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Yamoune A, Zdarska M, Depaepe T, Rudolfova A, Skalak J, Berendzen KW, Mira-Rodado V, Fitz M, Pekarova B, Nicolas Mala KL, Tarr P, Spackova E, Tomovicova L, Parizkova B, Franczyk A, Kovacova I, Dolgikh V, Zemlyanskaya E, Pernisova M, Novak O, Meyerowitz E, Harter K, Van Der Straeten D, Hejatko J. Cytokinins regulate spatially specific ethylene production to control root growth in Arabidopsis. PLANT COMMUNICATIONS 2024:101013. [PMID: 38961625 DOI: 10.1016/j.xplc.2024.101013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 06/03/2024] [Accepted: 06/28/2024] [Indexed: 07/05/2024]
Abstract
Two principal growth regulators, cytokinins and ethylene, are known to interact in the regulation of plant growth. However, information about the underlying molecular mechanism and positional specificity of cytokinin/ethylene crosstalk in the control of root growth is scarce. We have identified the spatial specificity of cytokinin-regulated root elongation and root apical meristem (RAM) size, both of which we demonstrate to be dependent on ethylene biosynthesis. Upregulation of the cytokinin biosynthetic gene ISOPENTENYLTRANSFERASE (IPT) in proximal and peripheral tissues leads to both root and RAM shortening. By contrast, IPT activation in distal and inner tissues reduces RAM size while leaving the root length comparable to that of mock-treated controls. We show that cytokinins regulate two steps specific to ethylene biosynthesis: production of the ethylene precursor 1-aminocyclopropane-1-carboxylate (ACC) by ACC SYNTHASEs (ACSs) and its conversion to ethylene by ACC OXIDASEs (ACOs). We describe cytokinin- and ethylene-specific regulation controlling the activity of ACSs and ACOs that are spatially discrete along both proximo/distal and radial root axes. Using direct ethylene measurements, we identify ACO2, ACO3, and ACO4 as being responsible for ethylene biosynthesis and ethylene-regulated root and RAM shortening in cytokinin-treated Arabidopsis. Direct interaction between ARABIDOPSIS RESPONSE REGULATOR 2 (ARR2), a member of the multistep phosphorelay cascade, and the C-terminal portion of ETHYLENE INSENSITIVE 2 (EIN2-C), a key regulator of canonical ethylene signaling, is involved in the cytokinin-induced, ethylene-mediated control of ACO4. We propose tight cooperation between cytokinin and ethylene signaling in the spatially specific regulation of ethylene biosynthesis as a key aspect of the hormonal control of root growth.
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Affiliation(s)
- Amel Yamoune
- CEITEC (Central European Institute of Technology), Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Marketa Zdarska
- CEITEC (Central European Institute of Technology), Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Thomas Depaepe
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, Gent, Belgium
| | - Anna Rudolfova
- CEITEC (Central European Institute of Technology), Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jan Skalak
- CEITEC (Central European Institute of Technology), Masaryk University, Brno, Czech Republic
| | | | | | - Michael Fitz
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Blanka Pekarova
- CEITEC (Central European Institute of Technology), Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Katrina Leslie Nicolas Mala
- CEITEC (Central European Institute of Technology), Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Paul Tarr
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Eliska Spackova
- CEITEC (Central European Institute of Technology), Masaryk University, Brno, Czech Republic
| | - Lucia Tomovicova
- CEITEC (Central European Institute of Technology), Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Barbora Parizkova
- Faculty of Science, Palacký University and Institute of Experimental Botany, The Czech Academy of Sciences, Olomouc, Czech Republic
| | - Abigail Franczyk
- CEITEC (Central European Institute of Technology), Masaryk University, Brno, Czech Republic
| | - Ingrid Kovacova
- CEITEC (Central European Institute of Technology), Masaryk University, Brno, Czech Republic
| | - Vladislav Dolgikh
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia; Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Elena Zemlyanskaya
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia; Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Marketa Pernisova
- CEITEC (Central European Institute of Technology), Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Ondrej Novak
- Faculty of Science, Palacký University and Institute of Experimental Botany, The Czech Academy of Sciences, Olomouc, Czech Republic
| | - Elliot Meyerowitz
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Klaus Harter
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | | | - Jan Hejatko
- CEITEC (Central European Institute of Technology), Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
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Ganesh A, Shukla V, Mohapatra A, George AP, Bhukya DPN, Das KK, Kola VSR, Suresh A, Ramireddy E. Root Cap to Soil Interface: A Driving Force Toward Plant Adaptation and Development. PLANT & CELL PHYSIOLOGY 2022; 63:1038-1051. [PMID: 35662353 DOI: 10.1093/pcp/pcac078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/05/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Land plants have developed robust roots to grow in diverse soil ecosystems. The distal end of the root tip has a specialized organ called the 'root cap'. The root cap assists the roots in penetrating the ground, absorbing water and minerals, avoiding heavy metals and regulating the rhizosphere microbiota. Furthermore, root-cap-derived auxin governs the lateral root patterning and directs root growth under varying soil conditions. The root cap formation is hypothesized as one of the key innovations during root evolution. Morphologically diversified root caps in early land plant lineage and later in angiosperms aid in improving the adaptation of roots and, thereby, plants in diverse soil environments. This review article presents a retrospective view of the root cap's important morphological and physiological characteristics for the root-soil interaction and their response toward various abiotic and biotic stimuli. Recent single-cell RNAseq data shed light on root cap cell-type-enriched genes. We compiled root cap cell-type-enriched genes from Arabidopsis, rice, maize and tomato and analyzed their transcription factor (TF) binding site enrichment. Further, the putative gene regulatory networks derived from root-cap-enriched genes and their TF regulators highlight the species-specific biological functions of root cap genes across the four plant species.
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Affiliation(s)
- Alagarasan Ganesh
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
| | - Vishnu Shukla
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
| | - Ankita Mohapatra
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
| | - Abin Panackal George
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
| | - Durga Prasad Naik Bhukya
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
| | - Krishna Kodappully Das
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
| | - Vijaya Sudhakara Rao Kola
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
| | - Aparna Suresh
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
| | - Eswarayya Ramireddy
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
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Tian J, Jiang W, Si J, Han Z, Li C, Chen D. Developmental Characteristics and Auxin Response of Epiphytic Root in Dendrobium catenatum. FRONTIERS IN PLANT SCIENCE 2022; 13:935540. [PMID: 35812932 PMCID: PMC9260429 DOI: 10.3389/fpls.2022.935540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Dendrobium catenatum, a traditional precious Chinese herbal medicine, belongs to epiphytic orchids. Its special life mode leads to the specialization of roots, but there is a lack of systematic research. The aerial root in D. catenatum displays diverse unique biological characteristics, and it initially originates from the opposite pole of the shoot meristem within the protocorm. The root development of D. catenatum is not only regulated by internal cues but also adjusts accordingly with the change in growth environments. D. catenatum root is highly tolerant to auxin, which may be closely related to its epiphytic life. Exogenous auxin treatment has dual effects on D. catenatum roots: relatively low concentration promotes root elongation, which is related to the induced expression of cell wall synthesis genes; excessive concentration inhibits the differentiation of velamen and exodermis and promotes the overproliferation of cortical cells, which is related to the significant upregulation of WOX11-WOX5 regeneration pathway genes and cell division regulatory genes. Overexpression of D. catenatum WOX12 (DcWOX12) in Arabidopsis inhibits cell and organ differentiation, but induces cell dedifferentiation and callus production. Therefore, DcWOX12 not only retains the characteristics of ancestors as stem cell regulators, but also obtains stronger cell fate transformation ability than homologous genes of other species. These findings suggest that the aerial root of D. catenatum evolves special structure and developmental characteristics to adapt to epiphytic life, providing insight into ideal root structure breeding of simulated natural cultivation in D. catenatum and a novel target gene for improving the efficiency of monocot plant transformation.
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Abstract
There can be no doubt that early land plant evolution transformed the planet but, until recently, how and when this was achieved was unclear. Coincidence in the first appearance of land plant fossils and formative shifts in atmospheric oxygen and CO2 are an artefact of the paucity of earlier terrestrial rocks. Disentangling the timing of land plant bodyplan assembly and its impact on global biogeochemical cycles has been precluded by uncertainty concerning the relationships of bryophytes to one another and to the tracheophytes, as well as the timescale over which these events unfolded. New genome and transcriptome sequencing projects, combined with the application of sophisticated phylogenomic modelling methods, have yielded increasing support for the Setaphyta clade of liverworts and mosses, within monophyletic bryophytes. We consider the evolution of anatomy, genes, genomes and of development within this phylogenetic context, concluding that many vascular plant (tracheophytes) novelties were already present in a comparatively complex last common ancestor of living land plants (embryophytes). Molecular clock analyses indicate that embryophytes emerged in a mid-Cambrian to early Ordovician interval, compatible with hypotheses on their role as geoengineers, precipitating early Palaeozoic glaciations.
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Affiliation(s)
- Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
| | - C Jill Harrison
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Jordi Paps
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Harald Schneider
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK; Center of Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, China
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5
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Fang T, Motte H, Parizot B, Beeckman T. Early "Rootprints" of Plant Terrestrialization: Selaginella Root Development Sheds Light on Root Evolution in Vascular Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:735514. [PMID: 34671375 PMCID: PMC8521068 DOI: 10.3389/fpls.2021.735514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
Roots provide multiple key functions for plants, including anchorage and capturing of water and nutrients. Evolutionarily, roots represent a crucial innovation that enabled plants to migrate from aquatic to terrestrial environment and to grow in height. Based on fossil evidence, roots evolved at least twice independently, once in the lycophyte clade and once in the euphyllophyte (ferns and seed plants) clade. In lycophytes, roots originated in a stepwise manner. Despite their pivotal position in root evolution, it remains unclear how root development is controlled in lycophytes. Getting more insight into lycophyte root development might shed light on how genetic players controlling the root meristem and root developmental processes have evolved. Unfortunately, genetic studies in lycophytes are lagging behind, lacking advanced biotechnological tools, partially caused by the limited economic value of this clade. The technology of RNA sequencing (RNA-seq) at least enabled transcriptome studies, which could enhance the understanding or discovery of genes involved in the root development of this sister group of euphyllophytes. Here, we provide an overview of the current knowledge on root evolution followed by a survey of root developmental events and how these are genetically and hormonally controlled, starting from insights obtained in the model seed plant Arabidopsis and where possible making a comparison with lycophyte root development. Second, we suggest possible key genetic regulators in root development of lycophytes mainly based on their expression profiles in Selaginella moellendorffii and phylogenetics. Finally, we point out challenges and possible future directions for research on root evolution.
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Affiliation(s)
- Tao Fang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hans Motte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Boris Parizot
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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Hetherington AJ, Bridson SL, Lee Jones A, Hass H, Kerp H, Dolan L. An evidence-based 3D reconstruction of Asteroxylon mackiei, the most complex plant preserved from the Rhynie chert. eLife 2021; 10:e69447. [PMID: 34425940 PMCID: PMC8384418 DOI: 10.7554/elife.69447] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/05/2021] [Indexed: 01/16/2023] Open
Abstract
The Early Devonian Rhynie chert preserves the earliest terrestrial ecosystem and informs our understanding of early life on land. However, our knowledge of the 3D structure, and development of these plants is still rudimentary. Here we used digital 3D reconstruction techniques to produce the first well-evidenced reconstruction of the structure and development of the rooting system of the lycopsid Asteroxylon mackiei, the most complex plant in the Rhynie chert. The reconstruction reveals the organisation of the three distinct axis types - leafy shoot axes, root-bearing axes, and rooting axes - in the body plan. Combining this reconstruction with developmental data from fossilised meristems, we demonstrate that the A. mackiei rooting axis - a transitional lycophyte organ between the rootless ancestral state and true roots - developed from root-bearing axes by anisotomous dichotomy. Our discovery demonstrates how this unique organ developed and highlights the value of evidence-based reconstructions for understanding the development and evolution of the first complex vascular plants on Earth.
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Affiliation(s)
| | - Siobhán L Bridson
- Department of Plant Sciences, University of OxfordOxfordUnited Kingdom
| | - Anna Lee Jones
- Department of Plant Sciences, University of OxfordOxfordUnited Kingdom
- Department of Plant Sciences, University of CambridgeCambridgeUnited Kingdom
| | - Hagen Hass
- Research Group for Palaeobotany, Institute for Geology and Palaeontology, Westfälische Wilhelms-Universität MünsterMünsterGermany
| | - Hans Kerp
- Research Group for Palaeobotany, Institute for Geology and Palaeontology, Westfälische Wilhelms-Universität MünsterMünsterGermany
| | - Liam Dolan
- Department of Plant Sciences, University of OxfordOxfordUnited Kingdom
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Aragón-Raygoza A, Vasco A, Blilou I, Herrera-Estrella L, Cruz-Ramírez A. Development and Cell Cycle Activity of the Root Apical Meristem in the Fern Ceratopteris richardii. Genes (Basel) 2020; 11:E1455. [PMID: 33291610 PMCID: PMC7761924 DOI: 10.3390/genes11121455] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 12/11/2022] Open
Abstract
Ferns are a representative clade in plant evolution although underestimated in the genomic era. Ceratopteris richardii is an emergent model for developmental processes in ferns, yet a complete scheme of the different growth stages is necessary. Here, we present a developmental analysis, at the tissue and cellular levels, of the first shoot-borne root of Ceratopteris. We followed early stages and emergence of the root meristem in sporelings. While assessing root growth, the first shoot-borne root ceases its elongation between the emergence of the fifth and sixth roots, suggesting Ceratopteris roots follow a determinate developmental program. We report cell division frequencies in the stem cell niche after detecting labeled nuclei in the root apical cell (RAC) and derivatives after 8 h of exposure. These results demonstrate the RAC has a continuous mitotic activity during root development. Detection of cell cycle activity in the RAC at early times suggests this cell acts as a non-quiescent organizing center. Overall, our results provide a framework to study root function and development in ferns and to better understand the evolutionary history of this organ.
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Affiliation(s)
- Alejandro Aragón-Raygoza
- Molecular and Developmental Complexity Group at Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, Irapuato 36821, Guanajuato, Mexico;
- Metabolic Engineering Group, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, Irapuato 36821, Guanajuato, Mexico;
| | - Alejandra Vasco
- Botanical Research Institute of Texas (BRIT), Fort Worth, TX 76107-3400, USA;
| | - Ikram Blilou
- Laboratory of Plant Cell and Developmental Biology, Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
| | - Luis Herrera-Estrella
- Metabolic Engineering Group, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, Irapuato 36821, Guanajuato, Mexico;
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
| | - Alfredo Cruz-Ramírez
- Molecular and Developmental Complexity Group at Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, Irapuato 36821, Guanajuato, Mexico;
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Delaux PM, Hetherington AJ, Coudert Y, Delwiche C, Dunand C, Gould S, Kenrick P, Li FW, Philippe H, Rensing SA, Rich M, Strullu-Derrien C, de Vries J. Reconstructing trait evolution in plant evo-devo studies. Curr Biol 2020; 29:R1110-R1118. [PMID: 31689391 DOI: 10.1016/j.cub.2019.09.044] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Our planet is teeming with an astounding diversity of plants. In a mere single group of closely related species, tremendous diversity can be observed in their form and function - the colour of petals in flowering plants, the shape of the fronds in ferns, and the branching pattern of the gametophyte in mosses. Diversity can also be found in subtler traits, such as the resistance to pathogens or the ability to recruit symbiotic microbes from the environment. Plant traits can also be highly conserved - at the cellular and metabolic levels, entire biosynthetic pathways are present in all plant groups, and morphological characteristics such as vascular tissues have been conserved for hundreds of millions of years. The research community that seeks to understand these traits - both the diverse and the conserved - by taking an evolutionary point-of-view on plant biology is growing. Here, we summarize a subset of the different aspects of plant evolutionary biology, provide a guide for structuring comparative biology approaches and discuss the pitfalls that (plant) researchers should avoid when embarking on such studies.
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Affiliation(s)
- Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Castanet-Tolosan, France.
| | | | - Yoan Coudert
- Laboratoire Reproduction et Développement des Plantes, Ecole Normale Supérieure de Lyon, CNRS, INRA, Université Claude Bernard Lyon 1, INRIA, 46 Allée d'Italie, Lyon, 69007, France
| | | | - Christophe Dunand
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Castanet-Tolosan, France
| | - Sven Gould
- Institute for Molecular Evolution, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Paul Kenrick
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA; Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Hervé Philippe
- Centre de Théorisation et de Modélisation de la Biodiversité, Station d'Écologie Théorique et Expérimentale, UMR CNRS 5321, Moulis, France; Département de Biochimie, Université de Montréal, Montréal, Québec, Canada
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043 Marburg, Germany; BIOSS Centre for Biological Signalling Studies, University Freiburg, Germany; SYNMIKRO Research Center, University of Marburg, 35043 Marburg, Germany
| | - Mélanie Rich
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Castanet-Tolosan, France
| | - Christine Strullu-Derrien
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK; Institut de Systématique, Évolution, Biodiversité, UMR 7205, Muséum National d'Histoire Naturelle, Paris, France
| | - Jan de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada; Institute of Microbiology, Technische Universitaet Braunschweig, 38106 Braunschweig, Germany; Institute for Microbiology and Genetics, Bioinformatics, University of Göttingen, Goldschmidtstr. 1, 37077 Göttingen, Germany
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Althoff F, Zachgo S. Transformation of Riccia fluitans, an Amphibious Liverwort Dynamically Responding to Environmental Changes. Int J Mol Sci 2020; 21:E5410. [PMID: 32751392 PMCID: PMC7432341 DOI: 10.3390/ijms21155410] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 01/21/2023] Open
Abstract
The colonization of land by streptophyte algae, ancestors of embryophyte plants, was a fundamental event in the history of life on earth. Bryophytes are early diversifying land plants that mark the transition from freshwater to terrestrial ecosystems. The amphibious liverwort Riccia fluitans can thrive in aquatic and terrestrial environments and thus represents an ideal organism to investigate this major transition. Therefore, we aimed to establish a transformation protocol for R. fluitans to make it amenable for genetic analyses. An Agrobacterium transformation procedure using R. fluitans callus tissue allows to generate stably transformed plants within 10 weeks. Furthermore, for comprehensive studies spanning all life stages, we demonstrate that the switch from vegetative to reproductive development can be induced by both flooding and poor nutrient availability. Interestingly, a single R. fluitans plant can consecutively adapt to different growth environments and forms distinctive and reversible features of the thallus, photosynthetically active tissue that is thus functionally similar to leaves of vascular plants. The morphological plasticity affecting vegetative growth, air pore formation, and rhizoid development realized by one genotype in response to two different environments makes R. fluitans ideal to study the adaptive molecular mechanisms enabling the colonialization of land by aquatic plants.
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Affiliation(s)
- Felix Althoff
- Botany Department, School of Biology and Chemistry, Osnabrück University, 49076 Osnabrück, Germany
| | - Sabine Zachgo
- Botany Department, School of Biology and Chemistry, Osnabrück University, 49076 Osnabrück, Germany
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Gerke P, Szövényi P, Neubauer A, Lenz H, Gutmann B, McDowell R, Small I, Schallenberg-Rüdinger M, Knoop V. Towards a plant model for enigmatic U-to-C RNA editing: the organelle genomes, transcriptomes, editomes and candidate RNA editing factors in the hornwort Anthoceros agrestis. THE NEW PHYTOLOGIST 2020; 225:1974-1992. [PMID: 31667843 DOI: 10.1111/nph.16297] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 10/20/2019] [Indexed: 06/10/2023]
Abstract
Hornworts are crucial to understand the phylogeny of early land plants. The emergence of 'reverse' U-to-C RNA editing accompanying the widespread C-to-U RNA editing in plant chloroplasts and mitochondria may be a molecular synapomorphy of a hornwort-tracheophyte clade. C-to-U RNA editing is well understood after identification of many editing factors in models like Arabidopsis thaliana and Physcomitrella patens, but there is no plant model yet to investigate U-to-C RNA editing. The hornwort Anthoceros agrestis is now emerging as such a model system. We report on the assembly and analyses of the A. agrestis chloroplast and mitochondrial genomes, their transcriptomes and editomes, and a large nuclear gene family encoding pentatricopeptide repeat (PPR) proteins likely acting as RNA editing factors. Both organelles in A. agrestis feature high amounts of RNA editing, with altogether > 1100 sites of C-to-U and 1300 sites of U-to-C editing. The nuclear genome reveals > 1400 genes for PPR proteins with variable carboxyterminal DYW domains. We observe significant variants of the 'classic' DYW domain, in the meantime confirmed as the cytidine deaminase for C-to-U editing, and discuss the first attractive candidates for reverse editing factors given their excellent matches to U-to-C editing targets according to the PPR-RNA binding code.
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Affiliation(s)
- Philipp Gerke
- Institut für Zelluläre und Molekulare Botanik (IZMB), University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstr. 107, 8008, Zürich, Switzerland
| | - Anna Neubauer
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstr. 107, 8008, Zürich, Switzerland
| | - Henning Lenz
- IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Bernard Gutmann
- EditForce Inc., West Zone #429, Kyushu University, 744 Motooka, Nishi-Ku, Fukuoka, 819-0395, Japan
| | - Rose McDowell
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia at Crawley, Perth, WA, 6009, Australia
| | - Ian Small
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia at Crawley, Perth, WA, 6009, Australia
| | | | - Volker Knoop
- Institut für Zelluläre und Molekulare Botanik (IZMB), University of Bonn, Kirschallee 1, 53115, Bonn, Germany
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11
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Hetherington AJ, Dolan L. Rhynie chert fossils demonstrate the independent origin and gradual evolution of lycophyte roots. CURRENT OPINION IN PLANT BIOLOGY 2019; 47:119-126. [PMID: 30562673 DOI: 10.1016/j.pbi.2018.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 12/03/2018] [Accepted: 12/04/2018] [Indexed: 05/13/2023]
Abstract
Mapping fossil traits onto the land plant phylogenetic framework indicates that there were at least two independent origins of roots among extant vascular plants - once in lycophytes and independently in euphyllophytes. At least two rooting structural types are found among extinct species preserved in the Rhynie chert. First, species that lacked roots and developed horizontal axes that developed rhizoids. Second, the rooting axes of Asteroxylon mackiei resembled the roots of extant lycopsids but lacked root hairs and root caps. These two rooting structures preceded the evolution of the roots of extant lycophytes comprising axes on which root hairs and root caps developed. These data demonstrate the defining root characters evolved gradually in the lycophyte lineage.
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Affiliation(s)
| | - Liam Dolan
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
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12
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13
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Edwards D, Kenrick P, Dolan L. History and contemporary significance of the Rhynie cherts-our earliest preserved terrestrial ecosystem. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2016.0489. [PMID: 29254954 DOI: 10.1098/rstb.2016.0489] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2017] [Indexed: 01/03/2023] Open
Abstract
The Rhynie cherts Unit is a 407 million-year old geological site in Scotland that preserves the most ancient known land plant ecosystem, including associated animals, fungi, algae and bacteria. The quality of preservation is astonishing, and the initial description of several plants 100 years ago had a huge impact on botany. Subsequent discoveries provided unparalleled insights into early life on land. These include the earliest records of plant life cycles and fungal symbioses, the nature of soil microorganisms and the diversity of arthropods. Today the Rhynie chert (here including the Rhynie and Windyfield cherts) takes on new relevance, especially in relation to advances in the fields of developmental genetics and Earth systems science. New methods and analytical techniques also contribute to a better understanding of the environment and its organisms. Key discoveries are reviewed, focusing on the geology of the site, the organisms and the palaeoenvironments. The plants and their symbionts are of particular relevance to understanding the early evolution of the plant life cycle and the origins of fundamental organs and tissue systems. The Rhynie chert provides remarkable insights into the structure and interactions of early terrestrial communities, and it has a significant role to play in developing our understanding of their broader impact on Earth systems.This article is part of a discussion meeting issue 'The Rhynie cherts: our earliest terrestrial ecosystem revisited'.
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Affiliation(s)
- Dianne Edwards
- School of Earth and Ocean Sciences, Cardiff University, Cardiff CF10 3AT, UK
| | - Paul Kenrick
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Liam Dolan
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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14
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Hetherington FM, Nützmann HW. Embracing the next generation of plant scientists. THE NEW PHYTOLOGIST 2018; 217:504-506. [PMID: 29271035 DOI: 10.1111/nph.14963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- Flora M Hetherington
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK
| | - Hans-Wilhelm Nützmann
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
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15
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Augstein F, Carlsbecker A. Getting to the Roots: A Developmental Genetic View of Root Anatomy and Function From Arabidopsis to Lycophytes. FRONTIERS IN PLANT SCIENCE 2018; 9:1410. [PMID: 30319672 PMCID: PMC6167918 DOI: 10.3389/fpls.2018.01410] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 09/05/2018] [Indexed: 05/11/2023]
Abstract
Roots attach plants to the ground and ensure efficient and selective uptake of water and nutrients. These functions are facilitated by the morphological and anatomical structures of the root, formed by the activity of the root apical meristem (RAM) and consecutive patterning and differentiation of specific tissues with distinct functions. Despite the importance of this plant organ, its evolutionary history is not clear, but fossils suggest that roots evolved at least twice, in the lycophyte (clubmosses and their allies) and in the euphyllophyte (ferns and seed plants) lineages. Both lycophyte and euphyllophyte roots grow indeterminately by the action of an apical meristem, which is protected by a root cap. They produce root hairs, and in most species the vascular stele is guarded by a specialized endodermal cell layer. Hence, most of these traits must have evolved independently in these lineages. This raises the question if the development of these apparently analogous tissues is regulated by distinct or homologous genes, independently recruited from a common ancestor of lycophytes and euphyllophytes. Currently, there are few studies of the genetic and molecular regulation of lycophyte and fern roots. Therefore, in this review, we focus on key regulatory networks that operate in root development in the model angiosperm Arabidopsis. We describe current knowledge of the mechanisms governing RAM maintenance as well as patterning and differentiation of tissues, such as the endodermis and the vasculature, and compare with other species. We discuss the importance of comparative analyses of anatomy and morphology of extant and extinct species, along with analyses of gene regulatory networks and, ultimately, gene function in plants holding key phylogenetic positions to test hypotheses of root evolution.
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