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Charting the genomic landscape of seed-free plants

Nature Plants volume 7, pages 554–565 (2021)Cite this article

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Abstract

During the past few years several high-quality genomes has been published from Charophyte algae, bryophytes, lycophytes and ferns. These genomes have not only elucidated the origin and evolution of early land plants, but have also provided important insights into the biology of the seed-free lineages. However, critical gaps across the phylogeny remain and many new questions have been raised through comparing seed-free and seed plant genomes. Here, we review the reference genomes available and identify those that are missing in the seed-free lineages. We compare patterns of various levels of genome and epigenomic organization found in seed-free plants to those of seed plants. Some genomic features appear to be fundamentally different. For instance, hornworts, Selaginella and most liverworts are devoid of whole-genome duplication, in stark contrast to other land plants. In addition, the distribution of genes and repeats appear to be less structured in seed-free genomes than in other plants, and the levels of gene body methylation appear to be much lower. Finally, we highlight the currently available (or needed) model systems, which are crucial to further our understanding about how changes in genes translate into evolutionary novelties.

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Fig. 1: Phylogeny of streptophytes (charophyte algae and land plants) and the available genomic resources.
Fig. 2: Distribution of gene/transposon density and DNA methylation.

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Acknowledgements

This project was supported by National Science Foundation grants IOS-1923011 and DEB-1831428 to F.-W.L., Swiss National Science Foundation grant nos. 160004, 131726 and 184826, the European Union’s Horizon 2020 Research and Innovation Programme (PlantHUB‐no. 722338), the Deutsche Forschungsgemeinschaft (German Research Foundation) under the Priority Programme ‘MAdLand—Molecular Adaptation to Land: Plant Evolution to Change’ (SPP 2237, 440370263), the Georges and Antoine Claraz Foundation, and the Forschungskredit and the University Research Priority Program ‘Evolution in Action’ of the University of Zurich to P.S. We thank K. Pryer and J. Banks for coining the term ‘seed-free plants’ and championing research in this area.

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  1. Department of Systematic and Evolutionary Botany, University of Zurich and Zurich-Basel Plant Science Center, Zurich, Switzerland

    Péter Szövényi

  2. Boyce Thompson Institute, Ithaca, NY, USA

    Andika Gunadi & Fay-Wei Li

  3. Plant Biology Section, Cornell University, Ithaca, NY, USA

    Fay-Wei Li

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  1. Péter Szövényi
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Szövényi, P., Gunadi, A. & Li, FW. Charting the genomic landscape of seed-free plants. Nat. Plants 7, 554–565 (2021). https://doi.org/10.1038/s41477-021-00888-z

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