tibet University, Lhasa, China
- 3Shandong Jianzhu University, Jinan, China
- 4Yichang Central People's Hospital, Yichang, China
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Abstract: In this study, we performed a comparative analysis of 11 newly identified species (Aframomum alboviolaceum, Amomum longipetiolatum, Amomum petaloideum, Amomum velutinum, Cautleya spicata, Cornukaempferia larsenii, Globba atrosanguinea, Globba variabilis, Hedychium aureum, Riedelia arfakensis, and Zingiber citriodorum) and 110 published data from the Zingiberaceae family, including their structure, codon usage, nucleotide polymorphisms, divergence time, and selection pressures. Our findings revealed a conserved structure within the chloroplast genomes of Zingiberaceae species, with no significant expansion or contraction detected during diversification. We identified four regions within proteincoding genes (atpH, rpl32, ndhA, and ycf1) and one intergenic region (psac-ndhE) prone to mutations, which could serve as valuable molecular markers for phylogeography and population genetics studies. Additionally, our analysis indicated that natural selection predominantly influences codon usage in the chloroplast genes of Zingiberaceae. Phylogenetic analysis supported the division of Zingiberaceae into two subfamilies. Our results confirmed that Globba is more closely related to Curcuma than to Hedychium, and Hedychium is more closely related to PommerescheaRhynchanthus than to Cautleya. Divergence time estimations revealed two rapid divergences among Zingiberoideae species, possibly influenced by the rapid uplift of the Tibetan Plateau and a cooling event in the Late Miocene caused by a decrease in CO2 levels. Results of ancestral range reconstruction indicate that Zingiberaceae species originated in Africa during the Cretaceous period and then spread to Southeast Asia and India. Most proteincoding genes in Zingiberaceae undergo negative selection, except for the ycf2 gene. Furthermore, we identified two positively selected genes (matK and ndhB) in highaltitude Roscoea species, which may be crucial for their adaptation to highland environments. In summary, our study provided new perspectives for crop identification, breeding, and conservation.
Keywords: Zingiberaceae, Chloroplast genome, phylogenetic analysis, biogeographic dispersal, positive selection
Received: 21 Jul 2025; Accepted: 01 Sep 2025.
Copyright: © 2025 Yuan, Lu, Yin, Luo, Chen, Wu, Zhang and Wei. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Tao Yuan, Wuhan University, Wuhan, China
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