Abstract
Seed plants overtook ferns to become the dominant plant group during the late Carboniferous, a period in which the climate became colder and dryer1,2. However, the specific innovations driving the success of seed plants are not clear. Here we report that the appearance of suberin lamellae (SL) contributed to the rise of seed plants. We show that the Casparian strip and SL vascular barriers evolved at different times, with the former originating in the most recent common ancestor (MRCA) of vascular plants and the latter in the MRCA of seed plants. Our results further suggest that most of the genes required for suberin formation arose through gene duplication in the MRCA of seed plants. We show that the appearance of the SL in the MRCA of seed plants enhanced drought tolerance through preventing water loss from the stele. We hypothesize that SL provide a decisive selective advantage over ferns in arid environments, resulting in the decline of ferns and the rise of gymnosperms. This study provides insights into the evolutionary success of seed plants and has implications for engineering drought-tolerant crops or fern varieties.
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Data availability
All the data required to assess the conclusions of this study are available in the paper or the Supplementary Information. Other relevant data are available from the corresponding authors upon request. Source data are provided with this paper.
References
Fich, E. A., Segerson, N. A. & Rose, J. K. C. The plant polyester cutin: biosynthesis, structure, and biological roles. Annu. Rev. Plant Biol. 67, 207–233 (2016).
Geldner, N. The endodermis. Annu. Rev. Plant Biol. 64, 531–558 (2013).
Calvo-Polanco, M. et al. Physiological roles of Casparian strips and suberin in the transport of water and solutes. New Phytol. 232, 2295–2307 (2021).
Niklas, K. J., Cobb, E. D. & Matas, A. J. The evolution of hydrophobic cell wall biopolymers: from algae to angiosperms. J. Exp. Bot. 68, 5261–5269 (2017).
Renault, H. et al. A phenol-enriched cuticle is ancestral to lignin evolution in land plants. Nat. Commun. 8, 14713 (2017).
Retallack, G. J. Permian–Triassic life crisis on land. Science 267, 77–80 (1995).
Nowak, H., Schneebeli-Hermann, E. & Kustatscher, E. No mass extinction for land plants at the Permian–Triassic transition. Nat. Commun. 10, 384 (2019).
Serra, O. & Geldner, N. The making of suberin. New Phytol. 235, 848–866 (2022).
Graca, J. Suberin: the biopolyester at the frontier of plants. Front. Chem. 3, 128–135 (2015).
Shukla, V. & Barberon, M. Building and breaking of a barrier: suberin plasticity and function in the endodermis. Curr. Opin. Plant Biol. 64, 102153 (2021).
Barberon, M. The endodermis as a checkpoint for nutrients. New Phytol. 213, 1604–1610 (2017).
Peterson, C. A., Peterson, R. L. & Robards, A. W. Correlated histochemical and ultrastructural-study of epidermis and hypodermis of onion roots. Protoplasma 96, 1–21 (1978).
Andersen, T. G., Barberon, M. & Geldner, N. Suberization—the second life of an endodermal cell. Curr. Opin. Plant Biol. 28, 9–15 (2015).
Kolattukudy, P. E. Biopolyester membranes of plants: cutin and suberin. Science 208, 990–1000 (1980).
Zhou, F. et al. Co-incidence of damage and microbial patterns controls localized immune responses in roots. Cell 180, 440–453.e18 (2020).
Barberon, M. et al. Adaptation of root function by nutrient-induced plasticity of endodermal differentiation. Cell 164, 447–459 (2016).
Barbosa, I. C. R., Rojas-Murcia, N. & Geldner, N. The Casparian strip—one ring to bring cell biology to lignification? Curr. Opin. Biotechnol. 56, 121–129 (2019).
Berhin, A. et al. The root cap cuticle: a cell wall structure for seedling establishment and lateral root formation. Cell 176, 1367–1378.e8 (2019).
Ursache, R. et al. GDSL-domain proteins have key roles in suberin polymerization and degradation. Nat. Plants 7, 353–364 (2021).
Nomberg, G., Marinov, O., Arya, G. C., Manasherova, E. & Cohen, H. The key enzymes in the suberin biosynthetic pathway in plants: an update. Plants (Basel) 11, 392 (2022).
Kim, G., Ryu, H. & Sung, J. Hormonal crosstalk and root suberization for drought stress tolerance in plants. Biomolecules 12, 811 (2022).
Shukla, V. et al. Suberin plasticity to developmental and exogenous cues is regulated by a set of MYB transcription factors. Proc. Natl Acad. Sci. USA 118, e2101730118 (2021).
Kosma, D. K. et al. AtMYB41 activates ectopic suberin synthesis and assembly in multiple plant species and cell types. Plant J. 80, 216–229 (2014).
Cohen, H., Fedyuk, V., Wang, C., Wu, S. & Aharoni, A. SUBERMAN regulates developmental suberization of the Arabidopsis root endodermis. Plant J. 102, 431–447 (2020).
Beisson, F., Li, Y. H., Bonaventure, G., Pollard, M. & Ohlrogge, J. B. The acyltransferase GPAT5 is required for the synthesis of suberin in seed coat and root of Arabidopsis. Plant Cell 19, 351–368 (2007).
Hofer, R. et al. The Arabidopsis cytochrome P450 CYP86A1 encodes a fatty acid omega-hydroxylase involved in suberin monomer biosynthesis. J. Exp. Bot. 59, 2347–2360 (2008).
Compagnon, V. et al. CYP86B1 is required for very long chain omega-hydroxyacid and alpha,omega-dicarboxylic acid synthesis in root and seed suberin polyester. Plant Physiol. 150, 1831–1843 (2009).
Franke, R. et al. The DAISY gene from Arabidopsis encodes a fatty acid elongase condensing enzyme involved in the biosynthesis of aliphatic suberin in roots and the chalaza-micropyle region of seeds. Plant J. 57, 80–95 (2009).
Lee, S. B. et al. Two Arabidopsis 3-ketoacyl CoA synthase genes, KCS20 and KCS2/DAISY, are functionally redundant in cuticular wax and root suberin biosynthesis, but differentially controlled by osmotic stress. Plant J. 60, 462–475 (2009).
Yang, W. et al. A land-plant-specific glycerol-3-phosphate acyltransferase family in Arabidopsis: substrate specificity, sn-2 preference, and evolution. Plant Physiol. 160, 638–652 (2012).
Domergue, F. et al. Three Arabidopsis fatty acyl-coenzyme A reductases, FAR1, FAR4, and FAR5, generate primary fatty alcohols associated with suberin deposition. Plant Physiol. 153, 1539–1554 (2010).
Yadav, V. et al. ABCG transporters are required for suberin and pollen wall extracellular barriers in Arabidopsis. Plant Cell 26, 3569–3588 (2014).
De Bellis, D. et al. Extracellular vesiculo-tubular structures associated with suberin deposition in plant cell walls. Nat. Commun. 13, 1489 (2022).
Gabaldon, T. & Koonin, E. V. Functional and evolutionary implications of gene orthology. Nat. Rev. Genet. 14, 360–366 (2013).
Cannell, N. et al. Multiple metabolic innovations and losses are associated with major transitions in land plant evolution. Curr. Biol. 30, 1783–1800.e11 (2020).
Baxter, I. et al. Root suberin forms an extracellular barrier that affects water relations and mineral nutrition in Arabidopsis. PLoS Genet. 5, e1000492 (2009).
de Silva, N. D. G. et al. Root suberin plays important roles in reducing water loss and sodium uptake in Arabidopsis thaliana. Metabolites 11, 735 (2021).
Feng, T. et al. Natural variation in root suberization is associated with local environment in Arabidopsis thaliana. New Phytol. 236, 385–398 (2022).
Pascut, F. C. et al. Non-invasive hydrodynamic imaging in plant roots at cellular resolution. Nat. Commun. 12, 4682 (2021).
Cuneo, I. F. et al. Differences in grapevine rootstock sensitivity and recovery from drought are linked to fine root cortical lacunae and root tip function. New Phytol. 229, 272–283 (2021).
Naseer, S. et al. Casparian strip diffusion barrier in Arabidopsis is made of a lignin polymer without suberin. Proc. Natl Acad. Sci. USA 109, 10101–10106 (2012).
DiMichele, W. A., Pfefferkorn, H. W. & Gastaldo, R. A. Response of Late Carboniferous and Early Permian plant communities to climate change. Annu. Rev. Earth Planet. Sci. 29, 461–487 (2001).
McElwain, J. C. Paleobotany and global change: important lessons for species to biomes from vegetation responses to past global change. Annu. Rev. Plant Biol. 69, 761–787 (2018).
Li, X. et al. A high-resolution climate simulation dataset for the past 540 million years. Sci. Data 9, 371 (2022).
Molina, I., Ohlrogge, J. B. & Pollard, M. Deposition and localization of lipid polyester in developing seeds of Brassica napus and Arabidopsis thaliana. Plant J. 53, 437–449 (2008).
Vishwanath, S. J. et al. Suberin-associated fatty alcohols in Arabidopsis: distributions in roots and contributions to seed coat barrier properties. Plant Physiol. 163, 1118–1132 (2013).
Lux, A., Morita, S., Abe, J. & Ito, K. An improved method for clearing and staining free-hand sections and whole-mount samples. Ann. Bot. 96, 989–996 (2005).
Ursache, R., Andersen, T. G., Marhavy, P. & Geldner, N. A protocol for combining fluorescent proteins with histological stains for diverse cell wall components. Plant J. 93, 399–412 (2018).
Wang, Z. G. et al. OsCASP1 is required for Casparian strip formation at endodermal cells of rice roots for selective uptake of mineral elements. Plant Cell 31, 2636–2648 (2019).
Kurihara, D., Mizuta, Y., Sato, Y. & Higashiyama, T. ClearSee: a rapid optical clearing reagent for whole-plant fluorescence imaging. Development 142, 4168–4179 (2015).
Wahrenburg, Z. et al. Transcriptional regulation of wound suberin deposition in potato cultivars with differential wound healing capacity. Plant J. 107, 77–99 (2021).
Leebens-Mack, J. H. et al. One thousand plant transcriptomes and the phylogenomics of green plants. Nature 574, 679–685 (2019).
Tatusov, R. L., Koonin, E. V. & Lipman, D. J. A genomic perspective on protein families. Science 278, 631–637 (1997).
Feng, T. et al. FAD2 gene radiation and positive selection contributed to polyacetylene metabolism evolution in campanulids. Plant Physiol. 181, 714–728 (2019).
Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinform. 10, 421 (2009).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
Capella-Gutierrez, S., Silla-Martinez, J. M. & Gabaldon, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).
Mirarab, S. et al. PASTA: ultra-large multiple sequence alignment for nucleotide and amino-acid sequences. J. Comput. Biol. 22, 377–386 (2015).
Zhang, C., Zhao, Y. M., Braun, E. L. & Mirarab, S. TAPER: pinpointing errors in multiple sequence alignments despite varying rates of evolution. Methods Ecol. Evol. 12, 2145–2158 (2021).
Andel, J., Perez, M. G. & Negrao, A. I. Estimating the dimension of a linear-model. Kybernetika 17, 514–525 (1981).
Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A. & Jermiin, L. S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587–589 (2017).
Kozlov, A. M., Darriba, D., Flouri, T., Morel, B. & Stamatakis, A. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35, 4453–4455 (2019).
Monakhova, Y. B. & Diehl, B. W. K. Multinuclear NMR screening of pharmaceuticals using standardization by H-2 integral of a deuterated solvent. J. Pharm. Biomed. 209, 114530 (2022).
Yang, Y. et al. Recent advances on phylogenomics of gymnosperms and a new classification. Plant Divers. 44, 340–350 (2022).
Qi, X. P. et al. A well-resolved fern nuclear phylogeny reveals the evolution history of numerous transcription factor families. Mol. Phylogenet. Evol. 127, 961–977 (2018).
Shekhar, V., Stӧckle, D., Thellmann, M. & Vermeer, J. E. M. The role of plant root systems in evolutionary adaptation. Curr. Top. Dev. Biol. 131, 55–80 (2019).
Acknowledgements
We thank J. Murray for suggestions and editing on this manuscript. We thank J. Vermeer and N. Geldner for kindly providing the A. thaliana mutant gelpquint-2 and the transgenetic line proCASP1::CDEF. We thank L. Xu, X. Gao, Z. Zhang, J. Li, W. Lan, S. Bu, W. Cai and S. Yin for their technical support. We also thank Y. He and the Experimental Auxiliary System, BL10U1 of Shanghai Synchrotron Radiation Facility for their support in using Raman microspectroscopy. This work was supported by the National Natural Science Foundation of China (grant nos. 31930024, 32070282 and U19A2026), Chinese Academy of Sciences (grant no. XDB27010103) and the Newton Fund (grant no. NAF\R1\201264).
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D.-Y.C., S.L., Y.S. and T.F. designed the study and wrote the manuscript. Y.S., T.F., C.-B.L., Y.-L.W., H.H., M.-L.H., X.F., X.Z., X.H., J.-C.W. and T.S. performed the experiments. Y.S., T.F. and C.-B.L. analysed the data. H.S., X.Y. and L.X. provided feedback on the manuscript.
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Extended data
Extended Data Fig. 1 Basic Fuchsin staining in root endodermis of the 18 species.
a, b, The positions for observing CS staining in dichotomous branching (a) and lateral branching (b) species as indicated by magenta or blue bars. c, Basic fuchsin staining pictures of endodermal cell walls at the positions as shown in (a) and (b). Species marked in magenta correspond to magenta bars in (a) and those marked in white correspond to blue bars in (b). These results were independently repeated three times. Lyj, Lycopodium japonicum; Sek, Selaginella kraussiana; Iss, Isoetes sinensis; Eqh, Equisetum hyemale; Opv, Ophioglossum vulgatum; Anf, Angiopteris fokiensis; Sac, Salvinia cucullata; Cer, Ceratopteris richardii; Nea, Nephrolepis auriculata; Pot, Polystichum tsus-simense; Adc, Adiantum capillus-veneris; Gib, Ginkgo biloba; Cyr, Cycas revoluta; Pib, Pinus bungeana; Tac, Taxus chinensis; Meg, Metasequoia glyptostroboides; Ors, Oryza sativa; Art, Arabidopsis thaliana. en, endodermis. Arrows pointed to the position of the Casparian strip. Scale bars: 10 µm.
Extended Data Fig. 2 Representative transmission electron microscopy pictures of endodermal cell walls.
a, b, The positions for observing CS staining in dichotomous branching (a) and lateral branching (b) species as indicated by magenta or blue bars. c, d, Ultrastructural observation of endodermal cells at the positions as shown in (a) and (b) after plasmolysis. Species marked in magenta correspond to magenta bars in (a) and those marked in white correspond to blue bars in (b). Plasmolysis was induced by incubating root sections in 0.8 M mannitol for 1 hour. c, The overview TEM pictures of endodermal cells after plasmolysis. Magenta dotted boxes show the cell wall between adjacent endodermal cells. Black asterisks (*) show the apoplastic space generated by plasmolysis. These results were independently repeated three times. en, endodermis; co, cortex; ste, stele; Scale bars: 5 µm. d, Details of the CS and the CSD-CS attachment.The arrows indicate attachment of CSD to CS after plasmolysis. These results were independently repeated three times. CS, Casparin strip. Scale bars: 500 nm. Lyj, Lycopodium japonicum; Sek, Selaginella kraussiana; Iss, Isoetes sinensis; Eqh, Equisetum hyemale; Opv, Ophioglossum vulgatum; Anf, Angiopteris fokiensis; Sac, Salvinia cucullata; Cer, Ceratopteris richardii; Nea, Nephrolepis auriculata; Pot, Polystichum tsus-simense; Adc, Adiantum capillus-veneris; Gib, Ginkgo biloba; Cyr, Cycas revoluta; Pib, Pinus bungeana; Tac, Taxus chinensis; Meg, Metasequoia glyptostroboides; Ors, Oryza sativa; Art, Arabidopsis thaliana.
Extended Data Fig. 3 Fluorol yellow staining in root endodermis at fully developed of the vascular plants.
a, b, The positions for observing CS staining in dichotomous branching (a) and lateral branching (b) species as indicated by colourful bars. c, d, FY 088 staining of roots at the positions as shown in (a) and (b). Species marked in magenta correspond to magenta bars in (a) and those marked in green and yellow species correspond to green and yellow bars respectively in (b). c, The overview FY 088 staining pictures of roots. These results were independently repeated three times. en, endodermis; Scale bars: 50 µm. d, Details of FY 088 staining pictures of the endodermal cells from three independent experiment. en, endodermis. Scale bars: 10 µm. Lyj, Lycopodium japonicum; Sek, Selaginella kraussiana; Iss, Isoetes sinensis; Eqh, Equisetum hyemale; Opv, Ophioglossum vulgatum; Anf, Angiopteris fokiensis; Sac, Salvinia cucullata; Cer, Ceratopteris richardii; Nea, Nephrolepis auriculata; Pot, Polystichum tsus-simense; Adc, Adiantum capillus-veneris; Gib, Ginkgo biloba; Cyr, Cycas revoluta; Pib, Pinus bungeana; Tac, Taxus chinensis; Meg, Metasequoia glyptostroboides; Ors, Oryza sativa; Art, Arabidopsis thaliana.
Extended Data Fig. 4 Phylogenetic tree of MYB41 family in plants.
The tree was inferred using maximum likelihood method with model Q.plant+R9. Numbers near nodes are bootstrap support values. The Arabidopsis MYB genes that are known to be involved in root suberization are in red. The genes used for function test are indicated by red star symbol.
Extended Data Fig. 5 The expression of 35S::MYBs-eYFP in tobacco leaves.
Expression and subcellular localization of the MYB homologs in epidermal cells of N. benthamiana leaves were observed under a confocal microscope. These results were independently repeated three times. DAPI was used as a nucler marker. The corresponding genes were cloned from Selaginella kraussiana, Salvinia cucullata, Adiantum capillus-veneris, Ginkgo biloba and Arabidopsis thaliana. Scale bars: 20 μm.
Extended Data Fig. 6 Raw data for Fig. 4c.
Raman spectra of D2O obtained from the mannitol after a 2-hour treatment. Shaded areas show the extent of one standard deviation on both sides of the mean values, n = 3. These results were independently repeated three times with similar outcomes.
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Su, Y., Feng, T., Liu, CB. et al. The evolutionary innovation of root suberin lamellae contributed to the rise of seed plants. Nat. Plants 9, 1968–1977 (2023). https://doi.org/10.1038/s41477-023-01555-1
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DOI: https://doi.org/10.1038/s41477-023-01555-1
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