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Jyoti TP, Chandel S, Singh R. Unveiling the epigenetic landscape of plants using flow cytometry approach. Cytometry A 2024; 105:231-241. [PMID: 38437027 DOI: 10.1002/cyto.a.24834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 01/12/2024] [Accepted: 02/22/2024] [Indexed: 03/06/2024]
Abstract
Plants are sessile creatures that have to adapt constantly changing environmental circumstances. Plants are subjected to a range of abiotic stressors as a result of unpredictable climate change. Understanding how stress-responsive genes are regulated can help us better understand how plants can adapt to changing environmental conditions. Epigenetic markers that dynamically change in response to stimuli, such as DNA methylation and histone modifications are known to regulate gene expression. Individual cells or particles' physical and/or chemical properties can be measured using the method known as flow cytometry. It may therefore be used to evaluate changes in DNA methylation, histone modifications, and other epigenetic markers, making it a potent tool for researching epigenetics in plants. We explore the use of flow cytometry as a technique for examining epigenetic traits in this thorough discussion. The separation of cell nuclei and their subsequent labeling with fluorescent antibodies, offering information on the epigenetic mechanisms in plants when utilizing flow cytometry. We also go through the use of high-throughput data analysis methods to unravel the complex epigenetic processes occurring inside plant systems.
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Affiliation(s)
- Thakur Prava Jyoti
- Department of Pharmacognosy, ISF College of Pharmacy, Moga, Punjab, India
| | - Shivani Chandel
- Department of Pharmacognosy, ISF College of Pharmacy, Moga, Punjab, India
| | - Rajveer Singh
- Department of Pharmacognosy, ISF College of Pharmacy, Moga, Punjab, India
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2
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Koutecký P, Smith T, Loureiro J, Kron P. Best practices for instrument settings and raw data analysis in plant flow cytometry. Cytometry A 2023; 103:953-966. [PMID: 37807676 DOI: 10.1002/cyto.a.24798] [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: 04/28/2022] [Revised: 05/26/2023] [Accepted: 09/12/2023] [Indexed: 10/10/2023]
Abstract
Flow cytometry (FCM) is now the most widely used method to determine ploidy levels and genome size of plants. To get reliable estimates and allow reproducibility of measurements, the methodology should be standardized and follow the best practices in the field. In this article, we discuss instrument calibration and quality control and various instrument and acquisition settings (parameters, flow rate, number of events, scales, use of discriminators, peak positions). These settings must be decided before measurements because they determine the amount and quality of the data and thus influence all downstream analyses. We describe the two main approaches to raw data analysis (gating and histogram modeling), and we discuss their advantages and disadvantages. Finally, we provide a summary of best practice recommendations for data acquisition and raw data analysis in plant FCM.
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Affiliation(s)
- Petr Koutecký
- Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Tyler Smith
- Agriculture and Agri-Food Canada (AAFC), Ottawa, Ontario, Canada
| | - João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Paul Kron
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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3
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Ptáček J, Ekrt L, Hornych O, Urfus T. Interploidy gene flow via a 'pentaploid bridge' and ploidy reduction in Cystopteris fragilis fern complex (Cystopteridaceae: Polypodiales). PLANT REPRODUCTION 2023; 36:321-331. [PMID: 37532893 DOI: 10.1007/s00497-023-00476-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 07/15/2023] [Indexed: 08/04/2023]
Abstract
KEY MESSAGE Our results indicate the existence of interploidy gene flow in Cystopteris fragilis, resulting in sexual triploid and diploid gametophytes from pentaploid parents. Similar evolutionary dynamics might operate in other fern complexes and need further investigation. Polyploidization and hybridization are a key evolutionary processes in ferns. Here, we outline an interploidy gene flow pathway operating in the polyploid Cystopteris fragilis complex. The conditions necessary for the existence of this pathway were tested. A total of 365 C. fragilis individuals were collected covering representatives of all three predominant ploidy levels (tetraploid, pentaploid, and hexaploid), cultivated, had their ploidy level estimated by flow cytometry, and their spores collected. The spores, as well as gametophytes and sporophytes established from them, were analysed by flow cytometry. Spore abortion rate was also estimated. In tetraploids, we observed the formation of unreduced (tetraploid) spores (ca 2%). Collected pentaploid individuals indicate ongoing hybridization between ploidy levels. Pentaploids formed up to 52% viable spores, ca 79% of them reduced, i.e. diploid and triploid. Reduced spores formed viable gametophytes, and, in the case of triploids, filial hexaploid sporophytes, showing evidence of sexual reproduction. Some tetraploid sporophytes reproduce apomictically (based on uniform ploidy of their metagenesis up to filial sporophytes). Triploid and diploid gametophytes from pentaploid parents are able to mate among themselves, or with "normal" reduced gametophytes from the sexual tetraploid sporophytes (the dominant ploidy level in the sporophytes in this populations), to produce tetraploid, pentaploid, and hexaploid sporophytes, allowing for geneflow from the pentaploids to both the tetraploid and hexaploid populations. Similar evolutionary dynamics might operate in other fern complexes and need further investigation.
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Affiliation(s)
- Jan Ptáček
- Department of Botany, Faculty of Science, Charles University, Benátská 2, , 128 00, Praha, Czech Republic
| | - Libor Ekrt
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
| | - Ondřej Hornych
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
| | - Tomáš Urfus
- Department of Botany, Faculty of Science, Charles University, Benátská 2, , 128 00, Praha, Czech Republic.
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4
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Loureiro J, Čertner M, Lučanová M, Sliwinska E, Kolář F, Doležel J, Garcia S, Castro S, Galbraith DW. The Use of Flow Cytometry for Estimating Genome Sizes and DNA Ploidy Levels in Plants. Methods Mol Biol 2023; 2672:25-64. [PMID: 37335468 DOI: 10.1007/978-1-0716-3226-0_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Flow cytometry has emerged as a uniquely flexible, accurate, and widely applicable technology for the analysis of plant cells. One of its most important applications centers on the measurement of nuclear DNA contents. This chapter describes the essential features of this measurement, outlining the overall methods and strategies, but going on to provide a wealth of technical details to ensure the most accurate and reproducible results. The chapter is aimed to be equally accessible to experienced plant cytometrists as well as those newly entering the field. Besides providing a step-by-step guide for estimating genome sizes and DNA-ploidy levels from fresh tissues, special attention is paid to the use of seeds and desiccated tissues for such purposes. Methodological aspects regarding field sampling, transport, and storage of plant material are also given in detail. Finally, troubleshooting information for the most common problems that may arise during the application of these methods is provided.
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Affiliation(s)
- João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal.
| | - Martin Čertner
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Magdalena Lučanová
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
- Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, Bydgoszcz University of Science and Technology, Bydgoszcz, Poland
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic
| | - Sònia Garcia
- Institut Botànic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Barcelona, Catalonia, Spain
| | - Sílvia Castro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - David W Galbraith
- School of Plant Sciences, BIO5 Institute, Arizona Cancer Center, Department of Biomedical Engineering, University of Arizona, Tucson, AZ, USA
- Henan University, School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, Kaifeng, China
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5
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Tang SK, Lee PH, Liou WT, Lin CH, Huang YM, Kuo LY. Fern Spores-"Ready-to-Use" Standards for Plant Genome Size Estimation Using a Flow Cytometric Approach. PLANTS (BASEL, SWITZERLAND) 2022; 12:140. [PMID: 36616269 PMCID: PMC9824788 DOI: 10.3390/plants12010140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/29/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Spores and pollen of plants were used as flow cytometric materials to efficiently infer genome sizes. Given this advantage, they hold great potential for various flow cytometric applications, particularly as plant genome size standards. To develop such novel standards, we investigated conditions of pretreatment (bead vortex), buffer, and reliable genome sizes of three fern spore collections-Cibotium taiwanense "Kuo4395", Sphaeropteris lepifera "Tang0001", and Alsophila metteniana "Lee s.n.". Additionally, up to 30 year-old spore collections were obtained from herbarium specimens and from samples stored at 4 °C; their spore nuclei were extracted, and the quality and quantity of these nucleus extractions through storage ages were examined. Nuclear extractions with a longer bead vortex duration or lower spore/bead ratio generally resulted in a higher recovered quantity but a lower quality or purity. For each spore standard, the protocol optimization was determined by their performance in bead vortex conditions, and a 1C genome size was further inferred by linear regression (C. taiwanense "Kuo4395" = 5.058 pg; S. lepifera "Tang0001" = 7.117 pg; and A. metteniana "Lee s.n." = 19.379 pg). Spore nucleus quality and quantity are significantly negatively correlated with storage ages. Nuclear extractions of 10-year-old refrigerated spores remained qualified as a genome size standard; however, none of the herbarium spore collections fit such criteria. Our study is the first to develop and apply dried and refrigerated spores for genome size standards. These standards are ready to use, easy to manipulate, and feature long-term storage in comparison with traditionally used standards of fresh leaves.
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Affiliation(s)
- Sheng-Kai Tang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu City 300, Taiwan
| | - Pei-Hsuan Lee
- Taiwan Forestry Research Institute, 53 Nan-Hai Road, Taipei City 100, Taiwan
| | - Wei-Ting Liou
- Experimental Forest, College of Bio-Resources and Agriculture, National Taiwan University, Nantou County 557, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung City 402, Taiwan
| | - Chen-Hsiang Lin
- Taoyuan District Agricultural Research and Extension Station, Council of Agriculture, Executive Yuan, Taoyuan City 327, Taiwan
| | - Yao-Moan Huang
- Taiwan Forestry Research Institute, 53 Nan-Hai Road, Taipei City 100, Taiwan
| | - Li-Yaung Kuo
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu City 300, Taiwan
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6
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Galbraith D, Loureiro J. Best practices in plant cytometry: The second tranche. Cytometry A 2022; 101:701-702. [PMID: 36047544 DOI: 10.1002/cyto.a.24681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2022] [Indexed: 11/10/2022]
Affiliation(s)
- David Galbraith
- University of Arizona, School of Plant Sciences, Tucson, USA.,School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
| | - João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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7
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Dunker S, Boyd M, Durka W, Erler S, Harpole WS, Henning S, Herzschuh U, Hornick T, Knight T, Lips S, Mäder P, Švara EM, Mozarowski S, Rakosy D, Römermann C, Schmitt‐Jansen M, Stoof‐Leichsenring K, Stratmann F, Treudler R, Virtanen R, Wendt‐Potthoff K, Wilhelm C. The potential of multispectral imaging flow cytometry for environmental monitoring. Cytometry A 2022; 101:782-799. [DOI: 10.1002/cyto.a.24658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 04/23/2022] [Accepted: 05/12/2022] [Indexed: 12/23/2022]
Affiliation(s)
- Susanne Dunker
- Department of Physiological Diversity Helmholtz‐Centre for Environmental Research (UFZ) Leipzig Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
| | - Matthew Boyd
- Department of Anthropology Lakehead University Thunder Bay Canada
| | - Walter Durka
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Community Ecology Helmholtz‐Centre for Environmental Research (UFZ) Halle Germany
| | - Silvio Erler
- Institute for Bee Protection, Julius Kühn Institute (JKI)‐Federal Research Centre for Cultivated Plants Braunschweig Germany
| | - W. Stanley Harpole
- Department of Physiological Diversity Helmholtz‐Centre for Environmental Research (UFZ) Leipzig Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Institute of Biology, Martin Luther University Halle‐Wittenberg Halle Germany
| | - Silvia Henning
- Department of Experimental Aerosol and Cloud Microphysics Leibniz Institute for Tropospheric Research (TROPOS) Leipzig Germany
| | - Ulrike Herzschuh
- Alfred‐Wegner‐Institute Helmholtz Centre of Polar and Marine Research Polar Terrestrial Environmental Systems Potsdam Germany
- Institute of Environmental Sciences and Geography University of Potsdam Potsdam Germany
- Institute of Biochemistry and Biology University of Potsdam Potsdam Germany
| | - Thomas Hornick
- Department of Physiological Diversity Helmholtz‐Centre for Environmental Research (UFZ) Leipzig Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
| | - Tiffany Knight
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Community Ecology Helmholtz‐Centre for Environmental Research (UFZ) Halle Germany
- Institute of Biology, Martin Luther University Halle‐Wittenberg Halle Germany
| | - Stefan Lips
- Department of Bioanalytical Ecotoxicology Helmholtz‐Centre for Environmental Research – UFZ Leipzig Germany
| | - Patrick Mäder
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Computer Science and Automation Technische Universität Ilmenau Ilmenau Germany
- Faculty of Biological Sciences Friedrich‐Schiller‐University Jena Jena Germany
| | - Elena Motivans Švara
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Community Ecology Helmholtz‐Centre for Environmental Research (UFZ) Halle Germany
- Institute of Biology, Martin Luther University Halle‐Wittenberg Halle Germany
| | | | - Demetra Rakosy
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Community Ecology Helmholtz‐Centre for Environmental Research (UFZ) Halle Germany
| | - Christine Römermann
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Institute of Ecology and Evolution Friedrich‐Schiller‐University Jena Jena Germany
| | - Mechthild Schmitt‐Jansen
- Department of Bioanalytical Ecotoxicology Helmholtz‐Centre for Environmental Research – UFZ Leipzig Germany
| | - Kathleen Stoof‐Leichsenring
- Alfred‐Wegner‐Institute Helmholtz Centre of Polar and Marine Research Polar Terrestrial Environmental Systems Potsdam Germany
| | - Frank Stratmann
- Department of Experimental Aerosol and Cloud Microphysics Leibniz Institute for Tropospheric Research (TROPOS) Leipzig Germany
| | - Regina Treudler
- Department of Dermatology, Venerology and Allergology University of Leipzig Medical Center Leipzig Germany
| | | | - Katrin Wendt‐Potthoff
- Department of Lake Research Helmholtz‐Centre for Environmental Research – UFZ Magdeburg Germany
| | - Christian Wilhelm
- Faculty of Life Sciences, Institute of Biology University of Leipzig Leipzig Germany
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8
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Čertner M, Lučanová M, Sliwinska E, Kolář F, Loureiro J. Plant material selection, collection, preservation, and storage for nuclear DNA content estimation. Cytometry A 2021; 101:737-748. [PMID: 34254737 DOI: 10.1002/cyto.a.24482] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 01/23/2023]
Abstract
In theory, any plant tissue providing intact nuclei in sufficient quantity is suitable for nuclear DNA content estimation using flow cytometry (FCM). While this certainly opens a wide variety of possible applications of FCM, especially when compared to classical karyological techniques restricted to tissues with active cell division, tissue selection and quality may directly affect the precision (and sometimes even reliability) of FCM measurements. It is usually convenient to first consider the goals of the study to either aim for the highest possible accuracy of estimates (e.g., for inferring genome size, detecting homoploid intraspecific genome size variation, aneuploidy, among others), or to decide that histograms of reasonable resolution provide sufficient information (e.g., ploidy level screening within a single model species). Here, a set of best practices guidelines for selecting the optimal plant tissue for FCM analysis, sampling of material, and material preservation and storage are provided. In addition, factors potentially compromising the quality of FCM estimates of nuclear DNA content and data interpretation are discussed.
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Affiliation(s)
- Martin Čertner
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Magdalena Lučanová
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic.,Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, UTP University of Science and Technology, Bydgoszcz, Poland
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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9
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Loureiro J, Kron P, Temsch EM, Koutecký P, Lopes S, Castro M, Castro S. Isolation of plant nuclei for estimation of nuclear DNA content: Overview and best practices. Cytometry A 2021; 99:318-327. [DOI: 10.1002/cyto.a.24331] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/01/2021] [Accepted: 02/24/2021] [Indexed: 11/07/2022]
Affiliation(s)
- João Loureiro
- Centre for Functional Ecology, Department of Life Sciences University of Coimbra Coimbra Portugal
| | - Paul Kron
- Department of Integrative Biology University of Guelph Guelph Ontario Canada
| | - Eva M. Temsch
- Department of Botany and Biodiversity Research University of Vienna Vienna Austria
| | - Petr Koutecký
- Department of Botany Faculty of Science, University of South Bohemia České Budějovice Czechia
| | - Sara Lopes
- Centre for Functional Ecology, Department of Life Sciences University of Coimbra Coimbra Portugal
| | - Mariana Castro
- Centre for Functional Ecology, Department of Life Sciences University of Coimbra Coimbra Portugal
| | - Sílvia Castro
- Centre for Functional Ecology, Department of Life Sciences University of Coimbra Coimbra Portugal
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