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Peer-reviewedCC BY 4.0Frontiers in Plant Science

Comparative organelle genome analysis of three medicinal species of the genus Woodwardia (Blechnaceae): new insights into the phylogeny and molecular identification

  • Yutong Huang1
  • Libao Feng1
  • Yanping Xing1
  • Wenxiao Men1
  • Yanchang Huang1
  • Tingguo Kang1
  • Yanyun Yang1
  • Liang Xu1,2
  1. 1School of Pharmacy, Liaoning University of Traditional Chinese Medicine
  2. 2Traditional Chinese Medicine Quality and Resource Development Professional Technology Innovation Center, Liaoning Provincial Department of Science and Technology
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Abstract

Introduction: Plants of the genus Woodwardia have a long history of medicinal use in China. Among these plants, Woodwardia japonica, Woodwardia unigemmata , and Woodwardia prolifera are the primary source species of Guan Zhong, a traditional Chinese medicine. However, because of morphological similarity among their dried herbal materials and limited availability of organellar (mitochondrial and chloroplast) genomic data, research on species identification, molecular evolution, and phylogeny has been impeded.

Methods: Organelle genomes of the three Woodwardia species were sequenced and assembled using the second- and third-generation sequencing technologies. In-depth analyses were conducted, including protein-coding genes (PCGs) presence/absence, non-synonymous/synonymous mutation ratios (Ka/Ks), codon usage bias, repeat sequence identification, RNA editing site prediction, synteny and mitochondrial–chloroplast homologous fragment (MTPT) identification, and molecular identification via mVISTA and nucleotide diversity. Finally, we employed both maximum likelihood (ML) and Bayesian (BI) methods, based on single-copy orthologous genes and secondary calibrations, to infer phylogenetic relationships and divergence times among Woodwardia and related ferns.

Results: The mitochondrial genomes of the three Woodwardia species exhibited notable differences in genome size and characteristics; while the chloroplast genomes were relatively conserved and highly similar. Phylogenetic and divergence time analyses indicated that W. unigemmata and W. prolifera are more closely related and diverged more recently. Integrated analyses of highly variable regions and phylogenetic revealed that the intergenic spacer rrn16–rps12_exon2 or rps12_exon2–rrn16 could effectively differentiate the three Guan Zhong-related Woodwardia species, suggesting their potential utility as reliable DNA barcodes for identifying medicinal materials.

Discussion: The results provide comprehensive insights and reliable, detailed organelle genomic data for the phylogeny and molecular identification of W. japonica, W. unigemmata , and W. prolifera .

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Cite

BibTeXRIS
BibTeX
@article{huang2026comparative,
  title = {{Comparative organelle genome analysis of three medicinal species of the genus Woodwardia (Blechnaceae): new insights into the phylogeny and molecular identification}},
  author = {Yutong Huang and Libao Feng and Yanping Xing and Wenxiao Men and Yanchang Huang and Tingguo Kang and Yanyun Yang and Liang Xu},
  journal = {Frontiers in Plant Science},
  year = {2026},
  month = oct,
  doi = {10.3389/fpls.2026.1905066},
  url = {https://www.frontiersin.org/articles/10.3389/fpls.2026.1905066/full},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Comparative organelle genome analysis of three medicinal species of the genus Woodwardia (Blechnaceae): new insights into the phylogeny and molecular identification
AU  - Yutong Huang
AU  - Libao Feng
AU  - Yanping Xing
AU  - Wenxiao Men
AU  - Yanchang Huang
AU  - Tingguo Kang
AU  - Yanyun Yang
AU  - Liang Xu
PY  - 2026
DA  - 2026/10/07
JO  - Frontiers in Plant Science
DO  - 10.3389/fpls.2026.1905066
UR  - https://www.frontiersin.org/articles/10.3389/fpls.2026.1905066/full
AB  - Introduction: Plants of the genus Woodwardia have a long history of medicinal use in China. Among these plants, Woodwardia japonica, Woodwardia unigemmata , and Woodwardia prolifera are the primary source species of Guan Zhong, a traditional Chinese medicine. However, because of morphological similarity among their dried herbal materials and limited availability of organellar (mitochondrial and chloroplast) genomic data, research on species identification, molecular evolution, and phylogeny has been impeded.  Methods: Organelle genomes of the three Woodwardia species were sequenced and assembled using the second- and third-generation sequencing technologies. In-depth analyses were conducted, including protein-coding genes (PCGs) presence/absence, non-synonymous/synonymous mutation ratios (Ka/Ks), codon usage bias, repeat sequence identification, RNA editing site prediction, synteny and mitochondrial–chloroplast homologous fragment (MTPT) identification, and molecular identification via mVISTA and nucleotide diversity. Finally, we employed both maximum likelihood (ML) and Bayesian (BI) methods, based on single-copy orthologous genes and secondary calibrations, to infer phylogenetic relationships and divergence times among Woodwardia and related ferns.  Results: The mitochondrial genomes of the three Woodwardia species exhibited notable differences in genome size and characteristics; while the chloroplast genomes were relatively conserved and highly similar. Phylogenetic and divergence time analyses indicated that W. unigemmata and W. prolifera are more closely related and diverged more recently. Integrated analyses of highly variable regions and phylogenetic revealed that the intergenic spacer rrn16–rps12_exon2 or rps12_exon2–rrn16 could effectively differentiate the three Guan Zhong-related Woodwardia species, suggesting their potential utility as reliable DNA barcodes for identifying medicinal materials.  Discussion: The results provide comprehensive insights and reliable, detailed organelle genomic data for the phylogeny and molecular identification of W. japonica, W. unigemmata , and W. prolifera .
SN  - 1664-462X
ER  -