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Bureš P, Elliott TL, Veselý P, Šmarda P, Forest F, Leitch IJ, Nic Lughadha E, Soto Gomez M, Pironon S, Brown MJM, Šmerda J, Zedek F. The global distribution of angiosperm genome size is shaped by climate. New Phytol 2024; 242:744-759. [PMID: 38264772 DOI: 10.1111/nph.19544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/03/2024] [Indexed: 01/25/2024]
Abstract
Angiosperms, which inhabit diverse environments across all continents, exhibit significant variation in genome sizes, making them an excellent model system for examining hypotheses about the global distribution of genome size. These include the previously proposed large genome constraint, mutational hazard, polyploidy-mediated, and climate-mediated hypotheses. We compiled the largest genome size dataset to date, encompassing 16 017 (> 5% of known) angiosperm species, and analyzed genome size distribution using a comprehensive geographic distribution dataset for all angiosperms. We observed that angiosperms with large range sizes generally had small genomes, supporting the large genome constraint hypothesis. Climate was shown to exert a strong influence on genome size distribution along the global latitudinal gradient, while the frequency of polyploidy and the type of growth form had negligible effects. In contrast to the unimodal patterns along the global latitudinal gradient shown by plant size traits and polyploid proportions, the increase in angiosperm genome size from the equator to 40-50°N/S is probably mediated by different (mostly climatic) mechanisms than the decrease in genome sizes observed from 40 to 50°N northward. Our analysis suggests that the global distribution of genome sizes in angiosperms is mainly shaped by climatically mediated purifying selection, genetic drift, relaxed selection, and environmental filtering.
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Affiliation(s)
- Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| | - Tammy L Elliott
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
- Department of Biological Sciences, University of Cape Town, Cape Town, 7700, South Africa
| | - Pavel Veselý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK
| | | | | | | | - Samuel Pironon
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK
- UN Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), Cambridge, CB3 0DL, UK
| | | | - Jakub Šmerda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| | - František Zedek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
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2
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Hu Y, Yu Z, Gao X, Liu G, Zhang Y, Šmarda P, Guo Q. Genetic diversity, population structure, and genome-wide association analysis of ginkgo cultivars. Hortic Res 2023; 10:uhad136. [PMID: 37564270 PMCID: PMC10410194 DOI: 10.1093/hr/uhad136] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 07/02/2023] [Indexed: 08/12/2023]
Abstract
Ginkgo biloba is an economically valuable tree worldwide. The species has nearly become extinct during the Quaternary, which has likely resulted in reduction of its genetic variability. The genetic variability is now conserved in few natural populations in China and a number of cultivars that are, however, derived from a few ancient trees, helping the species survive in China through medieval times. Despite the recent interest in ginkgo, however, detailed knowledge of its genetic diversity, conserved in cultivated trees and cultivars, has remained poor. This limits efficient conservation of its diversity as well as efficient use of the existing germplasm resources. Here we performed genotyping-by-sequencing (GBS) on 102 cultivated germplasms of ginkgo collected to explore their genetic structure, kinship, and inbreeding prediction. For the first time in ginkgo, a genome-wide association analysis study (GWAS) was used to attempt gene mapping of seed traits. The results showed that most of the germplasms did not show any obvious genetic relationship. The size of the ginkgo germplasm population expanded significantly around 1500 years ago during the Sui and Tang dynasties. Classification of seed cultivars based on a phylogenetic perspective does not support the current classification criteria based on phenotype. Twenty-four candidate genes were localized after performing GWAS on the seed traits. Overall, this study reveals the genetic basis of ginkgo seed traits and provides insights into its cultivation history. These findings will facilitate the conservation and utilization of the domesticated germplasms of this living fossil plant.
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Affiliation(s)
- Yaping Hu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Zhaoyan Yu
- Coconut Research Institute of Chinese Academy of Tropical Agricultural Science, Wenchang, Hainan 571339, China
| | - Xiaoge Gao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Ganping Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yun Zhang
- Institute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Koltlářská 2, Brno 61137, Czech Republic
| | - Qirong Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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3
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Šmarda P, Klem K, Knápek O, Veselá B, Veselá K, Holub P, Kuchař V, Šilerová A, Horová L, Bureš P. Growth, physiology, and stomatal parameters of plant polyploids grown under ice age, present-day, and future CO 2 concentrations. New Phytol 2023. [PMID: 37167007 DOI: 10.1111/nph.18955] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/24/2023] [Indexed: 05/12/2023]
Abstract
Polyploidy plays an important role in plant evolution, but knowledge of its eco-physiological consequences, such as of the putatively enlarged stomata of polyploid plants, remains limited. Enlarged stomata should disadvantage polyploids at low CO2 concentrations (namely during the Quaternary glacial periods) because larger stomata are viewed as less effective at CO2 uptake. We observed the growth, physiology, and epidermal cell features of 15 diploids and their polyploid relatives cultivated under glacial, present-day, and potential future atmospheric CO2 concentrations (200, 400, and 800 ppm respectively). We demonstrated some well-known polyploidy effects, such as faster growth and larger leaves, seeds, stomata, and other epidermal cells. The stomata of polyploids, however, tended to be more elongated than those of diploids, and contrary to common belief, they had no negative effect on the CO2 uptake capacity of polyploids. Moreover, polyploids grew comparatively better than diploids even at low, glacial CO2 concentrations. Higher polyploids with large genomes also showed increased operational stomatal conductance and consequently, a lower water-use efficiency. Our results point to a possible decrease in growth superiority of polyploids over diploids in a current and future high CO2 climactic scenarios, as well as the possible water and/or nutrient dependency of higher polyploids.
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Affiliation(s)
- Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2,, CZ-61137, Brno, Czech Republic
| | - Karel Klem
- Global Change Research Institute, Czech Academy of Sciences, Bělidla 986/4a,, CZ-60300, Brno, Czech Republic
| | - Ondřej Knápek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2,, CZ-61137, Brno, Czech Republic
| | - Barbora Veselá
- Global Change Research Institute, Czech Academy of Sciences, Bělidla 986/4a,, CZ-60300, Brno, Czech Republic
| | - Kristýna Veselá
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2,, CZ-61137, Brno, Czech Republic
| | - Petr Holub
- Global Change Research Institute, Czech Academy of Sciences, Bělidla 986/4a,, CZ-60300, Brno, Czech Republic
| | - Vít Kuchař
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2,, CZ-61137, Brno, Czech Republic
| | - Alexandra Šilerová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2,, CZ-61137, Brno, Czech Republic
| | - Lucie Horová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2,, CZ-61137, Brno, Czech Republic
| | - Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2,, CZ-61137, Brno, Czech Republic
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4
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Elliott TL, Zedek F, Barrett RL, Bruhl JJ, Escudero M, Hroudová Z, Joly S, Larridon I, Luceño M, Márquez-Corro JI, Martín-Bravo S, Muasya AM, Šmarda P, Thomas WW, Wilson KL, Bureš P. Chromosome size matters: genome evolution in the cyperid clade. Ann Bot 2022; 130:999-1014. [PMID: 36342743 PMCID: PMC9851305 DOI: 10.1093/aob/mcac136] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 11/03/2022] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS While variation in genome size and chromosome numbers and their consequences are often investigated in plants, the biological relevance of variation in chromosome size remains poorly known. Here, we examine genome and mean chromosome size in the cyperid clade (families Cyperaceae, Juncaceae and Thurniaceae), which is the largest vascular plant lineage with predominantly holocentric chromosomes. METHODS We measured genome size in 436 species of cyperids using flow cytometry, and augment these data with previously published datasets. We then separately compared genome and mean chromosome sizes (2C/2n) amongst the major lineages of cyperids and analysed how these two genomic traits are associated with various environmental factors using phylogenetically informed methods. KEY RESULTS We show that cyperids have the smallest mean chromosome sizes recorded in seed plants, with a large divergence between the smallest and largest values. We found that cyperid species with smaller chromosomes have larger geographical distributions and that there is a strong inverse association between mean chromosome size and number across this lineage. CONCLUSIONS The distinct patterns in genome size and mean chromosome size across the cyperids might be explained by holokinetic drive. The numerous small chromosomes might function to increase genetic diversity in this lineage where crossovers are limited during meiosis.
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Affiliation(s)
- Tammy L Elliott
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - František Zedek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Russell L Barrett
- National Herbarium of New South Wales, Australian Institute of Botanical Science, Australian Botanic Garden, Locked Bag 6002, Mount Annan, New South Wales 2567, Australia
| | - Jeremy J Bruhl
- Botany and N.C.W. Beadle Herbarium, School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Marcial Escudero
- Department of Plant Biology and Ecology, University of Seville, Reina Mercedes 6, 41012 Seville, Spain
| | - Zdenka Hroudová
- Institute of Botany of the Czech Academy of Sciences, 252 43 Průhonice, Czech Republic
- National Museum, Department of Botany, Cirkusová 1740, 193 00 Prague 9, Czech Republic
| | - Simon Joly
- Montreal Botanical Garden, 4101, Sherbrooke East, Montreal, QC H1X 2B2, Canada
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101, Sherbrooke East, Montreal, QC H1X 2B2, Canada
| | - Isabel Larridon
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - Modesto Luceño
- Botany Area, Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, ctra. de Utrera km. 1, 41013, Seville, Spain
| | - José Ignacio Márquez-Corro
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
- Botany Area, Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, ctra. de Utrera km. 1, 41013, Seville, Spain
| | - Santiago Martín-Bravo
- Botany Area, Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, ctra. de Utrera km. 1, 41013, Seville, Spain
| | - A Muthama Muasya
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africaand
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | | | - Karen L Wilson
- National Herbarium of New South Wales, Australian Institute of Botanical Science, Australian Botanic Garden, Locked Bag 6002, Mount Annan, New South Wales 2567, Australia
| | - Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
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5
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Sliwinska E, Loureiro J, Leitch IJ, Šmarda P, Bainard J, Bureš P, Chumová Z, Horová L, Koutecký P, Lučanová M, Trávníček P, Galbraith DW. Application-based guidelines for best practices in plant flow cytometry. Cytometry A 2021; 101:749-781. [PMID: 34585818 DOI: 10.1002/cyto.a.24499] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/10/2021] [Accepted: 08/26/2021] [Indexed: 12/15/2022]
Abstract
Flow cytometry (FCM) is currently the most widely-used method to establish nuclear DNA content in plants. Since simple, 1-3-parameter, flow cytometers, which are sufficient for most plant applications, are commercially available at a reasonable price, the number of laboratories equipped with these instruments, and consequently new FCM users, has greatly increased over the last decade. This paper meets an urgent need for comprehensive recommendations for best practices in FCM for different plant science applications. We discuss advantages and limitations of establishing plant ploidy, genome size, DNA base composition, cell cycle activity, and level of endoreduplication. Applications of such measurements in plant systematics, ecology, molecular biology research, reproduction biology, tissue cultures, plant breeding, and seed sciences are described. Advice is included on how to obtain accurate and reliable results, as well as how to manage troubleshooting that may occur during sample preparation, cytometric measurements, and data handling. Each section is followed by best practice recommendations; tips as to what specific information should be provided in FCM papers are also provided.
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Affiliation(s)
- Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, UTP University of Science and Technology, Bydgoszcz, Poland
| | - João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Ilia J Leitch
- Kew Science Directorate, Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jillian Bainard
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, Saskatchewan, Canada
| | - Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zuzana Chumová
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic.,Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Lucie Horová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Petr Koutecký
- Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, 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
| | - Pavel Trávníček
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - David W Galbraith
- School of Plant Sciences, BIO5 Institute, Arizona Cancer Center, Department of Biomedical Engineering, University of Arizona, Tucson, Arizona, 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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6
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Kiedrzyński M, Zielińska KM, Jedrzejczyk I, Kiedrzyńska E, Tomczyk PP, Rewicz A, Rewers M, Indreica A, Bednarska I, Stupar V, Roleček J, Šmarda P. Tetraploids expanded beyond the mountain niche of their diploid ancestors in the mixed-ploidy grass Festuca amethystina L. Sci Rep 2021; 11:18735. [PMID: 34548532 PMCID: PMC8455632 DOI: 10.1038/s41598-021-97767-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 08/30/2021] [Indexed: 02/08/2023] Open
Abstract
One promising area in understanding the responses of plants to ongoing global climate change is the adaptative effect of polyploidy. This work examines whether there is a coupling between the distribution of cytotypes and their biogeographical niche, and how different niches will affect their potential range. The study uses a range of techniques including flow cytometry, gradient and niche analysis, as well as distribution modelling. In addition, climatic, edaphic and habitat data was used to analyse environmental patterns and potential ranges of cytotypes in the first wide-range study of Festuca amethystina-a mixed-ploidy mountain grass. The populations were found to be ploidy homogeneous and demonstrate a parapatric pattern of cytotype distribution. Potential contact zones have been identified. The tetraploids have a geographically broader distribution than diploids; they also tend to occur at lower altitudes and grow in more diverse climates, geological units and habitats. Moreover, tetraploids have a more extensive potential range, being six-fold larger than diploids. Montane pine forests were found to be a focal environment suitable for both cytotypes, which has a central place in the environmental space of the whole species. Our findings present polyploidy as a visible driver of geographical, ecological and adaptive variation within the species.
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Affiliation(s)
- Marcin Kiedrzyński
- grid.10789.370000 0000 9730 2769Department of Biogeography, Paleoecology and Nature Conservation, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Katarzyna M. Zielińska
- grid.10789.370000 0000 9730 2769Department of Geobotany and Plant Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Iwona Jedrzejczyk
- grid.466210.70000 0004 4673 5993Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, Bydgoszcz University of Science and Technology, Bydgoszcz, Poland
| | - Edyta Kiedrzyńska
- grid.460361.60000 0004 4673 0316European Regional Centre for Ecohydrology of the Polish Academy of Sciences, Lodz, Poland ,grid.10789.370000 0000 9730 2769UNESCO Chair on Ecohydrology and Applied Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Przemysław P. Tomczyk
- grid.10789.370000 0000 9730 2769Department of Biogeography, Paleoecology and Nature Conservation, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland ,grid.460361.60000 0004 4673 0316European Regional Centre for Ecohydrology of the Polish Academy of Sciences, Lodz, Poland
| | - Agnieszka Rewicz
- grid.10789.370000 0000 9730 2769Department of Biogeography, Paleoecology and Nature Conservation, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Monika Rewers
- grid.466210.70000 0004 4673 5993Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, Bydgoszcz University of Science and Technology, Bydgoszcz, Poland
| | - Adrian Indreica
- grid.5120.60000 0001 2159 8361Department of Silviculture, Transilvania University of Brasov
, Brasov, Romania
| | - Iryna Bednarska
- Department of Nature Ecosystems Protection, Institute of Ecology of the Carpathians NASU, Lviv, Ukraine
| | - Vladimir Stupar
- grid.35306.330000 0000 9971 9023Faculty of Forestry, University of Banja Luka, Banja Luka, Bosnia and Herzegovina
| | - Jan Roleček
- grid.10267.320000 0001 2194 0956Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic ,grid.418095.10000 0001 1015 3316Department of Paleoecology, Institute of Botany, Czech Academy of Sciences, Brno, Czech Republic
| | - Petr Šmarda
- grid.10267.320000 0001 2194 0956Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
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7
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Temsch EM, Koutecký P, Urfus T, Šmarda P, Doležel J. Reference standards for flow cytometric estimation of absolute nuclear DNA content in plants. Cytometry A 2021; 101:710-724. [PMID: 34405937 PMCID: PMC9545105 DOI: 10.1002/cyto.a.24495] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/31/2021] [Accepted: 08/02/2021] [Indexed: 11/11/2022]
Abstract
The estimation of nuclear DNA content has been by far the most popular application of flow cytometry in plants. Because flow cytometry measures relative fluorescence intensities of nuclei stained by a DNA fluorochrome, ploidy determination, and estimation of the nuclear DNA content in absolute units both require comparison to a reference standard of known DNA content. This implies that the quality of the results obtained depends on the standard selection and use. Internal standardization, when the nuclei of an unknown sample and the reference standard are isolated, stained, and measured simultaneously, is mandatory for precise measurements. As DNA peaks representing G1/G0 nuclei of the sample and standard appear on the same histogram of fluorescence intensity, the quotient of their position on the fluorescence intensity axis provides the quotient of DNA amounts. For the estimation of DNA amounts in absolute units, a number of well‐established standards are now available to cover the range of known plant genome sizes. Since there are different standards in use, the standard and the genome size assigned to it has always to be reported. When none of the established standards fits, the introduction of a new standard species is needed. For this purpose, the regression line approach or simultaneous analysis of the candidate standard with several established standards should be prioritized. Moreover, the newly selected standard organism has to fulfill a number of requirements: it should be easy to identify and maintain, taxonomically unambiguous, globally available, with known genome size stability, lacking problematic metabolites, suitable for isolation of sufficient amounts of nuclei, and enabling measurements with low coefficients of variation of DNA peaks, hence suitable for the preparation of high quality samples.
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Affiliation(s)
- 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, Czech Republic
| | - Tomáš Urfus
- Department of Botany, Faculty of Science, Charles University, Prague 2, Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
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8
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Galbraith D, Loureiro J, Antoniadi I, Bainard J, Bureš P, Cápal P, Castro M, Castro S, Čertner M, Čertnerová D, Chumová Z, Doležel J, Giorgi D, Husband BC, Kolář F, Koutecký P, Kron P, Leitch IJ, Ljung K, Lopes S, Lučanová M, Lucretti S, Ma W, Melzer S, Molnár I, Novák O, Poulton N, Skalický V, Sliwinska E, Šmarda P, Smith TW, Sun G, Talhinhas P, Tárnok A, Temsch EM, Trávníček P, Urfus T. Best practices in plant cytometry. Cytometry A 2021; 99:311-317. [PMID: 33398930 DOI: 10.1002/cyto.a.24295] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/07/2020] [Accepted: 12/14/2020] [Indexed: 01/19/2023]
Affiliation(s)
- David Galbraith
- School of Plant Sciences, BIO5 Institute, Arizona Cancer Center, Department of Biomedical Engineering, University of Arizona, Tucson, Arizona, USA.,State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, Henan University, School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, Kaifeng, China
| | - João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Ioanna Antoniadi
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Jillian Bainard
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, Saskatchewan, Canada
| | - Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, CZ, Czech Republic
| | - Petr Cápal
- Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
| | - 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
| | - Martin Čertner
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Dora Čertnerová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Zuzana Chumová
- 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, Olomouc, Czech Republic
| | - Debora Giorgi
- Green Biotechnology Laboratory, Biotechnology and Agroindustry Division, Casaccia Research Center, ENEA - Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Brian C Husband
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Petr Koutecký
- Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Paul Kron
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Ilia J Leitch
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Richmond, UK
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Sara Lopes
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - 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
| | - Sergio Lucretti
- Green Biotechnology Laboratory, Biotechnology and Agroindustry Division, Casaccia Research Center, ENEA - Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Wen Ma
- School of Plant Sciences, BIO5 Institute, Arizona Cancer Center, Department of Biomedical Engineering, University of Arizona, Tucson, Arizona, USA.,State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, Henan University, School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, Kaifeng, China
| | - Susanne Melzer
- Clinical Trial Centre Leipzig, University Leipzig, Leipzig, Germany.,LIFE-Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - István Molnár
- Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
| | - Ondřej Novák
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.,Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science of Palacký University, Olomouc, Czech Republic
| | - Nicole Poulton
- Center for Aquatic Cytometry, Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
| | - Vladimír Skalický
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science of Palacký University, Olomouc, Czech Republic
| | - Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, UTP University of Science and Technology, Bydgoszcz, Poland
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, CZ, Czech Republic
| | - Tyler W Smith
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Guiling Sun
- School of Plant Sciences, BIO5 Institute, Arizona Cancer Center, Department of Biomedical Engineering, University of Arizona, Tucson, Arizona, USA.,State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, Henan University, School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, Kaifeng, China
| | - Pedro Talhinhas
- LEAF, Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Attila Tárnok
- LIFE-Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany.,Department of Precision Instruments, Tsinghua University, Beijing, China.,Department for Therapy Validation, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Eva M Temsch
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Pavel Trávníček
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Tomáš Urfus
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
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9
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Schnablová R, Huang L, Klimešová J, Šmarda P, Herben T. Inflorescence preformation prior to winter: a surprisingly widespread strategy that drives phenology of temperate perennial herbs. New Phytol 2021; 229:620-630. [PMID: 32805759 DOI: 10.1111/nph.16880] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/06/2020] [Indexed: 06/11/2023]
Abstract
Organ preformation in overwintering buds of perennial plants has been known for almost two centuries. It is hypothesized to underlie fast growth and early flowering, but its frequency, phylogenetic distribution, and ecological relevance have never been systematically examined. We microscopically observed inflorescence preformation in overwintering buds (IPB) in the autumn. We studied a phylogenetically and ecologically representative set of 330 species of temperate perennial angiosperms and linked these observations with quantitative data on species' flowering phenology, genome size, and ecology. IPB was observed in 34% of species examined (in 14% species the stamens and/or pistils were already developed). IPB is fairly phylogenetically conserved and frequent in many genera (Alchemilla, Carex, Euphorbia, Geranium, Primula, Pulmonaria) or families (Ranunculaceae, Euphorbiaceae, Violaceae, Boraginaceae). It was found in species of any genome size, although it was almost universal in those with large genomes. Compared with non-IPB species, IPB species flowered 38 d earlier on average and were more common in shaded and undisturbed habitats. IPB is a surprisingly widespread adaptation for early growth in predictable (undisturbed) conditions. It contributes to temporal niche differentiation and has important consequences for understanding plant phenology, genome size evolution, and phylogenetic structure of plant communities.
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Affiliation(s)
- Renáta Schnablová
- Department of Population Ecology, Institute of Botany of the Czech Academy of Sciences, Průhonice, 252 43, Czech Republic
| | - Lin Huang
- Department of Botany, Faculty of Science, Charles University, Praha 2, 128 43, Czech Republic
- Institute of Wetland Ecology & Clone Ecology, Taizhou University, Taizhou, 318000, China
| | - Jitka Klimešová
- Department of Functional Ecology, Institute of Botany of the Czech Academy of Sciences, Třeboň, 379 01, Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic
| | - Tomáš Herben
- Department of Population Ecology, Institute of Botany of the Czech Academy of Sciences, Průhonice, 252 43, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Praha 2, 128 43, Czech Republic
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10
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Zedek F, Plačková K, Veselý P, Šmerda J, Šmarda P, Horová L, Bureš P. Endopolyploidy is a common response to UV-B stress in natural plant populations, but its magnitude may be affected by chromosome type. Ann Bot 2020; 126:883-889. [PMID: 32582956 PMCID: PMC7750947 DOI: 10.1093/aob/mcaa109] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 06/18/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS Ultraviolet-B radiation (UV-B) radiation damages the DNA, cells and photosynthetic apparatus of plants. Plants commonly prevent this damage by synthetizing UV-B-protective compounds. Recent laboratory experiments in Arabidopsis and cucumber have indicated that plants can also respond to UV-B stress with endopolyploidy. Here we test the generality of this response in natural plant populations, considering their monocentric or holocentric chromosomal structure. METHODS We measured the endopolyploidy index (flow cytometry) and the concentration of UV-B-protective compounds in leaves of 12 herbaceous species (1007 individuals) from forest interiors and neighbouring clearings where they were exposed to increased UV-B radiation (103 forest + clearing populations). We then analysed the data using phylogenetic mixed models. KEY RESULTS The concentration of UV-B protectives increased with UV-B doses estimated from hemispheric photographs of the sky above sample collection sites, but the increase was more rapid in species with monocentric chromosomes. Endopolyploidy index increased with UV-B doses and with concentrations of UV-B-absorbing compounds only in species with monocentric chromosomes, while holocentric species responded negligibly. CONCLUSIONS Endopolyploidy seems to be a common response to increased UV-B in monocentric plants. Low sensitivity to UV-B in holocentric species might relate to their success in high-UV-stressed habitats and corroborates the hypothesized role of holocentric chromosomes in plant terrestrialization.
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Affiliation(s)
- František Zedek
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Klára Plačková
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Pavel Veselý
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Jakub Šmerda
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Lucie Horová
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Petr Bureš
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
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11
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Veleba A, Zedek F, Horová L, Veselý P, Srba M, Šmarda P, Bureš P. Is the evolution of carnivory connected with genome size reduction? Am J Bot 2020; 107:1253-1259. [PMID: 32882073 DOI: 10.1002/ajb2.1526] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 05/13/2020] [Indexed: 05/24/2023]
Abstract
PREMISE As repeatedly shown, the remarkable variation in the genome size of angiosperms can be shaped by extrinsic selective pressures, including nutrient availability. Carnivory has evolved independently in 10 angiosperm clades, but all carnivorous plants share a common affinity to nutrient-poor habitats. As such, carnivory and genome reduction could be responses to the same environmental pressure. Indeed, the smallest genomes among flowering plants are found in the carnivorous family Lentibulariaceae, where a unique mutation in cytochrome c oxidase (COX) is suspected to promote genome miniaturization. Despite these hypotheses, a phylogenetically informed test of genome size and nutrient availability across carnivorous clades has so far been missing. METHODS Using linear mixed models, we compared genome sizes of 127 carnivorous plants from 7 diverse angiosperm clades with 1072 of their noncarnivorous relatives. We also tested whether genome size in Lentibulariaceae reflects the presence of the COX mutation. RESULTS The genome sizes of carnivorous plants do not differ significantly from those of their noncarnivorous relatives. Based on available data, no significant association between the COX mutation and genome miniaturization could be confirmed, not even when considering polyploidy. CONCLUSIONS Carnivory alone does not seem to significantly affect genome size decrease. Plausibly, it might actually counterbalance the effect of nutrient limitation on genome size evolution. The role of the COX mutation in genome miniaturization needs to be evaluated by analysis of a broader data set because current knowledge of its presence across Lentibulariaceae covers less than 10% of the species diversity in this family.
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Affiliation(s)
- Adam Veleba
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ, 61137, Czech Republic
| | - František Zedek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ, 61137, Czech Republic
| | - Lucie Horová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ, 61137, Czech Republic
| | - Pavel Veselý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ, 61137, Czech Republic
| | - Miroslav Srba
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, Prague, CZ, 12844, Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ, 61137, Czech Republic
| | - Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ, 61137, Czech Republic
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12
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Veselý P, Šmarda P, Bureš P, Stirton C, Muasya AM, Mucina L, Horová L, Veselá K, Šilerová A, Šmerda J, Knápek O. Environmental pressures on stomatal size may drive plant genome size evolution: evidence from a natural experiment with Cape geophytes. Ann Bot 2020; 126:323-330. [PMID: 32474609 PMCID: PMC7380457 DOI: 10.1093/aob/mcaa095] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/21/2020] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS The idea that genome (size) evolution in eukaryotes could be driven by environmental factors is still vigorously debated. In extant plants, genome size correlates positively with stomatal size, leading to the idea that conditions enabling the existence of large stomata in fossil plants also supported growth of their genome size. We test this inductive assumption in drought-adapted, prostrate-leaved Cape (South Africa) geophytes where, compared with their upright-leaved geophytic ancestors, stomata develop in a favourably humid microclimate formed underneath their leaves. METHODS Stomatal parameters (leaf cuticle imprints) and genome size (flow cytometry) were measured in 16 closely related geophytic species pairs from seven plant families. In each pair, representing a different genus, we contrasted a prostrate-leaved species with its upright-leaved phylogenetic relative, the latter whose stomata are exposed to the ambient arid climate. KEY RESULTS Except for one, all prostrate-leaves species had larger stomata, and in 13 of 16 pairs they also had larger genomes than their upright-leaved relatives. Stomatal density and theoretical maximum conductance were less in prostrate-leaved species with small guard cells (<1 pL) but showed no systematic difference in species pairs with larger guard cells (>1 pL). Giant stomata were observed in the prostrate-leaved Satyrium bicorne (89-137 µm long), despite its relatively small genome (2C = 9 Gbp). CONCLUSIONS Our results imply that climate, through selection on stomatal size, might be able to drive genome size evolution in plants. The data support the idea that plants from 'greenhouse' geological periods with large stomata might have generally had larger genome sizes when compared with extant plants, though this might not have been solely due to higher atmospheric CO2 in these periods but could also have been due to humid conditions prevailing at fossil deposit sites.
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Affiliation(s)
- Pavel Veselý
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
- For correspondence. E-mail
| | - Petr Bureš
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
| | - Charles Stirton
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Rondebosch, Cape Town, South Africa
| | - A Muthama Muasya
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Rondebosch, Cape Town, South Africa
| | - Ladislav Mucina
- Iluka Chair in Vegetation Science and Biogeography, Harry Butler Institute, Murdoch University, Murdoch, Perth, Australia
- Department of Geography and Environmental Studies, Stellenbosch University, Matieland, Stellenbosch, South Africa
| | - Lucie Horová
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
| | - Kristýna Veselá
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
| | - Alexandra Šilerová
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
| | - Jakub Šmerda
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
| | - Ondřej Knápek
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
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13
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Rice A, Šmarda P, Novosolov M, Drori M, Glick L, Sabath N, Meiri S, Belmaker J, Mayrose I. The global biogeography of polyploid plants. Nat Ecol Evol 2019; 3:265-273. [PMID: 30697006 DOI: 10.1038/s41559-018-0787-9] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 12/11/2018] [Indexed: 11/09/2022]
Abstract
Deciphering the global distribution of polyploid plants is fundamental for understanding plant evolution and ecology. Many factors have been hypothesized to affect the uneven distribution of polyploid plants across the globe. Nevertheless, the lack of large comparative datasets has restricted such studies to local floras and to narrow taxonomical scopes, limiting our understanding of the underlying drivers of polyploid plant distribution. We present a map portraying the worldwide polyploid frequencies, based on extensive spatial data coupled with phylogeny-based polyploidy inference for tens of thousands of species. This allowed us to assess the potential global drivers affecting polyploid distribution. Our data reveal a clear latitudinal trend, with polyploid frequency increasing away from the equator. Climate, especially temperature, appears to be the most influential predictor of polyploid distribution. However, we find this effect to be mostly indirect, mediated predominantly by variation in plant lifeforms and, to a lesser extent, by taxonomical composition and species richness. Thus, our study presents an emerging view of polyploid distribution that highlights attributes that facilitate the establishment of new polyploid lineages by providing polyploids with sufficient time (that is, perenniality) and space (low species richness) to compete with pre-adapted diploid relatives.
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Affiliation(s)
- Anna Rice
- School of Plant Sciences and Food Security, Tel-Aviv University, Tel-Aviv, Israel
| | - Petr Šmarda
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Maria Novosolov
- School of Zoology, Tel-Aviv University, Tel-Aviv, Israel.,Steinhardt Museum of Natural History, Tel-Aviv University, Tel-Aviv, Israel
| | - Michal Drori
- School of Plant Sciences and Food Security, Tel-Aviv University, Tel-Aviv, Israel
| | - Lior Glick
- School of Plant Sciences and Food Security, Tel-Aviv University, Tel-Aviv, Israel
| | - Niv Sabath
- School of Plant Sciences and Food Security, Tel-Aviv University, Tel-Aviv, Israel
| | - Shai Meiri
- School of Zoology, Tel-Aviv University, Tel-Aviv, Israel.,Steinhardt Museum of Natural History, Tel-Aviv University, Tel-Aviv, Israel
| | - Jonathan Belmaker
- School of Zoology, Tel-Aviv University, Tel-Aviv, Israel.,Steinhardt Museum of Natural History, Tel-Aviv University, Tel-Aviv, Israel
| | - Itay Mayrose
- School of Plant Sciences and Food Security, Tel-Aviv University, Tel-Aviv, Israel.
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14
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Šmarda P, Horová L, Knápek O, Dieck H, Dieck M, Ražná K, Hrubík P, Orlóci L, Papp L, Veselá K, Veselý P, Bureš P. Multiple haploids, triploids, and tetraploids found in modern-day "living fossil" Ginkgo biloba. Hortic Res 2018; 5:55. [PMID: 30302259 PMCID: PMC6165845 DOI: 10.1038/s41438-018-0055-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 05/07/2018] [Accepted: 05/21/2018] [Indexed: 05/30/2023]
Abstract
Ginkgo biloba, the last extant representative of a lineage of Mesozoic gymnosperms, is one of the few seed plants with an exceptionally long (~300 Myr) evolutionary history free of genome-wide duplications (polyploidy). Despite this genome conservatism, we have recently found a viable spontaneous tetraploid Ginkgo sapling during routine screening of several plants, demonstrating that natural polyploidy is possible in Ginkgo. Here we provide a much wider flow cytometry survey of ploidy in some European Ginkgo collections, and own seedlings (>2200 individuals and ~200 cultivars). We found a surprisingly high level of ploidy variation in modern-day Ginkgo and documented altogether 13 haploid, 3 triploid, and 10 tetraploid Ginkgo plants or cultivars, most of them being morphologically distinct from common diploids. Haploids frequently produced polyploid (dihaploid) buds or branches. Tetraploids showed some genome size variation. The surveyed plants provide a unique resource for future Ginkgo research and breeding, and they might be used to accelerate the modern diversification of this nearly extinct plant lineage.
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Affiliation(s)
- Petr Šmarda
- Department of Botany and Zoology, Masaryk University, Koltlářská 2, CZ-61137 Brno, Czech Republic
| | - Lucie Horová
- Department of Botany and Zoology, Masaryk University, Koltlářská 2, CZ-61137 Brno, Czech Republic
| | - Ondřej Knápek
- Department of Botany and Zoology, Masaryk University, Koltlářská 2, CZ-61137 Brno, Czech Republic
| | - Heidi Dieck
- Herrenkamper Gärten, Herrenkamp 1, DE-27254 Siedenburg, Germany
| | - Martin Dieck
- Herrenkamper Gärten, Herrenkamp 1, DE-27254 Siedenburg, Germany
| | - Katarína Ražná
- Department of Genetics and Plant Breeding, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia
| | - Pavel Hrubík
- Slovak University of Agriculture in Nitra, Faculty of Horticulture and Landscape Engineering, Dunajská 16, 949 11 Nitra, Slovakia
| | - Laszlo Orlóci
- Botanical Garden of Eötvös University, Illés utca 25, Budapest, Hungary
| | - Laszlo Papp
- Botanical Garden of Eötvös University, Illés utca 25, Budapest, Hungary
| | - Kristýna Veselá
- Department of Botany and Zoology, Masaryk University, Koltlářská 2, CZ-61137 Brno, Czech Republic
| | - Pavel Veselý
- Department of Botany and Zoology, Masaryk University, Koltlářská 2, CZ-61137 Brno, Czech Republic
| | - Petr Bureš
- Department of Botany and Zoology, Masaryk University, Koltlářská 2, CZ-61137 Brno, Czech Republic
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15
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Veleba A, Šmarda P, Zedek F, Horová L, Šmerda J, Bureš P. Evolution of genome size and genomic GC content in carnivorous holokinetics (Droseraceae). Ann Bot 2017; 119:409-416. [PMID: 28025291 PMCID: PMC5314647 DOI: 10.1093/aob/mcw229] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 09/06/2016] [Accepted: 09/26/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS Studies in the carnivorous family Lentibulariaceae in the last years resulted in the discovery of the smallest plant genomes and an unusual pattern of genomic GC content evolution. However, scarcity of genomic data in other carnivorous clades still prevents a generalization of the observed patterns. Here the aim was to fill this gap by mapping genome evolution in the second largest carnivorous family, Droseraceae, where this evolution may be affected by chromosomal holokinetism in Drosera METHODS: The genome size and genomic GC content of 71 Droseraceae species were measured by flow cytometry. A dated phylogeny was constructed, and the evolution of both genomic parameters and their relationship to species climatic niches were tested using phylogeny-based statistics. KEY RESULTS The 2C genome size of Droseraceae varied between 488 and 10 927 Mbp, and the GC content ranged between 37·1 and 44·7 %. The genome sizes and genomic GC content of carnivorous and holocentric species did not differ from those of their non-carnivorous and monocentric relatives. The genomic GC content positively correlated with genome size and annual temperature fluctuations. The genome size and chromosome numbers were inversely correlated in the Australian clade of Drosera CONCLUSIONS: Our results indicate that neither carnivory (nutrient scarcity) nor the holokinetism have a prominent effect on size and DNA base composition of Droseraceae genomes. However, the holokinetic drive seems to affect karyotype evolution in one of the major clades of Drosera Our survey confirmed that the evolution of GC content is tightly connected with the evolution of genome size and also with environmental conditions.
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Affiliation(s)
- Adam Veleba
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ 61137, Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ 61137, Czech Republic
| | - František Zedek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ 61137, Czech Republic
| | - Lucie Horová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ 61137, Czech Republic
| | - Jakub Šmerda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ 61137, Czech Republic
| | - Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ 61137, Czech Republic
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16
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Affiliation(s)
- Petr Šmarda
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - Pavel Veselý
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - Jakub Šmerda
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - Petr Bureš
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - Ondřej Knápek
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - Magdaléna Chytrá
- Botanical Garden of the Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
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17
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Veleba A, Bureš P, Adamec L, Šmarda P, Lipnerová I, Horová L. Genome size and genomic GC content evolution in the miniature genome-sized family Lentibulariaceae. New Phytol 2014; 203:22-8. [PMID: 24661198 DOI: 10.1111/nph.12790] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Affiliation(s)
- Adam Veleba
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, Brno, CZ-61137, Czech Republic
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18
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Šmarda P, Hejcman M, Březinová A, Horová L, Steigerová H, Zedek F, Bureš P, Hejcmanová P, Schellberg J. Effect of phosphorus availability on the selection of species with different ploidy levels and genome sizes in a long-term grassland fertilization experiment. New Phytol 2013; 200:911-921. [PMID: 23819630 DOI: 10.1111/nph.12399] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 06/01/2013] [Indexed: 05/24/2023]
Abstract
Polyploidy and increased genome size are hypothesized to increase organismal nutrient demands, namely of phosphorus (P), which is an essential and abundant component of nucleic acids. Therefore, polyploids and plants with larger genomes are expected to be selectively disadvantaged in P-limited environments. However, this hypothesis has yet to be experimentally tested. We measured the somatic DNA content and ploidy level in 74 vascular plant species in a long-term fertilization experiment. The differences between the fertilizer treatments regarding the DNA content and ploidy level of the established species were tested using phylogeny-based statistics. The percentage and biomass of polyploid species clearly increased with soil P in particular fertilizer treatments, and a similar but weaker trend was observed for the DNA content. These increases were associated with the dominance of competitive life strategy (particularly advantageous in the P-treated plots) in polyploids and the enhanced competitive ability of dominant polyploid grasses at high soil P concentrations, indicating their increased P limitation. Our results verify the hypothesized effect of P availability on the selection of polyploids and plants with increased genome sizes, although the relative contribution of increased P demands vs increased competitiveness as causes of the observed pattern requires further evaluation.
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Affiliation(s)
- Petr Šmarda
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - Michal Hejcman
- Faculty of Environmental Sciences, Czech University of Life Sciences, Kamýcká 1176, CZ-16521, Prague 6, Suchdol, Czech Republic
| | - Alexandra Březinová
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - Lucie Horová
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - Helena Steigerová
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - František Zedek
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - Petr Bureš
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - Pavla Hejcmanová
- Institute of Tropics and Subtropics, Czech University of Life Sciences, Kamýcká 129, CZ-16521, Prague 6, Suchdol, Czech Republic
| | - Jürgen Schellberg
- Institute of Crop Science and Resource Conservation, University of Bonn, Katzenburgweg 5, D-53115, Bonn, Germany
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Veselý P, Bureš P, Šmarda P. Nutrient reserves may allow for genome size increase: evidence from comparison of geophytes and their sister non-geophytic relatives. Ann Bot 2013; 112:1193-200. [PMID: 23960044 PMCID: PMC3783246 DOI: 10.1093/aob/mct185] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 06/24/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS The genome size of an organism is determined by its capacity to tolerate genome expansion, given the species' life strategy and the limits of a particular environment, and the ability for retrotransposon suppression and/or removal. In some giant-genomed bulb geophytes, this tolerance is explained by their ability to pre-divide cells in the dormant stages or by the selective advantage of larger cells in the rapid growth of their fleshy body. In this study, a test shows that the tendency for genome size expansion is a more universal feature of geophytes, and is a subject in need of more general consideration. METHODS Differences in monoploid genome sizes were compared using standardized phylogenetically independent contrasts in 47 sister pairs of geophytic and non-geophytic taxa sampled across all the angiosperms. The genome sizes of 96 species were adopted from the literature and 53 species were newly measured using flow cytometry with propidium iodide staining. KEY RESULTS The geophytes showed increased genome sizes compared with their non-geophytic relatives, regardless of the storage organ type and regardless of whether or not vernal geophytes, polyploids or annuals were included in the analyses. CONCLUSIONS The universal tendency of geophytes to possess a higher genome size suggests the presence of a universal mechanism allowing for genome expansion. It is assumed that this is primarily due to the nutrient and energetic independence of geophytes perhaps allowing continuous synthesis of DNA, which is known to proceed in the extreme cases of vernal geophytes even in dormant stages. This independence may also be assumed as a reason for allowing large genomes in some parasitic plants, as well as the nutrient limitation of small genomes of carnivorous plants.
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Affiliation(s)
- Pavel Veselý
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
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Zedek F, Šmerda J, Šmarda P, Bureš P. Correlated evolution of LTR retrotransposons and genome size in the genus Eleocharis. BMC Plant Biol 2010; 10:265. [PMID: 21118487 PMCID: PMC3095338 DOI: 10.1186/1471-2229-10-265] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 11/30/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND Transposable elements (TEs) are considered to be an important source of genome size variation and genetic and phenotypic plasticity in eukaryotes. Most of our knowledge about TEs comes from large genomic projects and studies focused on model organisms. However, TE dynamics among related taxa from natural populations and the role of TEs at the species or supra-species level, where genome size and karyotype evolution are modulated in concert with polyploidy and chromosomal rearrangements, remain poorly understood. We focused on the holokinetic genus Eleocharis (Cyperaceae), which displays large variation in genome size and the occurrence of polyploidy and agmatoploidy/symploidy. We analyzed and quantified the long terminal repeat (LTR) retrotransposons Ty1-copia and Ty3-gypsy in relation to changes in both genome size and karyotype in Eleocharis. We also examined how this relationship is reflected in the phylogeny of Eleocharis. RESULTS Using flow cytometry, we measured the genome sizes of members of the genus Eleocharis (Cyperaceae). We found positive correlation between the independent phylogenetic contrasts of genome size and chromosome number in Eleocharis. We analyzed PCR-amplified sequences of various reverse transcriptases of the LTR retrotransposons Ty1-copia and Ty3-gypsy (762 sequences in total). Using real-time PCR and dot blot approaches, we quantified the densities of Ty1-copia and Ty3-gypsy within the genomes of the analyzed species. We detected an increasing density of Ty1-copia elements in evolutionarily younger Eleocharis species and found a positive correlation between Ty1-copia densities and C/n-values (an alternative measure of monoploid genome size) in the genus phylogeny. In addition, our analysis of Ty1-copia sequences identified a novel retrotransposon family named Helos1, which is responsible for the increasing density of Ty1-copia. The transition:transversion ratio of Helos1 sequences suggests that Helos1 recently transposed in later-diverging Eleocharis species. CONCLUSIONS Using several different approaches, we were able to distinguish between the roles of LTR retrotransposons, polyploidy and agmatoploidy/symploidy in shaping Eleocharis genomes and karyotypes. Our results confirm the occurrence of both polyploidy and agmatoploidy/symploidy in Eleocharis. Additionally, we introduce a new player in the process of genome evolution in holokinetic plants: LTR retrotransposons.
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Affiliation(s)
- František Zedek
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Jakub Šmerda
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Petr Bureš
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
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Šmarda P, Horová L, Bureš P, Hralová I, Marková M. Stabilizing selection on genome size in a population of Festuca pallens under conditions of intensive intraspecific competition. New Phytol 2010; 187:1195-1204. [PMID: 20561203 DOI: 10.1111/j.1469-8137.2010.03335.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
*Stabilizing selection is a key evolutionary mechanism for which there is relatively little experimental evidence. To date, stabilizing selection has never been observed at the whole-genome level. *We tested the effect of selection on genome size in a field experiment using seeds collected in a population of Festuca pallens with a highly variable genome size. Using flow cytometry, we measured the genome size in germinating seedlings and juvenile plants grown with or without high intraspecific competition (908 individuals). Above-ground biomass and leaf number were used as measurements of individual vegetative performance. The possible confounding effect of seed weight was controlled for in a separate experiment. *Growth under high competition had a significant stabilizing effect on genome size. Because no relationship was observed between genome size and vegetative performance, we assume that the elimination of plants with extreme genome sizes was the result of decreased survival as a consequence of some unrecognized stress. *Our results indicate that genome size may be under direct selection. The equal disadvantaging of either large or small genomes indicates that the selection for optimum genome size in species may be fully context dependent. This study demonstrates the power of competition experiments for the detection of weak selection processes.
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Affiliation(s)
- Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
| | - Lucie Horová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
| | - Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
| | - Ivana Hralová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
| | - Michaela Marková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
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