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

Nature Plants volume 11, pages 1028–1048 (2025)Cite this article

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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.

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Fig. 1: Sampling, transcriptome assembly and species tree of major representatives of ferns.
Fig. 2: Gene functions in ferns.
Fig. 3: Lignin analysis of ferns.
Fig. 4: Polysaccharide analysis.
Fig. 5: Independent duplication of cell-wall-related modules in ferns.

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Data availability

The raw sequencing data are available at E-MTAB-13848, and the coding and protein sequences are available via Figshare at https://doi.org/10.6084/m9.figshare.26347330 (ref. 164). The co-expression networks are available at https://conekt.sbs.ntu.edu.sg/species/.

Code availability

The code used to perform the analyses is available on request.

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Acknowledgements

We acknowledge J. Fangel for contributions to Fig. 4e and S. Daniel for help with lignin biochemistry. We thank D. Maizels (http://www.scientific-art.com/) for the illustrations in Fig. 1. M.M. acknowledges funding from Singaporean Ministry of Education grant no. MOE-MOET32022-0002 ‘From tough pollen to soft matter’ and a Novo Nordisk Starting Grant. L.P. and B.C. (project no. 440046237) and J.d.V. (project no. 440231723; VR 132/4-2) acknowledge funding within the framework of MAdLand (http://madland.science), priority programme 2237 of the German Research Foundation (DFG). J.d.V. further thanks the European Research Council for funding under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 852725; ERC-StG ‘TerreStriAL’). S.d.V. acknowledges funding from the Lower Saxony Ministry of Science and Culture (Niedersachsen Vorab initiative) and DFG project no. 515101361. We thank L. Saulnier for discussion and help with identifying the unknown sugar. We also thank E. Haswell (https://elizabethhaswell.carrd.co) for her help with proofreading the manuscript. Finally, we thank J. C. Goh for his help in starting the project.

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Authors and Affiliations

  1. School of Biological Sciences, Nanyang Technological University, Singapore, Singapore

    Zahin Ali, Qiao Wen Tan, Peng Ken Lim, Irene Julca, Jia Min Lee & Marek Mutwil

  2. Department of Applied Bioinformatics, Institute for Microbiology and Genetics, Goettingen Center for Molecular Biosciences, Campus Institute Data Science, University of Goettingen, Göttingen, Germany

    Zahin Ali, Sophie de Vries & Jan de Vries

  3. Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium

    Hengchi Chen & Yves Van de Peer

  4. VIB Center for Plant Systems Biology, VIB, Ghent, Belgium

    Hengchi Chen & Yves Van de Peer

  5. Pharmaceutical Institute, Department of Pharmaceutical Biology, Christian-Albrechts-University of Kiel, Kiel, Germany

    Lukas Pfeifer & Birgit Classen

  6. University of Lausanne, Lausanne, Switzerland

    Irene Julca

  7. Department of Computational Biology, University of Lausanne, Lausanne, Switzerland

    Irene Julca

  8. INRAE, UR 1268 BIA, Nantes, France

    Fanny Vinter, Camille Alvarado, Amandine Layens & Richard Sibout

  9. Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa

    Eshchar Mizrachi & Yves Van de Peer

  10. Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark

    Mohammed Saddik Motawie, Bodil Joergensen, Peter Ulvskov & Marek Mutwil

  11. College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China

    Yves Van de Peer

  12. Singapore Botanic Gardens, National Parks Board, Singapore, Republic of Singapore

    Boon Chuan Ho

  13. Department of Biological Sciences, National University of Singapore, Singapore, Republic of Singapore

    Boon Chuan Ho

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  1. Zahin Ali
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Contributions

Z.M.A. and B.C.H. were involved in the sampling of ferns. Z.M.A., Q.W.T., H.C., P.K.L., I.J., J.M.L., S.d.V., J.d.V., E.M. and Y.V.d.P. were involved in the bioinformatical analysis of the data. L.P. and B.C. were involved in the GC–MS and bioinformatical analyses. F.V., C.A., A.L. and R.S. were involved in tissue sectioning and microscopy and the lignin and sugar analyses. M.S.M. performed the sugar synthesis and analysis. B.J. and P.U. performed the CoMPP analysis. Z.M.A. and M.M. wrote the paper with help from all authors. M.M. conceptualized and supervised the project.

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Correspondence to Marek Mutwil.

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Nature Plants thanks Thais Almeida and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

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Supplementary Figs. 1–19.

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Supplementary Methods.

Supplementary Data 1

Co-expression networks.

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Supplementary Tables 1–15.

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Ali, Z., Tan, Q.W., Lim, P.K. et al. Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls. Nat. Plants 11, 1028–1048 (2025). https://doi.org/10.1038/s41477-025-01978-y

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