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ORIGINAL RESEARCH article

Front. Plant Sci.

Sec. Plant Systematics and Evolution

Comparative analysis of mitochondrial genomes of Epimedium L. reveals heterogeneity in structure, synteny, intercellular gene transfer, and RNA editing

Provisionally accepted
De XuDe Xu1Juan HuangJuan Huang1Qianqian MaQianqian Ma1Tao WangTao Wang1Zheming ZhangZheming Zhang1Qiang WangQiang Wang1Zhide WangZhide Wang1Zhou XieZhou Xie1Xue LiuXue Liu2*Liang FuLiang Fu1*
  • 1Dazhou Academy of Agricultural Sciences, DaZhou, China
  • 2Chongqing Academy of Chinese Materia Medica, Chongqing, China

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Epimedium L. is a taxonomically complex genus comprising 68 species worldwide, yet its mitochondrial genome (mitogenome) remains unexplored. We assembled the complete of E. pubescens, E. wushanense, and E. sagittatum using Illumina and Nanopore sequencing. The Epimedium mitogenomes displayed diverse structural variation, including a single circular molecule in E. sagittatum (324,345 bp), two circular molecules in E. wushanense (281,026 bp and 72,800 bp), and a multipartite structure with three circular (171,784 bp, 76,915 bp, and 71,519 bp) and one linear chromosome (26,149 bp) in E. pubescens. Each species contained 58 unique genes, including 36 protein-coding genes (PCGs), 19 tRNAs, 3 rRNAs and abundant repetitive elements (77–89 SSRs and 169–380 dispersed repeats). A total of 642 C-to-U RNA editing sites were predicted across 35–36 PCGs, with three 删除[office]: ) 删除[l]: experimentally validated edits generating start and stop codons, revealing species-specific editing profiles. Nine mitochondrial plastid DNA fragments (MTPTs; 4.4–7.5 Kb) were identified per species, containing 6–9 complete genes Three Epimedium species and related taxa exhibited conserved mitogenome regions alongside extensive gene rearrangements and inversions. Phylogenetic analysis based on 29 conserved PCGs strongly supported a monophyletic Epimedium clade (100% bootstrap), with E. sagittatum and E. pubescens forming a sister group to E. wushanense. This study provides the first comprehensive view of Epimedium mitogenome architecture, RNA editing, and evolutionary relationships, enriching our understanding of its mitochondrial evolution and taxonomy.

Keywords: Epimedium L., Mitochondrial Genome, comparative analysis, gene transfer, RNA editing events

Received: 09 Sep 2025; Accepted: 07 Nov 2025.

Copyright: © 2025 Xu, Huang, Ma, Wang, Zhang, Wang, Wang, Xie, Liu and Fu. 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:
Xue Liu, liu0906xue@163.com
Liang Fu, fuliangrain@126.com

Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.

Supplementary Material