1
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Arnoux-Courseaux M, Coudert Y. Re-examining meristems through the lens of evo-devo. TRENDS IN PLANT SCIENCE 2024; 29:413-427. [PMID: 38040554 DOI: 10.1016/j.tplants.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 12/03/2023]
Abstract
The concept of the meristem was introduced in 1858 to characterize multicellular, formative, and proliferative tissues that give rise to the entire plant body, based on observations of vascular plants. Although its original definition did not encompass bryophytes, this concept has been used and continuously refined over the past 165 years to describe the diverse apices of all land plants. Here, we re-examine this matter in light of recent evo-devo research and show that, despite displaying high anatomical diversity, land plant meristems are unified by shared genetic control. We also propose a modular view of meristem function and highlight multiple evolutionary mechanisms that are likely to have contributed to the assembly and diversification of the varied meristems during the course of plant evolution.
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Affiliation(s)
- Moïra Arnoux-Courseaux
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, INRIA, Lyon 69007, France; Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des Martyrs, F-38054, Grenoble, France
| | - Yoan Coudert
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, INRIA, Lyon 69007, France.
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2
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Demko V, Belova T, Messerer M, Hvidsten TR, Perroud PF, Ako AE, Johansen W, Mayer KFX, Olsen OA, Lang D. Regulation of developmental gatekeeping and cell fate transition by the calpain protease DEK1 in Physcomitrium patens. Commun Biol 2024; 7:261. [PMID: 38438476 PMCID: PMC10912778 DOI: 10.1038/s42003-024-05933-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 02/19/2024] [Indexed: 03/06/2024] Open
Abstract
Calpains are cysteine proteases that control cell fate transitions whose loss of function causes severe, pleiotropic phenotypes in eukaryotes. Although mainly considered as modulatory proteases, human calpain targets are directed to the N-end rule degradation pathway. Several such targets are transcription factors, hinting at a gene-regulatory role. Here, we analyze the gene-regulatory networks of the moss Physcomitrium patens and characterize the regulons that are misregulated in mutants of the calpain DEFECTIVE KERNEL1 (DEK1). Predicted cleavage patterns of the regulatory hierarchies in five DEK1-controlled subnetworks are consistent with a pleiotropic and regulatory role during cell fate transitions targeting multiple functions. Network structure suggests DEK1-gated sequential transitions between cell fates in 2D-to-3D development. Our method combines comprehensive phenotyping, transcriptomics and data science to dissect phenotypic traits, and our model explains the protease function as a switch gatekeeping cell fate transitions potentially also beyond plant development.
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Affiliation(s)
- Viktor Demko
- Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 84104, Bratislava, Slovakia
- Plant Science and Biodiversity Center, Slovak Academy of Sciences, Dubravska cesta 9, 84104, Bratislava, Slovakia
| | - Tatiana Belova
- Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
| | - Maxim Messerer
- Plant Genome and Systems Biology, Helmholtz Center Munich-Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Torgeir R Hvidsten
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Pierre-François Perroud
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Ako Eugene Ako
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 31, 2318, Hamar, Norway
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Brackenhurst Campus, Southwell, Nottinghamshire, NG25 0QF, UK
| | - Wenche Johansen
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 31, 2318, Hamar, Norway
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Center Munich-Research Center for Environmental Health, 85764, Neuherberg, Germany
- School of Life Sciences, Technical University Munich, 85354, Freising, Germany
| | - Odd-Arne Olsen
- Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Daniel Lang
- Plant Genome and Systems Biology, Helmholtz Center Munich-Research Center for Environmental Health, 85764, Neuherberg, Germany.
- Bundeswehr Institute of Microbiology, Microbial Genomics and Bioforensics, 80937, Munich, Germany.
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3
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Cammarata J, Roeder AHK, Scanlon MJ. The ratio of auxin to cytokinin controls leaf development and meristem initiation in Physcomitrium patens. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6541-6550. [PMID: 37498739 DOI: 10.1093/jxb/erad299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
Abstract
Crosstalk between auxin and cytokinin contributes to widespread developmental processes, including root and shoot meristem maintenance, phyllotaxy, and vascular patterning. However, our understanding of crosstalk between these hormones is limited primarily to angiosperms. The moss Physcomitrium patens (formerly Physcomitrella patens) is a powerful system for studying plant hormone function. Auxin and cytokinin play similar roles in regulating moss gametophore (shoot) architecture, to those in flowering plant shoots. However, auxin-cytokinin crosstalk is poorly understood in moss. Here we find that the ratio of auxin to cytokinin is an important determinant of development in P. patens, especially during leaf development and branch stem cell initiation. Addition of high levels of auxin to P. patens gametophores blocks leaf outgrowth. However, simultaneous addition of high levels of both auxin and cytokinin partially restores leaf outgrowth, suggesting that the ratio of these hormones is the predominant factor. Likewise, during branch initiation and outgrowth, chemical inhibition of auxin synthesis phenocopies cytokinin application. Finally, cytokinin-insensitive mutants resemble plants with altered auxin signaling and are hypersensitive to auxin. In summary, our results suggest that the ratio between auxin and cytokinin signaling is the basis for developmental decisions in the moss gametophore.
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Affiliation(s)
- Joseph Cammarata
- School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Adrienne H K Roeder
- School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Michael J Scanlon
- School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, NY 14853, USA
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4
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Garcias-Morales D, Palomar VM, Charlot F, Nogué F, Covarrubias AA, Reyes JL. N 6 -Methyladenosine modification of mRNA contributes to the transition from 2D to 3D growth in the moss Physcomitrium patens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:7-22. [PMID: 36794900 DOI: 10.1111/tpj.16149] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Plants colonized the land approximately 470 million years ago, coinciding with the development of apical cells that divide in three planes. The molecular mechanisms that underly the development of the 3D growth pattern are poorly understood, mainly because 3D growth in seed plants starts during embryo development. In contrast, the transition from 2D to 3D growth in the moss Physcomitrium patens has been widely studied, and it involves a large turnover of the transcriptome to allow the establishment of stage-specific transcripts that facilitate this developmental transition. N6 -Methyladenosine (m6 A) is the most abundant, dynamic and conserved internal nucleotide modification present on eukaryotic mRNA and serves as a layer of post-transcriptional regulation directly affecting several cellular processes and developmental pathways in many organisms. In Arabidopsis, m6 A has been reported to be essential for organ growth and determination, embryo development and responses to environmental signals. In this study, we identified the main genes of the m6 A methyltransferase complex (MTC), MTA, MTB and FIP37, in P. patens and demonstrate that their inactivation leads to the loss of m6 A in mRNA, a delay in the formation of gametophore buds and defects in spore development. Genome-wide analysis revealed several transcripts affected in the Ppmta background. We demonstrate that the PpAPB1-PpAPB4 transcripts, encoding central factors orchestrating the transition from 2D to 3D growth in P. patens, are modified by m6 A, whereas in the Ppmta mutant the lack of the m6 A marker is associated with a corresponding decrease in transcript accumulation. Overall, we suggest that m6 A is essential to enable the proper accumulation of these and other bud-specific transcripts directing the turnover of stage-specific transcriptomes, and thus promoting the transition from protonema to gametophore buds in P. patens.
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Affiliation(s)
- David Garcias-Morales
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, UNAM, Av. Universidad 2001, Cuernavaca, CP, 62210, Mexico
| | - V Miguel Palomar
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 1105 N. University Ave, Ann Arbor, MI, 48109-1085, USA
| | - Florence Charlot
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Fabien Nogué
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Alejandra A Covarrubias
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, UNAM, Av. Universidad 2001, Cuernavaca, CP, 62210, Mexico
| | - José L Reyes
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, UNAM, Av. Universidad 2001, Cuernavaca, CP, 62210, Mexico
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5
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Kapoor B, Kumar P, Verma V, Irfan M, Sharma R, Bhargava B. How plants conquered land: evolution of terrestrial adaptation. J Evol Biol 2023; 36:5-14. [PMID: 36083189 DOI: 10.1111/jeb.14062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 01/11/2023]
Abstract
The transition of plants from water to land is considered one of the most significant events in the evolution of life on Earth. The colonization of land by plants, accompanied by their morphological, physiological and developmental changes, resulted in plant biodiversity. Besides significantly influencing oxygen levels in the air and on land, plants manufacture organic matter from CO2 and water with the help of sunlight, paving the way for the diversification of nonplant lineages ranging from microscopic organisms to animals. Land plants regulate the climate by adjusting total biomass and energy flow. At the genetic level, these innovations are achieved through the rearrangement of pre-existing genetic information. Advances in genome sequencing technology are revamping our understanding of plant evolution. This study highlights the morphological and genomic innovations that allow plants to integrate life on Earth.
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Affiliation(s)
- Bhuvnesh Kapoor
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Pankaj Kumar
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Vipasha Verma
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Mohammad Irfan
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, New York, USA
| | - Rajnish Sharma
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Bhavya Bhargava
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
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6
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Zhou P, Chen H, Dang J, Shi Z, Shao Y, Liu C, Fan L, Wu Q. Single-cell transcriptome of Nepeta tenuifolia leaves reveal differentiation trajectories in glandular trichomes. FRONTIERS IN PLANT SCIENCE 2022; 13:988594. [PMID: 36340347 PMCID: PMC9627484 DOI: 10.3389/fpls.2022.988594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
The peltate glandular trichomes (PGTs) on Nepeta tenuifolia leaves can secrete and store bioactive essential oils. ScRNA-seq is a powerful tool for uncovering heterogeneous cells and exploring the development and differentiation of specific cells. Due to leaves rich in PGTs, the young leaves were used to isolated protoplasts and successfully captured 33,254 protoplasts for sequencing purposes. After cell type annotation, all the cells were partitioned into six broad populations with 19 clusters. Cells from PGTs were identified based on the expression patterns of trichome-specific genes, monoterpene biosynthetic genes, and metabolic analysis of PGT secretions. The developmental trajectories of PGTs were delineated by pseudotime analysis. Integrative analysis of scRNA-seq data from N. tenuifolia leaves and Arabidopsis thaliana shoot revealed that PGTs were specific to N. tenuifolia. Thus, our results provide a promising basis for exploring cell development and differentiation in plants, especially glandular trichome initiation and development.
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Affiliation(s)
- Peina Zhou
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Hongyu Chen
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Jingjie Dang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Zunrui Shi
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Yongfang Shao
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Chanchan Liu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Longjiang Fan
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Qinan Wu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, China
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7
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Fouracre JP, Harrison CJ. How was apical growth regulated in the ancestral land plant? Insights from the development of non-seed plants. PLANT PHYSIOLOGY 2022; 190:100-112. [PMID: 35771646 PMCID: PMC9434304 DOI: 10.1093/plphys/kiac313] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Land plant life cycles are separated into distinct haploid gametophyte and diploid sporophyte stages. Indeterminate apical growth evolved independently in bryophyte (moss, liverwort, and hornwort) and fern gametophytes, and tracheophyte (vascular plant) sporophytes. The extent to which apical growth in tracheophytes co-opted conserved gametophytic gene networks, or exploited ancestral sporophytic networks, is a long-standing question in plant evolution. The recent phylogenetic confirmation of bryophytes and tracheophytes as sister groups has led to a reassessment of the nature of the ancestral land plant. Here, we review developmental genetic studies of apical regulators and speculate on their likely evolutionary history.
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Affiliation(s)
| | - C Jill Harrison
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
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8
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Kleist TJ, Bortolazzo A, Keyser ZP, Perera AM, Irving TB, Venkateshwaran M, Atanjaoui F, Tang RJ, Maeda J, Cartwright HN, Christianson ML, Lemaux PG, Luan S, Ané JM. Stress-associated developmental reprogramming in moss protonemata by synthetic activation of the common symbiosis pathway. iScience 2022; 25:103754. [PMID: 35146383 PMCID: PMC8819110 DOI: 10.1016/j.isci.2022.103754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 12/22/2021] [Accepted: 01/07/2022] [Indexed: 11/19/2022] Open
Abstract
Symbioses between angiosperms and rhizobia or arbuscular mycorrhizal fungi are controlled through a conserved signaling pathway. Microbe-derived, chitin-based elicitors activate plant cell surface receptors and trigger nuclear calcium oscillations, which are decoded by a calcium/calmodulin-dependent protein kinase (CCaMK) and its target transcription factor interacting protein of DMI3 (IPD3). Genes encoding CCaMK and IPD3 have been lost in multiple non-mycorrhizal plant lineages yet retained among non-mycorrhizal mosses. Here, we demonstrated that the moss Physcomitrium is equipped with a bona fide CCaMK that can functionally complement a Medicago loss-of-function mutant. Conservation of regulatory phosphosites allowed us to generate predicted hyperactive forms of Physcomitrium CCaMK and IPD3. Overexpression of synthetically activated CCaMK or IPD3 in Physcomitrium led to abscisic acid (ABA) accumulation and ectopic development of brood cells, which are asexual propagules that facilitate escape from local abiotic stresses. We therefore propose a functional role for Physcomitrium CCaMK-IPD3 in stress-associated developmental reprogramming.
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Affiliation(s)
- Thomas J. Kleist
- Department of Plant & Microbial Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Plant Biology, Carnegie Institute for Science, Stanford, CA 94305, USA
- Institute for Molecular Physiology, Department of Biology, Heinrich Heine University, Düsseldorf 40225, Germany
- Corresponding author
| | - Anthony Bortolazzo
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zachary P. Keyser
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Adele M. Perera
- Department of Plant & Microbial Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Thomas B. Irving
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Fatiha Atanjaoui
- Institute for Molecular Physiology, Department of Biology, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Ren-Jie Tang
- Department of Plant & Microbial Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Junko Maeda
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Heather N. Cartwright
- Department of Plant Biology, Carnegie Institute for Science, Stanford, CA 94305, USA
| | - Michael L. Christianson
- Department of Plant & Microbial Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Peggy G. Lemaux
- Department of Plant & Microbial Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Sheng Luan
- Department of Plant & Microbial Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706, USA
- Corresponding author
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9
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Hata Y, Kyozuka J. Fundamental mechanisms of the stem cell regulation in land plants: lesson from shoot apical cells in bryophytes. PLANT MOLECULAR BIOLOGY 2021; 107:213-225. [PMID: 33609252 PMCID: PMC8648652 DOI: 10.1007/s11103-021-01126-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/01/2021] [Indexed: 05/02/2023]
Abstract
This review compares the molecular mechanisms of stem cell control in the shoot apical meristems of mosses and angiosperms and reveals the conserved features and evolution of plant stem cells. The establishment and maintenance of pluripotent stem cells in the shoot apical meristem (SAM) are key developmental processes in land plants including the most basal, bryophytes. Bryophytes, such as Physcomitrium (Physcomitrella) patens and Marchantia polymorpha, are emerging as attractive model species to study the conserved features and evolutionary processes in the mechanisms controlling stem cells. Recent studies using these model bryophyte species have started to uncover the similarities and differences in stem cell regulation between bryophytes and angiosperms. In this review, we summarize findings on stem cell function and its regulation focusing on different aspects including hormonal, genetic, and epigenetic control. Stem cell regulation through auxin, cytokinin, CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) signaling and chromatin modification by Polycomb Repressive Complex 2 (PRC2) and PRC1 is well conserved. Several transcription factors crucial for SAM regulation in angiosperms are not involved in the regulation of the SAM in mosses, but similarities also exist. These findings provide insights into the evolutionary trajectory of the SAM and the fundamental mechanisms involved in stem cell regulation that are conserved across land plants.
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Affiliation(s)
- Yuki Hata
- Graduate School of Life Sciences, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan.
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Abstract
High-throughput single-cell transcriptomic approaches have revolutionized our view of gene expression at the level of individual cells, providing new insights into their heterogeneity, identities, and functions. Recently, technical challenges to the application of single-cell transcriptomics to plants have been overcome, and many plant organs and tissues have now been subjected to analyses at single-cell resolution. In this review, we describe these studies and their impact on our understanding of the diversity, differentiation, and activities of plant cells. We particularly highlight their impact on plant cell identity, including unprecedented views of cell transitions and definitions of rare and novel cell types. We also point out current challenges and future opportunities for the application and analyses of single-cell transcriptomics in plants. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Kook Hui Ryu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; , ,
| | - Yan Zhu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; , ,
| | - John Schiefelbein
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; , ,
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11
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Wang Y, Huan Q, Li K, Qian W. Single-cell transcriptome atlas of the leaf and root of rice seedlings. J Genet Genomics 2021; 48:881-898. [PMID: 34340913 DOI: 10.1016/j.jgg.2021.06.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 12/14/2022]
Abstract
As a multicellular organism, rice flourishes relying on gene expression diversity among cells of various functions. However, cellular-resolution transcriptome features are yet to be fully recognized, let alone cell-specific transcriptional responses to environmental stimuli. In this study, we apply single-cell RNA sequencing to both shoot and root of rice seedlings growing in Kimura B nutrient solution or exposed to various abiotic stresses and characterize transcriptomes for a total of 237,431 individual cells. We identify 15 and nine cell types in the leaf and root, respectively, and observe that common transcriptome features are often shared between leaves and roots in the same tissue layer, except for endodermis or epidermis. Abiotic stress stimuli alter gene expression largely in a cell type-specific manner, but for a given cell type, different stresses often trigger transcriptional regulation of roughly the same set of genes. Besides, we detect proportional changes in cell populations in response to abiotic stress and investigate the underlying molecular mechanisms through single-cell reconstruction of the developmental trajectory. Collectively, our study represents a benchmark-setting data resource of single-cell transcriptome atlas for rice seedlings and an illustration of exploiting such resources to drive discoveries in plant biology.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing Huan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Ke Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenfeng Qian
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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12
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Véron E, Vernoux T, Coudert Y. Phyllotaxis from a Single Apical Cell. TRENDS IN PLANT SCIENCE 2021; 26:124-131. [PMID: 33097400 DOI: 10.1016/j.tplants.2020.09.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/21/2020] [Accepted: 09/25/2020] [Indexed: 05/27/2023]
Abstract
Phyllotaxis, the geometry of leaf arrangement around stems, determines plant architecture. Molecular interactions coordinating the formation of phyllotactic patterns have mainly been studied in multicellular shoot apical meristems of flowering plants. Phyllotaxis evolved independently in the major land plant lineages. In mosses, it arises from a single apical cell, raising the question of how asymmetric divisions of a single-celled meristem create phyllotactic patterns and whether associated genetic processes are shared across lineages. We present an overview of the mechanisms governing shoot apical cell specification and activity in the model moss, Physcomitrium patens, and argue that similar molecular regulatory modules have been deployed repeatedly across evolution to operate at different scales and drive apical function in convergent shoot forms.
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Affiliation(s)
- Elsa Véron
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, INRIA, Lyon 69007, France
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, INRIA, Lyon 69007, France.
| | - Yoan Coudert
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, INRIA, Lyon 69007, France.
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Moody LA, Kelly S, Clayton R, Weeks Z, Emms DM, Langdale JA. NO GAMETOPHORES 2 Is a Novel Regulator of the 2D to 3D Growth Transition in the Moss Physcomitrella patens. Curr Biol 2020; 31:555-563.e4. [PMID: 33242390 DOI: 10.1016/j.cub.2020.10.077] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/01/2020] [Accepted: 10/26/2020] [Indexed: 12/31/2022]
Abstract
The colonization of land by plants was one of the most transformative events in the history of life on Earth. The transition from water, which coincided with and was likely facilitated by the evolution of three-dimensional (3D) growth, enabled the generation of morphological diversity on land. In many plants, the transition from two-dimensional (2D) to 3D growth occurs during embryo development. However, in the early divergent moss Physcomitrella patens, 3D growth is preceded by an extended filamentous phase that can be maintained indefinitely. Here, we describe the identification of the cytokinin-responsive NO GAMETOPHORES 2 (PpNOG2) gene, which encodes a shikimate o-hydroxycinnamoyltransferase. In mutants lacking PpNOG2 function, transcript levels of CLAVATA and SCARECROW genes are significantly reduced, excessive gametophore initial cells are produced, and buds undergo premature developmental arrest. Mutants also exhibit misregulation of auxin-responsive genes. Our results suggest that PpNOG2 functions in the ascorbic acid pathway leading to cuticle formation and that NOG2-related genes were co-opted into the lignin biosynthesis pathway after the divergence of bryophytes and vascular plants. We present a revised model of 3D growth in which PpNOG2 comprises part of a feedback mechanism that is required for the modulation of gametophore initial cell frequency. We also propose that the 2D to 3D growth transition in P. patens is underpinned by complex auxin-cytokinin crosstalk that is regulated, at least in part, by changes in flavonoid metabolism.
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Affiliation(s)
- Laura A Moody
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Roxaana Clayton
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Zoe Weeks
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - David M Emms
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Jane A Langdale
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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14
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Haas FB, Fernandez-Pozo N, Meyberg R, Perroud PF, Göttig M, Stingl N, Saint-Marcoux D, Langdale JA, Rensing SA. Single Nucleotide Polymorphism Charting of P. patens Reveals Accumulation of Somatic Mutations During in vitro Culture on the Scale of Natural Variation by Selfing. FRONTIERS IN PLANT SCIENCE 2020; 11:813. [PMID: 32733496 PMCID: PMC7358436 DOI: 10.3389/fpls.2020.00813] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/20/2020] [Indexed: 06/01/2023]
Abstract
Introduction: Physcomitrium patens (Hedw.) Mitten (previously known as Physcomitrella patens) was collected by H.L.K. Whitehouse in Gransden Wood (Huntingdonshire, United Kingdom) in 1962 and distributed across the globe starting in 1974. Hence, the Gransden accession has been cultured in vitro in laboratories for half a century. Today, there are more than 13 different pedigrees derived from the original accession. Additionally, accessions from other sites worldwide were collected during the last decades. Methods and Results: In this study, 250 high throughput RNA sequencing (RNA-seq) samples and 25 gDNA samples were used to detect single nucleotide polymorphisms (SNPs). Analyses were performed using five different P. patens accessions and 13 different Gransden pedigrees. SNPs were overlaid with metadata and known phenotypic variations. Unique SNPs defining Gransden pedigrees and accessions were identified and experimentally confirmed. They can be successfully employed for PCR-based identification. Conclusion: We show independent mutations in different Gransden laboratory pedigrees, demonstrating that somatic mutations occur and accumulate during in vitro culture. The frequency of such mutations is similar to those observed in naturally occurring populations. We present evidence that vegetative propagation leads to accumulation of deleterious mutations, and that sexual reproduction purges those. Unique SNP sets for five different P. patens accessions were isolated and can be used to determine individual accessions as well as Gransden pedigrees. Based on that, laboratory methods to easily determine P. patens accessions and Gransden pedigrees are presented.
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Affiliation(s)
- Fabian B. Haas
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Noe Fernandez-Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Rabea Meyberg
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | | | - Marco Göttig
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Nora Stingl
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Denis Saint-Marcoux
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
- Université de Lyon, UJM-Saint-Etienne, CNRS, Laboratoire BVpam - FRE 3727, Saint-Étienne, France
| | - Jane A. Langdale
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Stefan A. Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- SYNMIKRO Center for Synthetic Microbiology, University of Marburg, Marburg, Germany
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15
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A mycorrhizae-like gene regulates stem cell and gametophore development in mosses. Nat Commun 2020; 11:2030. [PMID: 32332755 PMCID: PMC7181705 DOI: 10.1038/s41467-020-15967-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/02/2020] [Indexed: 12/14/2022] Open
Abstract
Plant colonization of land has been intimately associated with mycorrhizae or mycorrhizae-like fungi. Despite the pivotal role of fungi in plant adaptation, it remains unclear whether and how gene acquisition following fungal interaction might have affected the development of land plants. Here we report a macro2 domain gene in bryophytes that is likely derived from Mucoromycota, a group that includes some mycorrhizae-like fungi found in the earliest land plants. Experimental and transcriptomic evidence suggests that this macro2 domain gene in the moss Physcomitrella patens, PpMACRO2, is important in epigenetic modification, stem cell function, cell reprogramming and other processes. Gene knockout and over-expression of PpMACRO2 significantly change the number and size of gametophores. These findings provide insights into the role of fungal association and the ancestral gene repertoire in the early evolution of land plants.
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16
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Tang H, Duijts K, Bezanilla M, Scheres B, Vermeer JEM, Willemsen V. Geometric cues forecast the switch from two- to three-dimensional growth in Physcomitrella patens. THE NEW PHYTOLOGIST 2020; 225:1945-1955. [PMID: 31639220 PMCID: PMC7027797 DOI: 10.1111/nph.16276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/12/2019] [Indexed: 05/02/2023]
Abstract
During land colonization, plants acquired a range of body plan adaptations, of which the innovation of three-dimensional (3D) tissues increased organismal complexity and reproductivity. In the moss, Physcomitrella patens, a 3D leafy gametophore originates from filamentous cells that grow in a two-dimensional (2D) plane through a series of asymmetric cell divisions. Asymmetric cell divisions that coincide with different cell division planes and growth directions enable the developmental switch from 2D to 3D, but insights into the underlying mechanisms coordinating this switch are still incomplete. Using 2D and 3D imaging and image segmentation, we characterized two geometric cues, the width of the initial cell and the angle of the transition division plane, which sufficiently distinguished a gametophore initial cell from a branch initial cell. These identified cues were further confirmed in gametophore formation mutants. The identification of a fluorescent marker allowed us to successfully predict the gametophore initial cell with > 90% accuracy before morphological changes, supporting our hypothesis that, before the transition division, parental cells of the gametophore initials possess different properties from those of the branch initials. Our results suggest that the cell fate decision of the initial cell is determined in the parental cell, before the transition division.
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Affiliation(s)
- Han Tang
- Laboratory of Plant Developmental BiologyWageningen University & Research6708 PBWageningenthe Netherlands
- Laboratory of Cell BiologyWageningen University & Research6708 PEWageningenthe Netherlands
| | - Kilian Duijts
- Laboratory of Cell BiologyWageningen University & Research6708 PEWageningenthe Netherlands
| | | | - Ben Scheres
- Laboratory of Plant Developmental BiologyWageningen University & Research6708 PBWageningenthe Netherlands
| | - Joop E. M. Vermeer
- Laboratory of Cell and Molecular BiologyInstitute of BiologyUniversity of Neuchâtel2000NeuchâtelSwitzerland
| | - Viola Willemsen
- Laboratory of Plant Developmental BiologyWageningen University & Research6708 PBWageningenthe Netherlands
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17
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Agudelo-Romero P, Fortes AM, Suárez T, Lascano HR, Saavedra L. Evolutionary insights into FYVE and PHOX effector proteins from the moss Physcomitrella patens. PLANTA 2020; 251:62. [PMID: 32040768 DOI: 10.1007/s00425-020-03354-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/01/2020] [Indexed: 06/10/2023]
Abstract
Genome-wide identification, together with gene expression patterns and promoter region analysis of FYVE and PHOX proteins in Physcomitrella patens, emphasized their importance in regulating mainly developmental processes in P. patens. Phosphatidylinositol 3-phosphate (PtdIns3P) is a signaling phospholipid, which regulates several aspects of plant growth and development, as well as responses to biotic and abiotic stresses. The mechanistic insights underlying PtdIns3P mode of action, specifically through effector proteins have been partially explored in plants, with main focus on Arabidopsis thaliana. In this study, we searched for genes coding for PtdIns3P-binding proteins such as FYVE and PHOX domain-containing sequences from different photosynthetic organisms to gather evolutionary insights on these phosphoinositide binding domains, followed by an in silico characterization of the FYVE and PHOX gene families in the moss Physcomitrella patens. Phylogenetic analysis showed that PpFYVE proteins can be grouped in 7 subclasses, with an additional subclass whose FYVE domain was lost during evolution to higher plants. On the other hand, PpPHOX proteins are classified into 5 subclasses. Expression analyses based on RNAseq data together with the analysis of cis-acting regulatory elements and transcription factor (TF) binding sites in promoter regions suggest the importance of these proteins in regulating stress responses but mainly developmental processes in P. patens. The results provide valuable information and robust candidate genes for future functional analysis aiming to further explore the role of this signaling pathway mainly during growth and development of tip growing cells and during the transition from 2 to 3D growth. These studies would identify ancestral regulatory players undertaken during plant evolution.
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Affiliation(s)
- Patricia Agudelo-Romero
- The UWA Institute of Agriculture, The University of Western Australia, M082, Perth, 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, M316 Perth, Perth, 6009, Australia
- Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - Ana Margarida Fortes
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Trinidad Suárez
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
- Facultad de Ciencias Químicas, Centro de Investigaciones en Química Biológica de Córdoba, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Hernán Ramiro Lascano
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
- CONICET-Instituto de Fisiología y Recursos Genéticos Vegetales, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (INTA), Córdoba, Argentina
| | - Laura Saavedra
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina.
- Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina.
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18
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Motte H, Parizot B, Fang T, Beeckman T. The evolutionary trajectory of root stem cells. CURRENT OPINION IN PLANT BIOLOGY 2020; 53:23-30. [PMID: 31707318 DOI: 10.1016/j.pbi.2019.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/05/2019] [Accepted: 09/19/2019] [Indexed: 06/10/2023]
Abstract
Root stem cells are crucial for the establishment of roots and are therefore a major evolutionary innovation that enabled land plants to spread on land. Despite their importance, not too much is known about the origin and the molecular players installing and maintaining them. Although still fragmentary, the recent availability of new data for early land plants can be used to identify and analyze the conservation of key regulators of root meristems. In this review, we evaluate the possible conservation of important root stem cell regulators to suggest pathways that might have been important at the origin of roots.
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Affiliation(s)
- Hans Motte
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Boris Parizot
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Tao Fang
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Tom Beeckman
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
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19
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A KNOX-Cytokinin Regulatory Module Predates the Origin of Indeterminate Vascular Plants. Curr Biol 2019; 29:2743-2750.e5. [DOI: 10.1016/j.cub.2019.06.083] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 06/10/2019] [Accepted: 06/27/2019] [Indexed: 12/29/2022]
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20
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Lloyd JPB, Lang D, Zimmer AD, Causier B, Reski R, Davies B. The loss of SMG1 causes defects in quality control pathways in Physcomitrella patens. Nucleic Acids Res 2019; 46:5822-5836. [PMID: 29596649 PMCID: PMC6009662 DOI: 10.1093/nar/gky225] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 03/16/2018] [Indexed: 12/16/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is important for RNA quality control and gene regulation in eukaryotes. NMD targets aberrant transcripts for decay and also directly influences the abundance of non-aberrant transcripts. In animals, the SMG1 kinase plays an essential role in NMD by phosphorylating the core NMD factor UPF1. Despite SMG1 being ubiquitous throughout the plant kingdom, little is known about its function, probably because SMG1 is atypically absent from the genome of the model plant, Arabidopsis thaliana. By combining our previously established SMG1 knockout in moss with transcriptome-wide analysis, we reveal the range of processes involving SMG1 in plants. Machine learning assisted analysis suggests that 32% of multi-isoform genes produce NMD-targeted transcripts and that splice junctions downstream of a stop codon act as the major determinant of NMD targeting. Furthermore, we suggest that SMG1 is involved in other quality control pathways, affecting DNA repair and the unfolded protein response, in addition to its role in mRNA quality control. Consistent with this, smg1 plants have increased susceptibility to DNA damage, but increased tolerance to unfolded protein inducing agents. The potential involvement of SMG1 in RNA, DNA and protein quality control has major implications for the study of these processes in plants.
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Affiliation(s)
- James P B Lloyd
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, UK
| | - Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Andreas D Zimmer
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Barry Causier
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, UK
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.,BIOSS - Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Brendan Davies
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, UK
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21
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Yao H, Skirpan A, Wardell B, Matthes MS, Best NB, McCubbin T, Durbak A, Smith T, Malcomber S, McSteen P. The barren stalk2 Gene Is Required for Axillary Meristem Development in Maize. MOLECULAR PLANT 2019; 12:374-389. [PMID: 30690173 DOI: 10.1016/j.molp.2018.12.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 12/08/2018] [Accepted: 12/21/2018] [Indexed: 06/09/2023]
Abstract
The diversity of plant architecture is determined by axillary meristems (AMs). AMs are produced from small groups of stem cells in the axils of leaf primordia and generate vegetative branches and reproductive inflorescences. Previous studies identified genes critical for AM development that function in auxin biosynthesis, transport, and signaling. barren stalk1 (ba1), a basic helix-loop-helix transcription factor, acts downstream of auxin to control AM formation. Here, we report the cloning and characterization of barren stalk2 (ba2), a mutant that fails to produce ears and has fewer branches and spikelets in the tassel, indicating that ba2 functions in reproductive AM development. Furthermore, the ba2 mutation suppresses tiller growth in the teosinte branched1 mutant, indicating that ba2 also plays an essential role in vegetative AM development. The ba2 gene encodes a protein that co-localizes and heterodimerizes with BA1 in the nucleus. Characterization of the genetic interaction between ba2 and ba1 demonstrates that ba1 shows a gene dosage effect in ba2 mutants, providing further evidence that BA1 and BA2 act together in the same pathway. Characterization of the molecular and genetic interaction between ba2 and additional genes required for the regulation of ba1 further supports this finding. The ba1 and ba2 genes are orthologs of rice genes, LAX PANICLE1 (LAX1) and LAX2, respectively, hence providing insights into pathways controlling AMs development in grasses.
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Affiliation(s)
- Hong Yao
- Division of Biological Sciences, Interdisciplinary Plant Group, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Andrea Skirpan
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Brian Wardell
- Department of Biological Sciences, California State University, Long Beach, CA 90840, USA
| | - Michaela S Matthes
- Division of Biological Sciences, Interdisciplinary Plant Group, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Norman B Best
- Division of Biological Sciences, Interdisciplinary Plant Group, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Tyler McCubbin
- Division of Biological Sciences, Interdisciplinary Plant Group, Columbia, MO 65211, USA
| | - Amanda Durbak
- Division of Biological Sciences, Interdisciplinary Plant Group, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Taylor Smith
- Division of Biological Sciences, Interdisciplinary Plant Group, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Simon Malcomber
- Department of Biological Sciences, California State University, Long Beach, CA 90840, USA
| | - Paula McSteen
- Division of Biological Sciences, Interdisciplinary Plant Group, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
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22
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Moody LA. The 2D to 3D growth transition in the moss Physcomitrella patens. CURRENT OPINION IN PLANT BIOLOGY 2019; 47:88-95. [PMID: 30399606 DOI: 10.1016/j.pbi.2018.10.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 10/01/2018] [Accepted: 10/03/2018] [Indexed: 05/18/2023]
Abstract
The colonization of land by plants coincided with and was most likely facilitated by the evolution of 3-dimensional (3D) growth. 3D growth is a pivotal feature of all land plants, but most develop in a way that precludes genetic investigation. In the moss Physcomitrella patens, 3D growth (gametophores) is preceded by an extended 2-dimensional (2D) growth phase (protonemata) that can be propagated indefinitely. Studies using P. patens have thus elucidated some of the molecular mechanisms underlying 3D growth regulation. This review summarizes the known molecular mechanisms underlying both the formation of gametophore initial cells and the development of the 3D growth in gametophores.
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Affiliation(s)
- Laura A Moody
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
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23
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24
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Whitewoods CD, Cammarata J, Nemec Venza Z, Sang S, Crook AD, Aoyama T, Wang XY, Waller M, Kamisugi Y, Cuming AC, Szövényi P, Nimchuk ZL, Roeder AHK, Scanlon MJ, Harrison CJ. CLAVATA Was a Genetic Novelty for the Morphological Innovation of 3D Growth in Land Plants. Curr Biol 2018; 28:2365-2376.e5. [PMID: 30033333 PMCID: PMC6089843 DOI: 10.1016/j.cub.2018.05.068] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/10/2018] [Accepted: 05/23/2018] [Indexed: 11/24/2022]
Abstract
How genes shape diverse plant and animal body forms is a key question in biology. Unlike animal cells, plant cells are confined by rigid cell walls, and cell division plane orientation and growth rather than cell movement determine overall body form. The emergence of plants on land coincided with a new capacity to rotate stem cell divisions through multiple planes, and this enabled three-dimensional (3D) forms to arise from ancestral forms constrained to 2D growth. The genes involved in this evolutionary innovation are largely unknown. The evolution of 3D growth is recapitulated during the development of modern mosses when leafy shoots arise from a filamentous (2D) precursor tissue. Here, we show that a conserved, CLAVATA peptide and receptor-like kinase pathway originated with land plants and orients stem cell division planes during the transition from 2D to 3D growth in a moss, Physcomitrella. We find that this newly identified role for CLAVATA in regulating cell division plane orientation is shared between Physcomitrella and Arabidopsis. We report that roles for CLAVATA in regulating cell proliferation and cell fate are also shared and that CLAVATA-like peptides act via conserved receptor components in Physcomitrella. Our results suggest that CLAVATA was a genetic novelty enabling the morphological innovation of 3D growth in land plants.
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Affiliation(s)
- Chris D Whitewoods
- Plant Sciences Department, Cambridge University, Downing Street, Cambridge CB2 3EA, UK
| | - Joseph Cammarata
- Plant Sciences Department, Cambridge University, Downing Street, Cambridge CB2 3EA, UK; Plant Biology Section, School of Integrative Plant Science, Cornell University, Tower Road, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Zoe Nemec Venza
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Stephanie Sang
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Ashley D Crook
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tsuyoshi Aoyama
- Plant Sciences Department, Cambridge University, Downing Street, Cambridge CB2 3EA, UK; School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Xiao Y Wang
- Plant Sciences Department, Cambridge University, Downing Street, Cambridge CB2 3EA, UK
| | - Manuel Waller
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Andrew C Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Adrienne H K Roeder
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Tower Road, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Michael J Scanlon
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Tower Road, Ithaca, NY 14853, USA
| | - C Jill Harrison
- Plant Sciences Department, Cambridge University, Downing Street, Cambridge CB2 3EA, UK; School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.
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25
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Ding X, Pervere LM, Bascom C, Bibeau JP, Khurana S, Butt AM, Orr RG, Flaherty PJ, Bezanilla M, Vidali L. Conditional genetic screen in Physcomitrella patens reveals a novel microtubule depolymerizing-end-tracking protein. PLoS Genet 2018; 14:e1007221. [PMID: 29746462 PMCID: PMC5944918 DOI: 10.1371/journal.pgen.1007221] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 01/24/2018] [Indexed: 11/19/2022] Open
Abstract
Our ability to identify genes that participate in cell growth and division is limited because their loss often leads to lethality. A solution to this is to isolate conditional mutants where the phenotype is visible under restrictive conditions. Here, we capitalize on the haploid growth-phase of the moss Physcomitrella patens to identify conditional loss-of-growth (CLoG) mutants with impaired growth at high temperature. We used whole-genome sequencing of pooled segregants to pinpoint the lesion of one of these mutants (clog1) and validated the identified mutation by rescuing the conditional phenotype by homologous recombination. We found that CLoG1 is a novel and ancient gene conserved in plants. At the restrictive temperature, clog1 plants have smaller cells but can complete cell division, indicating an important role of CLoG1 in cell growth, but not an essential role in cell division. Fluorescent protein fusions of CLoG1 indicate it is localized to microtubules with a bias towards depolymerizing microtubule ends. Silencing CLoG1 decreases microtubule dynamics, suggesting that CLoG1 plays a critical role in regulating microtubule dynamics. By discovering a novel gene critical for plant growth, our work demonstrates that P. patens is an excellent genetic system to study genes with a fundamental role in plant cell growth.
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Affiliation(s)
- Xinxin Ding
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA
| | - Leah M. Pervere
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA
| | - Carl Bascom
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA
- Department of Biological Sciences, Dartmouth College, Hanover, NH
| | - Jeffrey P. Bibeau
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA
| | - Sakshi Khurana
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA
| | - Allison M. Butt
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA
| | - Robert G. Orr
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA
| | - Patrick J. Flaherty
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA
- Department of Mathematics and Statistics, University of Massachusetts, Amherst, MA
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA
| | | | - Luis Vidali
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA
- * E-mail:
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26
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Chandler JW. Class VIIIb APETALA2 Ethylene Response Factors in Plant Development. TRENDS IN PLANT SCIENCE 2018; 23:151-162. [PMID: 29074232 DOI: 10.1016/j.tplants.2017.09.016] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/22/2017] [Accepted: 09/25/2017] [Indexed: 05/21/2023]
Abstract
The APETALA2 (AP2) transcription factor superfamily in many plant species is extremely large. In addition to well-documented roles in stress responses, some AP2 members in arabidopsis, such as those of subgroup VIIIb, which includes DORNRÖSCHEN, DORNRÖSCHEN-LIKE, PUCHI, and LEAFY PETIOLE, are also important developmental regulators throughout the plant life cycle. Information is accumulating from orthologs of these proteins in important crop species that they influence key agronomic traits, such as the release of bud-burst in woody perennials and floral meristem identity and branching in cereals, and thereby represent potential for agronomic improvement. Given the increasing recognition of their developmental significance, this review highlights the function of these proteins and addresses their phylogenetic and evolutionary relationships.
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Affiliation(s)
- John W Chandler
- Institute for Developmental Biology, Cologne Biocenter, University of Cologne, Zuelpicher Strasse 47b, D-50674 Cologne, Germany.
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27
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Frangedakis E, Saint‐Marcoux D, Moody LA, Rabbinowitsch E, Langdale JA. Nonreciprocal complementation of KNOX gene function in land plants. THE NEW PHYTOLOGIST 2017; 216:591-604. [PMID: 27886385 PMCID: PMC5637896 DOI: 10.1111/nph.14318] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 09/30/2016] [Indexed: 05/02/2023]
Abstract
Class I KNOTTED-LIKE HOMEOBOX (KNOX) proteins regulate development of the multicellular diploid sporophyte in both mosses and flowering plants; however, the morphological context in which they function differs. In order to determine how Class I KNOX function was modified as land plants evolved, phylogenetic analyses and cross-species complementation assays were performed. Our data reveal that a duplication within the charophyte sister group to land plants led to distinct Class I and Class II KNOX gene families. Subsequently, Class I sequences diverged substantially in the nonvascular bryophyte groups (liverworts, mosses and hornworts), with moss sequences being most similar to those in vascular plants. Despite this similarity, moss mutants were not complemented by vascular plant KNOX genes. Conversely, the Arabidopsis brevipedicellus (bp-9) mutant was complemented by the PpMKN2 gene from the moss Physcomitrella patens. Lycophyte KNOX genes also complemented bp-9 whereas fern genes only partially complemented the mutant. This lycophyte/fern distinction is mirrored in the phylogeny of KNOX-interacting BELL proteins, in that a gene duplication occurred after divergence of the two groups. Together, our results imply that the moss MKN2 protein can function in a broader developmental context than vascular plant KNOX proteins, the narrower scope having evolved progressively as lycophytes, ferns and flowering plants diverged.
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Affiliation(s)
| | - Denis Saint‐Marcoux
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Laura A. Moody
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Ester Rabbinowitsch
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Jane A. Langdale
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
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Jill Harrison C. Development and genetics in the evolution of land plant body plans. Philos Trans R Soc Lond B Biol Sci 2017; 372:20150490. [PMID: 27994131 PMCID: PMC5182422 DOI: 10.1098/rstb.2015.0490] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2016] [Indexed: 12/22/2022] Open
Abstract
The colonization of land by plants shaped the terrestrial biosphere, the geosphere and global climates. The nature of morphological and molecular innovation driving land plant evolution has been an enigma for over 200 years. Recent phylogenetic and palaeobotanical advances jointly demonstrate that land plants evolved from freshwater algae and pinpoint key morphological innovations in plant evolution. In the haploid gametophyte phase of the plant life cycle, these include the innovation of mulitcellular forms with apical growth and multiple growth axes. In the diploid phase of the life cycle, multicellular axial sporophytes were an early innovation priming subsequent diversification of indeterminate branched forms with leaves and roots. Reverse and forward genetic approaches in newly emerging model systems are starting to identify the genetic basis of such innovations. The data place plant evo-devo research at the cusp of discovering the developmental and genetic changes driving the radiation of land plant body plans.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- C Jill Harrison
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
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