ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Systematics and Evolution
This article is part of the Research TopicEvolution and Adaptive Implications of Intragenomic Elements in Plant GenomesView all articles
Comparative plastome analyses and evolutionary relationships of Drynaria
Provisionally accepted
- 1Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Shenzhen, China
- 2Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen, China
- 3Shanghai Chenshan Plant Science Research Center, Shanghai, China
- 4Guangdong Pharmaceutical University, Guangzhou, China
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The genus Drynaria, a member of the Polypodiaceae family, exhibits substantial medicinal and ornamental value. Although molecular biological studies have elucidated the phylogenetic relationships in Drynaria, the characteristics of its plastome and the mechanisms underlying its adaptive evolution remain inadequately understood. This study performed a comprehensive comparative genomic analysis based on the plastomes of 15 Drynaria species. The research analyzed codon usage bias and identified positively selected genes within this genus. A well-supported phylogenetic tree was constructed using plastome data, and divergence times were measured at key nodes. The analysis revealed that the plastomes of the 15 Drynaria species varied in size from 151,473 bp (D. speciosa) to 163,438 bp (D. parishii), each with 133 genes. Comparative analysis demonstrated conserved gene content, order, and orientation across all examined species, with no inversions or rearrangements except for a non-coding region rearrangement in the large single copy region of D. roosii and the small single copy region of D. meyeniana. Nucleotide diversity analysis identified seven hypervariable regions. The study detected 691 simple sequence repeats, 136 tandem repeats, and 750 dispersed repeats. Codon usage bias in Drynaria plastomes was predominantly influenced by natural selection. Phylogenetic reconstruction based on complete plastomes produced congruent topologies. Divergence time estimation suggested that Drynaria originated in the mid-Paleocene (59.75 Ma), with major diversification events occurring during the late Miocene (6–5 Ma). Selection pressure analysis revealed positive selection of petA and ycf3 in branch models, while ccsA, ycf1, and rpoC2 exhibited evidence of positive selection in branch-site models. These findings provide insights into the evolutionary adaptations and genomic features of this ecologically and economically significant fern genus.
Keywords: Chloroplast genomes, Drynaria, evolution, fERN, phylogeny
Received: 19 Aug 2025; Accepted: 05 Dec 2025.
Copyright: © 2025 Chen, SHU, Li, Yan, Zheng and Gu. 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:
Yue-Hong Yan
Xi-Long Zheng
Yu-Feng Gu
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