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Chandler JO, Wilhelmsson PKI, Fernandez-Pozo N, Graeber K, Arshad W, Pérez M, Steinbrecher T, Ullrich KK, Nguyen TP, Mérai Z, Mummenhoff K, Theißen G, Strnad M, Scheid OM, Schranz ME, Petřík I, Tarkowská D, Novák O, Rensing SA, Leubner-Metzger G. The dimorphic diaspore model Aethionema arabicum (Brassicaceae): Distinct molecular and morphological control of responses to parental and germination temperatures. THE PLANT CELL 2024; 36:2465-2490. [PMID: 38513609 PMCID: PMC11218780 DOI: 10.1093/plcell/koae085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/23/2024]
Abstract
Plants in habitats with unpredictable conditions often have diversified bet-hedging strategies that ensure fitness over a wider range of variable environmental factors. A striking example is the diaspore (seed and fruit) heteromorphism that evolved to maximize species survival in Aethionema arabicum (Brassicaceae) in which external and endogenous triggers allow the production of two distinct diaspores on the same plant. Using this dimorphic diaspore model, we identified contrasting molecular, biophysical, and ecophysiological mechanisms in the germination responses to different temperatures of the mucilaginous seeds (M+ seed morphs), the dispersed indehiscent fruits (IND fruit morphs), and the bare non-mucilaginous M- seeds obtained by pericarp (fruit coat) removal from IND fruits. Large-scale comparative transcriptome and hormone analyses of M+ seeds, IND fruits, and M- seeds provided comprehensive datasets for their distinct thermal responses. Morph-specific differences in co-expressed gene modules in seeds, as well as in seed and pericarp hormone contents, identified a role of the IND pericarp in imposing coat dormancy by generating hypoxia affecting abscisic acid (ABA) sensitivity. This involved expression of morph-specific transcription factors, hypoxia response, and cell wall remodeling genes, as well as altered ABA metabolism, transport, and signaling. Parental temperature affected ABA contents and ABA-related gene expression and altered IND pericarp biomechanical properties. Elucidating the molecular framework underlying the diaspore heteromorphism can provide insight into developmental responses to globally changing temperatures.
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Affiliation(s)
- Jake O Chandler
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Per K I Wilhelmsson
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg 35043, Germany
| | - Noe Fernandez-Pozo
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg 35043, Germany
- Institute for Mediterranean and Subtropical Horticulture “La Mayora” (IHSM-CSIC-UMA), Málaga 29010, Spain
| | - Kai Graeber
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Waheed Arshad
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Marta Pérez
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Tina Steinbrecher
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Kristian K Ullrich
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg 35043, Germany
| | - Thu-Phuong Nguyen
- Biosystematics Group, Wageningen University, PB Wageningen 6708, The Netherlands
| | - Zsuzsanna Mérai
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Klaus Mummenhoff
- Department of Biology, Botany, University of Osnabrück, Osnabrück 49076, Germany
| | - Günter Theißen
- Matthias Schleiden Institute/Department of Genetics, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, Czech Academy of Sciences, Olomouc 78371, Czech Republic
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, PB Wageningen 6708, The Netherlands
| | - Ivan Petřík
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, Czech Academy of Sciences, Olomouc 78371, Czech Republic
| | - Danuše Tarkowská
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, Czech Academy of Sciences, Olomouc 78371, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, Czech Academy of Sciences, Olomouc 78371, Czech Republic
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg 35043, Germany
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg 79104, Germany
| | - Gerhard Leubner-Metzger
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, Czech Academy of Sciences, Olomouc 78371, Czech Republic
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2
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Arshad W, Steinbrecher T, Wilhelmsson PK, Fernandez-Pozo N, Pérez M, Mérai Z, Rensing SA, Chandler JO, Leubner-Metzger G. Aethionema arabicum dimorphic seed trait resetting during transition to seedlings. FRONTIERS IN PLANT SCIENCE 2024; 15:1358312. [PMID: 38525145 PMCID: PMC10957558 DOI: 10.3389/fpls.2024.1358312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/19/2024] [Indexed: 03/26/2024]
Abstract
The transition from germinating seeds to emerging seedlings is one of the most vulnerable plant life cycle stages. Heteromorphic diaspores (seed and fruit dispersal units) are an adaptive bet-hedging strategy to cope with spatiotemporally variable environments. While the roles and mechanisms of seedling traits have been studied in monomorphic species, which produce one type of diaspore, very little is known about seedlings in heteromorphic species. Using the dimorphic diaspore model Aethionema arabicum (Brassicaceae), we identified contrasting mechanisms in the germination responses to different temperatures of the mucilaginous seeds (M+ seed morphs), the dispersed indehiscent fruits (IND fruit morphs), and the bare non-mucilaginous M- seeds obtained from IND fruits by pericarp (fruit coat) removal. What follows the completion of germination is the pre-emergence seedling growth phase, which we investigated by comparative growth assays of early seedlings derived from the M+ seeds, bare M- seeds, and IND fruits. The dimorphic seedlings derived from M+ and M- seeds did not differ in their responses to ambient temperature and water potential. The phenotype of seedlings derived from IND fruits differed in that they had bent hypocotyls and their shoot and root growth was slower, but the biomechanical hypocotyl properties of 15-day-old seedlings did not differ between seedlings derived from germinated M+ seeds, M- seeds, or IND fruits. Comparison of the transcriptomes of the natural dimorphic diaspores, M+ seeds and IND fruits, identified 2,682 differentially expressed genes (DEGs) during late germination. During the subsequent 3 days of seedling pre-emergence growth, the number of DEGs was reduced 10-fold to 277 root DEGs and 16-fold to 164 shoot DEGs. Among the DEGs in early seedlings were hormonal regulators, in particular for auxin, ethylene, and gibberellins. Furthermore, DEGs were identified for water and ion transporters, nitrate transporter and assimilation enzymes, and cell wall remodeling protein genes encoding enzymes targeting xyloglucan and pectin. We conclude that the transcriptomes of seedlings derived from the dimorphic diaspores, M+ seeds and IND fruits, undergo transcriptional resetting during the post-germination pre-emergence growth transition phase from germinated diaspores to growing seedlings.
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Affiliation(s)
- Waheed Arshad
- Seed Biology and Technology Group, Department of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
| | - Tina Steinbrecher
- Seed Biology and Technology Group, Department of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
| | | | - Noe Fernandez-Pozo
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
- Department Plant Breeding and Physiology, Institute for Mediterranean and Subtropical Horticulture “La Mayora” (IHSM-CSIC-UMA), Málaga, Spain
| | - Marta Pérez
- Seed Biology and Technology Group, Department of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
| | - Zsuzsanna Mérai
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Stefan A. Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg, Germany
- Faculty of Chemistry and Pharmacy, University of Freiburg, Freiburg, Germany
| | - Jake O. Chandler
- Seed Biology and Technology Group, Department of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
| | - Gerhard Leubner-Metzger
- Seed Biology and Technology Group, Department of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, Czech Academy of Sciences, Olomouc, Czechia
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3
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Krzyszton M, Yatusevich R, Wrona M, Sacharowski SP, Adamska D, Swiezewski S. Single seeds exhibit transcriptional heterogeneity during secondary dormancy induction. PLANT PHYSIOLOGY 2022; 190:211-225. [PMID: 35670742 PMCID: PMC9438484 DOI: 10.1093/plphys/kiac265] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
Seeds are highly resilient to the external environment, which allows plants to persist in unpredictable and unfavorable conditions. Some plant species have adopted a bet-hedging strategy to germinate a variable fraction of seeds in any given condition, and this could be explained by population-based threshold models. Here, in the model plant Arabidopsis (Arabidopsis thaliana), we induced secondary dormancy (SD) to address the transcriptional heterogeneity among seeds that leads to binary germination/nongermination outcomes. We developed a single-seed RNA-seq strategy that allowed us to observe a reduction in seed transcriptional heterogeneity as seeds enter stress conditions, followed by an increase during recovery. We identified groups of genes whose expression showed a specific pattern through a time course and used these groups to position the individual seeds along the transcriptional gradient of germination competence. In agreement, transcriptomes of dormancy-deficient seeds (mutant of DELAY OF GERMINATION 1) showed a shift toward higher values of the germination competence index. Interestingly, a significant fraction of genes with variable expression encoded translation-related factors. In summary, interrogating hundreds of single-seed transcriptomes during SD-inducing treatment revealed variability among the transcriptomes that could result from the distribution of population-based sensitivity thresholds. Our results also showed that single-seed RNA-seq is the method of choice for analyzing seed bet-hedging-related phenomena.
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Affiliation(s)
| | | | - Magdalena Wrona
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, PAS, Warsaw 02-106, Poland
| | - Sebastian P Sacharowski
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, PAS, Warsaw 02-106, Poland
| | - Dorota Adamska
- Genomics Core Facility, Centre of New Technologies, University of Warsaw, Warsaw 02-097, Poland
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Hourston JE, Steinbrecher T, Chandler JO, Pérez M, Dietrich K, Turečková V, Tarkowská D, Strnad M, Weltmeier F, Meinhard J, Fischer U, Fiedler‐Wiechers K, Ignatz M, Leubner‐Metzger G. Cold-induced secondary dormancy and its regulatory mechanisms in Beta vulgaris. PLANT, CELL & ENVIRONMENT 2022; 45:1315-1332. [PMID: 35064681 PMCID: PMC9305896 DOI: 10.1111/pce.14264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 10/26/2021] [Accepted: 11/18/2021] [Indexed: 06/14/2023]
Abstract
The dynamic behaviour of seeds in soil seed banks depends on their ability to act as sophisticated environmental sensors to adjust their sensitivity thresholds for germination by dormancy mechanisms. Here we show that prolonged incubation of sugar beet fruits at low temperature (chilling at 5°C, generally known to release seed dormancy of many species) can induce secondary nondeep physiological dormancy of an apparently nondormant crop species. The physiological and biophysical mechanisms underpinning this cold-induced secondary dormancy include the chilling-induced accumulation of abscisic acid in the seeds, a reduction in the embryo growth potential and a block in weakening of the endosperm covering the embryonic root. Transcriptome analysis revealed distinct gene expression patterns in the different temperature regimes and upon secondary dormancy induction and maintenance. The chilling caused reduced expression of cell wall remodelling protein genes required for embryo cell elongation growth and endosperm weakening, as well as increased expression of seed maturation genes, such as for late embryogenesis abundant proteins. A model integrating the hormonal signalling and master regulator expression with the temperature-control of seed dormancy and maturation programmes is proposed. The revealed mechanisms of the cold-induced secondary dormancy are important for climate-smart agriculture and food security.
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Affiliation(s)
- James E. Hourston
- Department of Biological SciencesRoyal Holloway University of LondonEghamUK
| | - Tina Steinbrecher
- Department of Biological SciencesRoyal Holloway University of LondonEghamUK
| | - Jake O. Chandler
- Department of Biological SciencesRoyal Holloway University of LondonEghamUK
| | - Marta Pérez
- Department of Biological SciencesRoyal Holloway University of LondonEghamUK
| | | | - Veronika Turečková
- Laboratory of Growth Regulators, Palacký University and Institute of Experimental BotanyCzech Academy of SciencesOlomoucCzech Republic
| | - Danuše Tarkowská
- Laboratory of Growth Regulators, Palacký University and Institute of Experimental BotanyCzech Academy of SciencesOlomoucCzech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Palacký University and Institute of Experimental BotanyCzech Academy of SciencesOlomoucCzech Republic
| | | | | | | | | | - Michael Ignatz
- Department of Biological SciencesRoyal Holloway University of LondonEghamUK
| | - Gerhard Leubner‐Metzger
- Department of Biological SciencesRoyal Holloway University of LondonEghamUK
- Laboratory of Growth Regulators, Palacký University and Institute of Experimental BotanyCzech Academy of SciencesOlomoucCzech Republic
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5
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Steinbrecher T, Leubner-Metzger G. Xyloglucan remodelling enzymes and the mechanics of plant seed and fruit biology. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1253-1257. [PMID: 35235657 PMCID: PMC8890615 DOI: 10.1093/jxb/erac020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This article comments on: Di Marzo M, Ebeling Viana V, Banfi C, Cassina V, Corti R, Herrera-Ubaldo H, Babolin N, Guazzotti A, Kiegle E, Gregis V, de Folter S, Sampedro J, Mantegazza F, Colombo L, Ezquer I. 2022. Cell wall modifications by α-XYLOSIDASE1 are required for the control of seed and fruit size. Journal of Experimental Botany 73, 1499–1515.
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Affiliation(s)
- Tina Steinbrecher
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Gerhard Leubner-Metzger
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
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6
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Malovichko YV, Shikov AE, Nizhnikov AA, Antonets KS. Temporal Control of Seed Development in Dicots: Molecular Bases, Ecological Impact and Possible Evolutionary Ramifications. Int J Mol Sci 2021; 22:ijms22179252. [PMID: 34502157 PMCID: PMC8430901 DOI: 10.3390/ijms22179252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 12/21/2022] Open
Abstract
In flowering plants, seeds serve as organs of both propagation and dispersal. The developing seed passes through several consecutive stages, following a conserved general outline. The overall time needed for a seed to develop, however, may vary both within and between plant species, and these temporal developmental properties remain poorly understood. In the present paper, we summarize the existing data for seed development alterations in dicot plants. For genetic mutations, the reported cases were grouped in respect of the key processes distorted in the mutant specimens. Similar phenotypes arising from the environmental influence, either biotic or abiotic, were also considered. Based on these data, we suggest several general trends of timing alterations and how respective mechanisms might add to the ecological plasticity of the families considered. We also propose that the developmental timing alterations may be perceived as an evolutionary substrate for heterochronic events. Given the current lack of plausible models describing timing control in plant seeds, the presented suggestions might provide certain insights for future studies in this field.
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Affiliation(s)
- Yury V. Malovichko
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (Y.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anton E. Shikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (Y.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (Y.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (Y.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Correspondence:
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Arshad W, Lenser T, Wilhelmsson PKI, Chandler JO, Steinbrecher T, Marone F, Pérez M, Collinson ME, Stuppy W, Rensing SA, Theißen G, Leubner-Metzger G. A tale of two morphs: developmental patterns and mechanisms of seed coat differentiation in the dimorphic diaspore model Aethionema arabicum (Brassicaceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:166-181. [PMID: 33945185 DOI: 10.1111/tpj.15283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
The developmental transition from a fertilized ovule to a dispersed diaspore (seed or fruit) involves complex differentiation processes of the ovule's integuments leading to the diversity in mature seed coat structures in angiosperms. In this study, comparative imaging and transcriptome analysis were combined to investigate the morph-specific developmental differences during outer seed coat differentiation and mucilage production in Aethionema arabicum, the Brassicaceae model for diaspore dimorphism. One of the intriguing adaptations of this species is the production and dispersal of morphologically distinct, mucilaginous and non-mucilaginous diaspores from the same plant (dimorphism). The dehiscent fruit morph programme producing multiple mucilaginous seed diaspores was used as the default trait combination, similar to Arabidopsis thaliana, and was compared with the indehiscent fruit morph programme leading to non-mucilaginous diaspores. Synchrotron-based radiation X-ray tomographic microscopy revealed a co-ordinated framework of morph-specific early changes in internal anatomy of developing A. arabicum gynoecia including seed abortion in the indehiscent programme and mucilage production by the mucilaginous seed coat. The associated comparative analysis of the gene expression patterns revealed that the unique seed coat dimorphism of Ae. arabicum provides an excellent model system for comparative study of the control of epidermal cell differentiation and mucilage biosynthesis by the mucilage transcription factor cascade and their downstream cell wall and mucilage remodelling genes. Elucidating the underlying molecular framework of the dimorphic diaspore syndrome is key to understanding differential regulation of bet-hedging survival strategies in challenging environments, timely in the face of global climatic change.
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Affiliation(s)
- Waheed Arshad
- Department of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Teresa Lenser
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Jena, D-07743, Germany
| | - Per K I Wilhelmsson
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, D-35043, Germany
| | - Jake O Chandler
- Department of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Tina Steinbrecher
- Department of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Federica Marone
- Swiss Light Source, Paul Scherrer Institute, Villigen, CH-5232, Switzerland
| | - Marta Pérez
- Department of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Margaret E Collinson
- Department of Earth Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Wolfgang Stuppy
- Botanischer Garten der Ruhr-Universität Bochum, Universitätsstraße 150, Bochum, D-44780, Germany
- The Royal Botanic Gardens, Kew, Wellcome Trust Millennium Building, Wakehurst Place, Ardingly, West Sussex, RH17 6TN, UK
| | - Stefan A Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, D-35043, Germany
| | - Günter Theißen
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Jena, D-07743, Germany
| | - Gerhard Leubner-Metzger
- Department of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
- Laboratory of Growth Regulators, Palacký University, Institute of Experimental Botany, Czech Academy of Sciences, Olomouc, CZ-78371, Czech Republic
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The EpiDiverse Plant Epigenome-Wide Association Studies (EWAS) Pipeline. EPIGENOMES 2021; 5:epigenomes5020012. [PMID: 34968299 PMCID: PMC8594691 DOI: 10.3390/epigenomes5020012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 11/29/2022] Open
Abstract
Bisulfite sequencing is a widely used technique for determining DNA methylation and its relationship with epigenetics, genetics, and environmental parameters. Various techniques were implemented for epigenome-wide association studies (EWAS) to reveal meaningful associations; however, there are only very few plant studies available to date. Here, we developed the EpiDiverse EWAS pipeline and tested it using two plant datasets, from P. abies (Norway spruce) and Q. lobata (valley oak). Hence, we present an EWAS implementation tested for non-model plant species and describe its use.
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9
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Fernandez‐Pozo N, Metz T, Chandler JO, Gramzow L, Mérai Z, Maumus F, Mittelsten Scheid O, Theißen G, Schranz ME, Leubner‐Metzger G, Rensing SA. Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:275-293. [PMID: 33453123 PMCID: PMC8641386 DOI: 10.1111/tpj.15161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/31/2020] [Accepted: 01/08/2021] [Indexed: 05/06/2023]
Abstract
Aethionema arabicum is an important model plant for Brassicaceae trait evolution, particularly of seed (development, regulation, germination, dormancy) and fruit (development, dehiscence mechanisms) characters. Its genome assembly was recently improved but the gene annotation was not updated. Here, we improved the Ae. arabicum gene annotation using 294 RNA-seq libraries and 136 307 full-length PacBio Iso-seq transcripts, increasing BUSCO completeness by 11.6% and featuring 5606 additional genes. Analysis of orthologs showed a lower number of genes in Ae. arabicum than in other Brassicaceae, which could be partially explained by loss of homeologs derived from the At-α polyploidization event and by a lower occurrence of tandem duplications after divergence of Aethionema from the other Brassicaceae. Benchmarking of MADS-box genes identified orthologs of FUL and AGL79 not found in previous versions. Analysis of full-length transcripts related to ABA-mediated seed dormancy discovered a conserved isoform of PIF6-β and antisense transcripts in ABI3, ABI4 and DOG1, among other cases found of different alternative splicing between Turkey and Cyprus ecotypes. The presented data allow alternative splicing mining and proposition of numerous hypotheses to research evolution and functional genomics. Annotation data and sequences are available at the Ae. arabicum DB (https://plantcode.online.uni-marburg.de/aetar_db).
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Affiliation(s)
- Noe Fernandez‐Pozo
- Plant Cell BiologyDepartment of BiologyUniversity of MarburgMarburgGermany
| | - Timo Metz
- Plant Cell BiologyDepartment of BiologyUniversity of MarburgMarburgGermany
| | - Jake O. Chandler
- School of Biological SciencesRoyal Holloway University of LondonEghamSurreyUK
| | - Lydia Gramzow
- Matthias Schleiden Institute/GeneticsFriedrich Schiller University JenaJenaGermany
| | - Zsuzsanna Mérai
- Gregor Mendel Institute of Molecular Plant BiologyAustrian Academy of SciencesVienna BioCenter (VBC)ViennaAustria
| | | | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant BiologyAustrian Academy of SciencesVienna BioCenter (VBC)ViennaAustria
| | - Günter Theißen
- Matthias Schleiden Institute/GeneticsFriedrich Schiller University JenaJenaGermany
| | - M. Eric Schranz
- Biosystematics GroupWageningen UniversityWageningenThe Netherlands
| | - Gerhard Leubner‐Metzger
- School of Biological SciencesRoyal Holloway University of LondonEghamSurreyUK
- Laboratory of Growth RegulatorsCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University and Institute of Experimental BotanyAcademy of Sciences of the Czech RepublicOlomoucCzech Republic
| | - Stefan A. Rensing
- Plant Cell BiologyDepartment of BiologyUniversity of MarburgMarburgGermany
- BIOSS Centre for Biological Signaling StudiesUniversity of FreiburgFreiburgGermany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO)University of MarburgMarburgGermany
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10
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Gianella M, Bradford KJ, Guzzon F. Ecological, (epi)genetic and physiological aspects of bet-hedging in angiosperms. PLANT REPRODUCTION 2021; 34:21-36. [PMID: 33449209 PMCID: PMC7902588 DOI: 10.1007/s00497-020-00402-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/28/2020] [Indexed: 06/01/2023]
Abstract
KEY MESSAGE Bet-hedging is a complex evolutionary strategy involving morphological, eco-physiological, (epi)genetic and population dynamics aspects. We review these aspects in flowering plants and propose further research needed for this topic. Bet-hedging is an evolutionary strategy that reduces the temporal variance in fitness at the expense of a lowered arithmetic mean fitness. It has evolved in organisms subjected to variable cues from the external environment, be they abiotic or biotic stresses such as irregular rainfall or predation. In flowering plants, bet-hedging is exhibited by hundreds of species and is mainly exerted by reproductive organs, in particular seeds but also embryos and fruits. The main example of bet-hedging in angiosperms is diaspore heteromorphism in which the same individual produces different seed/fruit morphs in terms of morphology, dormancy, eco-physiology and/or tolerance to biotic and abiotic stresses in order to 'hedge its bets' in unpredictable environments. The objective of this review is to provide a comprehensive overview of the ecological, genetic, epigenetic and physiological aspects involved in shaping bet-hedging strategies, and how these can affect population dynamics. We identify several open research questions about bet-hedging strategies in plants: 1) understanding ecological trade-offs among different traits; 2) producing more comprehensive phylogenetic analyses to understand the diffusion and evolutionary implications of this strategy; 3) clarifying epigenetic mechanisms related to bet-hedging and plant responses to environmental cues; and 4) applying multi-omics approaches to study bet-hedging at different levels of detail. Clarifying those aspects of bet-hedging will deepen our understanding of this fascinating evolutionary strategy.
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Affiliation(s)
- Maraeva Gianella
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Kent J Bradford
- Department of Plant Sciences, Seed Biotechnology Center, University of California, Davis, USA
| | - Filippo Guzzon
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz, Km. 45, El Batán, 56237, Texcoco, Mexico State, Mexico.
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Yin X, Liu Y, Zeb R, Chen F, Chen H, Wang KJ. The intergenerational toxic effects on offspring of medaka fish Oryzias melastigma from parental benzo[a]pyrene exposure via interference of the circadian rhythm. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 267:115437. [PMID: 32866872 DOI: 10.1016/j.envpol.2020.115437] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 08/10/2020] [Accepted: 08/13/2020] [Indexed: 06/11/2023]
Abstract
Benzo[a]pyrene (BaP), a widely existed polycyclic aromatic hydrocarbon pollutant in aquatic environment, has toxic effects on marine animals and their generations, but the intergenerational immunotoxic mechanism underlying has not been clearly understood. In the study, the offspring of marine medaka (oryzias melastigma) which were exposed to 0.5 μg L-1 BaP suffered from circadian rhythm oscillation disorders and severe DNA damage. Many clock-associated genes like per1 were significantly modulated in offspring, both per1 and p53 were significantly inhibited that altered the progression of cell cycle and inhibited DNA repair, which possibly resulted in the increased mortality of offspring. The hypermethylation of the per1 promotor and abnormal levels of N6-methyladenosine (m6A) suggested that the underlying mechanism was probably related to the epigenetic modification. Moreover, the offspring from paternal BaP exposure had more severe DNA damage and a higher degree of hypermethylation than those from maternal exposure. F1 larvae from BaP-exposed parents were more sensitive to BaP exposure, showing that the expression of immune and metabolism-related genes were significantly up-regulated. Taken together, the parental toxicity induced by BaP could be passed to F1 generation and the mechanism underlying was probably associated with a characteristic circadian rhythm disorder.
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Affiliation(s)
- Xiaohan Yin
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Yong Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Rabia Zeb
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Fangyi Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China; State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Huiyun Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China; State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Ke-Jian Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China; State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China.
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Landis JB, Kurti A, Lawhorn AJ, Litt A, McCarthy EW. Differential Gene Expression with an Emphasis on Floral Organ Size Differences in Natural and Synthetic Polyploids of Nicotiana tabacum (Solanaceae). Genes (Basel) 2020; 11:E1097. [PMID: 32961813 PMCID: PMC7563459 DOI: 10.3390/genes11091097] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 11/16/2022] Open
Abstract
Floral organ size, especially the size of the corolla, plays an important role in plant reproduction by facilitating pollination efficiency. Previous studies have outlined a hypothesized organ size pathway. However, the expression and function of many of the genes in the pathway have only been investigated in model diploid species; therefore, it is unknown how these genes interact in polyploid species. Although correlations between ploidy and cell size have been shown in many systems, it is unclear whether there is a difference in cell size between naturally occurring and synthetic polyploids. To address these questions comparing floral organ size and cell size across ploidy, we use natural and synthetic polyploids of Nicotiana tabacum (Solanaceae) as well as their known diploid progenitors. We employ a comparative transcriptomics approach to perform analyses of differential gene expression, focusing on candidate genes that may be involved in floral organ size, both across developmental stages and across accessions. We see differential expression of several known floral organ candidate genes including ARF2, BIG BROTHER, and GASA/GAST1. Results from linear models show that ploidy, cell width, and cell number positively influence corolla tube circumference; however, the effect of cell width varies by ploidy, and diploids have a significantly steeper slope than both natural and synthetic polyploids. These results demonstrate that polyploids have wider cells and that polyploidy significantly increases corolla tube circumference.
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Affiliation(s)
- Jacob B. Landis
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA; (A.K.); (A.J.L.); (A.L.)
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY 14853, USA
| | - Amelda Kurti
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA; (A.K.); (A.J.L.); (A.L.)
| | - Amber J. Lawhorn
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA; (A.K.); (A.J.L.); (A.L.)
| | - Amy Litt
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA; (A.K.); (A.J.L.); (A.L.)
| | - Elizabeth W. McCarthy
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA; (A.K.); (A.J.L.); (A.L.)
- Department of Biology, SUNY Cortland, Cortland, NY 13045, USA
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Puglia GD, Prjibelski AD, Vitale D, Bushmanova E, Schmid KJ, Raccuia SA. Hybrid transcriptome sequencing approach improved assembly and gene annotation in Cynara cardunculus (L.). BMC Genomics 2020; 21:317. [PMID: 32819282 PMCID: PMC7441626 DOI: 10.1186/s12864-020-6670-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 03/13/2020] [Indexed: 12/11/2022] Open
Abstract
Background The investigation of transcriptome profiles using short reads in non-model organisms, which lack of well-annotated genomes, is limited by partial gene reconstruction and isoform detection. In contrast, long-reads sequencing techniques revealed their potential to generate complete transcript assemblies even when a reference genome is lacking. Cynara cardunculus var. altilis (DC) (cultivated cardoon) is a perennial hardy crop adapted to dry environments with many industrial and nutraceutical applications due to the richness of secondary metabolites mostly produced in flower heads. The investigation of this species benefited from the recent release of a draft genome, but the transcriptome profile during the capitula formation still remains unexplored. In the present study we show a transcriptome analysis of vegetative and inflorescence organs of cultivated cardoon through a novel hybrid RNA-seq assembly approach utilizing both long and short RNA-seq reads. Results The inclusion of a single Nanopore flow-cell output in a hybrid sequencing approach determined an increase of 15% complete assembled genes and 18% transcript isoforms respect to short reads alone. Among 25,463 assembled unigenes, we identified 578 new genes and updated 13,039 gene models, 11,169 of which were alternatively spliced isoforms. During capitulum development, 3424 genes were differentially expressed and approximately two-thirds were identified as transcription factors including bHLH, MYB, NAC, C2H2 and MADS-box which were highly expressed especially after capitulum opening. We also show the expression dynamics of key genes involved in the production of valuable secondary metabolites of which capitulum is rich such as phenylpropanoids, flavonoids and sesquiterpene lactones. Most of their biosynthetic genes were strongly transcribed in the flower heads with alternative isoforms exhibiting differentially expression levels across the tissues. Conclusions This novel hybrid sequencing approach allowed to improve the transcriptome assembly, to update more than half of annotated genes and to identify many novel genes and different alternatively spliced isoforms. This study provides new insights on the flowering cycle in an Asteraceae plant, a valuable resource for plant biology and breeding in Cynara and an effective method for improving gene annotation.
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Affiliation(s)
- Giuseppe D Puglia
- Institute for Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Fruwirthstrasse 21, 70599, Stuttgart, Germany. .,Consiglio Nazionale delle Ricerche, Istituto per i Sistemi Agricoli e Forestali del Mediterraneo (CNR-ISAFOM) U.O.S. Catania, Via Empedocle, 58, 95128, Catania, Italy.
| | - Andrey D Prjibelski
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Domenico Vitale
- Consiglio Nazionale delle Ricerche, Istituto per i Sistemi Agricoli e Forestali del Mediterraneo (CNR-ISAFOM) U.O.S. Catania, Via Empedocle, 58, 95128, Catania, Italy
| | - Elena Bushmanova
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Karl J Schmid
- Institute for Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Fruwirthstrasse 21, 70599, Stuttgart, Germany.
| | - Salvatore A Raccuia
- Consiglio Nazionale delle Ricerche, Istituto per i Sistemi Agricoli e Forestali del Mediterraneo (CNR-ISAFOM) U.O.S. Catania, Via Empedocle, 58, 95128, Catania, Italy
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Genome Improvement and Genetic Map Construction for Aethionema arabicum, the First Divergent Branch in the Brassicaceae Family. G3-GENES GENOMES GENETICS 2019; 9:3521-3530. [PMID: 31554715 PMCID: PMC6829135 DOI: 10.1534/g3.119.400657] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The genus Aethionema is a sister-group to the core-group of the Brassicaceae family that includes Arabidopsis thaliana and the Brassica crops. Thus, Aethionema is phylogenetically well-placed for the investigation and understanding of genome and trait evolution across the family. We aimed to improve the quality of the reference genome draft version of the annual species Aethionema arabicum. Second, we constructed the first Ae. arabicum genetic map. The improved reference genome and genetic map enabled the development of each other. We started with the initially published genome (version 2.5). PacBio and MinION sequencing together with genetic map v2.5 were incorporated to produce the new reference genome v3.0. The improved genome contains 203 MB of sequence, with approximately 94% of the assembly made up of called (non-gap) bases, assembled into 2,883 scaffolds (with only 6% of the genome made up of non-called bases (Ns)). The N50 (10.3 MB) represents an 80-fold increase over the initial genome release. We generated a Recombinant Inbred Line (RIL) population that was derived from two ecotypes: Cyprus and Turkey (the reference genotype. Using a Genotyping by Sequencing (GBS) approach, we generated a high-density genetic map with 749 (v2.5) and then 632 SNPs (v3.0) was generated. The genetic map and reference genome were integrated, thus greatly improving the scaffolding of the reference genome into 11 linkage groups. We show that long-read sequencing data and genetics are complementary, resulting in an improved genome assembly in Ae. arabicum. They will facilitate comparative genetic mapping work for the Brassicaceae family and are also valuable resources to investigate wide range of life history traits in Aethionema.
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