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Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls

Zahin Ali, Qiao Wen Tan, Peng Ken Lim, Hengchi Chen (UGent) , Lukas Pfeifer, Irene Julca, Jia Min Lee, Birgit Classen, Sophie de Vries, Jan de Vries, et al.
(2025) NATURE PLANTS. 11. p.1028-1048
Author
Organization
Abstract
Ferns are essential for understanding plant evolution; however, their large and intricate genomes have kept their genetic landscape largely unexplored, with only a few genomes sequenced and limited transcriptomic data available. To bridge this gap, we generated extensive RNA-sequencing data across various organs from 22 representative fern species, resulting in high-quality transcriptome assemblies. These data enabled us to construct a time-calibrated phylogeny for ferns, encompassing all major clades, which revealed numerous instances of whole-genome duplication. We highlighted the distinctiveness of fern genetics, discovering that half of the identified gene families are unique to ferns. Our exploration of fern cell walls through biochemical and immunological analyses uncovered the presence of the lignin syringyl unit, along with evidence of its independent evolution in ferns. Additionally, the identification of an unusual sugar in fern cell walls suggests a divergent evolutionary trajectory in cell wall biochemistry, probably influenced by gene duplication and sub-functionalization. To facilitate further research, we have developed an online database that includes preloaded genomic and transcriptomic data for ferns and other land plants. We used this database to demonstrate the independent evolution of lignocellulosic gene modules in ferns. Our findings provide a comprehensive framework illustrating the unique evolutionary journey ferns have undertaken since diverging from the last common ancestor of euphyllophytes more than 360 million years ago
Keywords
MULTIPLE SEQUENCE ALIGNMENT, CELLULOSE SYNTHASE, SYRINGYL LIGNIN, ARABIDOPSIS-THALIANA, PLANT EVOLUTION, MIXED-LINKAGE, GENOME SIZE, INSIGHTS, PROVIDES, ACID

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MLA
Ali, Zahin, et al. “Comparative Transcriptomics in Ferns Reveals Key Innovations and Divergent Evolution of the Secondary Cell Walls.” NATURE PLANTS, vol. 11, 2025, pp. 1028–48, doi:10.1038/s41477-025-01978-y.
APA
Ali, Z., Tan, Q. W., Lim, P. K., Chen, H., Pfeifer, L., Julca, I., … Mutwil, M. (2025). Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls. NATURE PLANTS, 11, 1028–1048. https://doi.org/10.1038/s41477-025-01978-y
Chicago author-date
Ali, Zahin, Qiao Wen Tan, Peng Ken Lim, Hengchi Chen, Lukas Pfeifer, Irene Julca, Jia Min Lee, et al. 2025. “Comparative Transcriptomics in Ferns Reveals Key Innovations and Divergent Evolution of the Secondary Cell Walls.” NATURE PLANTS 11: 1028–48. https://doi.org/10.1038/s41477-025-01978-y.
Chicago author-date (all authors)
Ali, Zahin, Qiao Wen Tan, Peng Ken Lim, Hengchi Chen, Lukas Pfeifer, Irene Julca, Jia Min Lee, Birgit Classen, Sophie de Vries, Jan de Vries, Fanny Vinter, Camille Alvarado, Amandine Layens, Eshchar Mizrachi, Mohammed Saddik Motawie, Bodil Joergensen, Peter Ulvskov, Yves Van de Peer, Boon Chuan Ho, Richard Sibout, and Marek Mutwil. 2025. “Comparative Transcriptomics in Ferns Reveals Key Innovations and Divergent Evolution of the Secondary Cell Walls.” NATURE PLANTS 11: 1028–1048. doi:10.1038/s41477-025-01978-y.
Vancouver
1.
Ali Z, Tan QW, Lim PK, Chen H, Pfeifer L, Julca I, et al. Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls. NATURE PLANTS. 2025;11:1028–48.
IEEE
[1]
Z. Ali et al., “Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls,” NATURE PLANTS, vol. 11, pp. 1028–1048, 2025.
@article{01JTFTWMFQDQY8DTV355KVRGDD,
  abstract     = {{Ferns are essential for understanding plant evolution; however, their large and intricate genomes have kept their genetic landscape largely unexplored, with only a few genomes sequenced and limited transcriptomic data available. To bridge this gap, we generated extensive RNA-sequencing data across various organs from 22 representative fern species, resulting in high-quality transcriptome assemblies. These data enabled us to construct a time-calibrated phylogeny for ferns, encompassing all major clades, which revealed numerous instances of whole-genome duplication. We highlighted the distinctiveness of fern genetics, discovering that half of the identified gene families are unique to ferns. Our exploration of fern cell walls through biochemical and immunological analyses uncovered the presence of the lignin syringyl unit, along with evidence of its independent evolution in ferns. Additionally, the identification of an unusual sugar in fern cell walls suggests a divergent evolutionary trajectory in cell wall biochemistry, probably influenced by gene duplication and sub-functionalization. To facilitate further research, we have developed an online database that includes preloaded genomic and transcriptomic data for ferns and other land plants. We used this database to demonstrate the independent evolution of lignocellulosic gene modules in ferns. Our findings provide a comprehensive framework illustrating the unique evolutionary journey ferns have undertaken since diverging from the last common ancestor of euphyllophytes more than 360 million years ago}},
  author       = {{Ali, Zahin and Tan, Qiao Wen and Lim, Peng Ken and Chen, Hengchi and Pfeifer, Lukas and Julca, Irene and Lee, Jia Min and Classen, Birgit and de Vries, Sophie and de Vries, Jan and Vinter, Fanny and Alvarado, Camille and Layens, Amandine and Mizrachi, Eshchar and Motawie, Mohammed Saddik and Joergensen, Bodil and Ulvskov, Peter and Van de Peer, Yves and Ho, Boon Chuan and Sibout, Richard and Mutwil, Marek}},
  issn         = {{2055-026X}},
  journal      = {{NATURE PLANTS}},
  keywords     = {{MULTIPLE SEQUENCE ALIGNMENT,CELLULOSE SYNTHASE,SYRINGYL LIGNIN,ARABIDOPSIS-THALIANA,PLANT EVOLUTION,MIXED-LINKAGE,GENOME SIZE,INSIGHTS,PROVIDES,ACID}},
  language     = {{eng}},
  pages        = {{1028--1048}},
  title        = {{Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls}},
  url          = {{http://doi.org/10.1038/s41477-025-01978-y}},
  volume       = {{11}},
  year         = {{2025}},
}
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