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Charalambous I, Ioannou N, Kyratzis AC, Kourtellarides D, Hagidimitriou M, Nikoloudakis N. Genome Size Variation across a Cypriot Fabeae Tribe Germplasm Collection. PLANTS (BASEL, SWITZERLAND) 2023; 12:1469. [PMID: 37050095 PMCID: PMC10096862 DOI: 10.3390/plants12071469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/23/2023] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
DNA content is an important trait linked to the evolutionary routes of taxa and often connected to speciation. In the present study, we studied C-values variation across the Cypriot Fabeae gene pool. Several hundred plants (Vicia spp., Lens spp., Pisum spp.) were sampled across Cyprus. Accurate estimates were established by flow cytometry and propidium iodine staining for 155 discrete populations/accessions. A ten-fold variation was detected across lineages with 1C DNA content varying from 1.584 pg for V. cretica (ARI02420) to 13.983 pg for V. faba (ARI00187). In general, flow cytometry was precise for the characterization of species, even though there were instances of genome overlapping across taxa. Most analyses in the current work refer to species that have not been characterized before by flow cytometry (or any other DNA content estimation method). Still, a correlation to C-values previously reported in Kew Plant DNA C-values database was attempted. A high degree of correlation except for V. dalmatica was established. The evaluation of genome size trait in relation with the Fabeae phylogeny, revealed that Pisum and Lens genera were rather homogenous, but an astonishing fluctuation was shown for Vicia spp. Moreover, it was established that genome up- or down-scaling was not directly linked to speciation drivers. The genomic size measurements presented here could deliver extra quality control for the identification and characterization of taxa in germplasm collections, particularly in cases where species share morphological characters.
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Affiliation(s)
- Iliana Charalambous
- Department of Agricultural Science, Biotechnology and Food Science, Cyprus University of Technology, 3036 Limassol, Cyprus; (I.C.); (N.I.)
| | - Nektaria Ioannou
- Department of Agricultural Science, Biotechnology and Food Science, Cyprus University of Technology, 3036 Limassol, Cyprus; (I.C.); (N.I.)
| | - Angelos C. Kyratzis
- Vegetable Crop Sector, Agricultural Research Institute-Ministry of Agriculture, Rural Development and Environment, 1516 Nicosia, Cyprus; (A.C.K.); (D.K.)
| | - Dimitrios Kourtellarides
- Vegetable Crop Sector, Agricultural Research Institute-Ministry of Agriculture, Rural Development and Environment, 1516 Nicosia, Cyprus; (A.C.K.); (D.K.)
| | | | - Nikolaos Nikoloudakis
- Department of Agricultural Science, Biotechnology and Food Science, Cyprus University of Technology, 3036 Limassol, Cyprus; (I.C.); (N.I.)
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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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3
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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] [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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Conservation implications of widespread polyploidy and apomixis: a case study in the genus Pomaderris (Rhamnaceae). CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01184-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Wu H, Ma Z, Wang MM, Qin AL, Ran JH, Wang XQ. A high frequency of allopolyploid speciation in the gymnospermous genus Ephedra and its possible association with some biological and ecological features. Mol Ecol 2016; 25:1192-210. [PMID: 26800145 PMCID: PMC7168403 DOI: 10.1111/mec.13538] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 11/30/2022]
Abstract
The origin and evolution of polyploids have been studied extensively in angiosperms and ferns but very rarely in gymnosperms. With the exception of three species of conifers, all natural polyploid species of gymnosperms belong to Ephedra, in which more than half of the species show polyploid cytotypes. Here, we investigated the origin and evolution of polyploids of Ephedra distributed in the Qinghai–Tibetan Plateau (QTP) and neighbouring areas. Flow cytometry (FCM) was used to measure the ploidy levels of the sampled species that are represented by multiple individuals from different populations, and then, two single‐copy nuclear genes (LFY and DDB2) and two chloroplast DNA fragments were used to unravel the possible origins and maternal donors of the polyploids. The results indicate that the studied polyploid species are allopolyploids, and suggest that allotetraploidy is a dominant mode of speciation in Ephedra. The high percentage of polyploids in the genus could be related to some of its biological attributes such as vegetative propagation, a relatively high rate of unreduced gamete formation, and a small genome size relative to most other gymnosperms. Significant ecological divergences between allotetraploids and their putative progenitors were detected by PCAs and anova and Tukey's tests, with the exception of E. saxatilis. The overlap of geographical distributions and ecological niches of some diploid species could have provided opportunities for interspecific hybridization and allopolyploid speciation.
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Affiliation(s)
- Hui Wu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Zhen Ma
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ming-Ming Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ai-Li Qin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jin-Hua Ran
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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Sénéchal H, Visez N, Charpin D, Shahali Y, Peltre G, Biolley JP, Lhuissier F, Couderc R, Yamada O, Malrat-Domenge A, Pham-Thi N, Poncet P, Sutra JP. A Review of the Effects of Major Atmospheric Pollutants on Pollen Grains, Pollen Content, and Allergenicity. ScientificWorldJournal 2015; 2015:940243. [PMID: 26819967 PMCID: PMC4706970 DOI: 10.1155/2015/940243] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 10/30/2015] [Accepted: 11/09/2015] [Indexed: 12/12/2022] Open
Abstract
This review summarizes the available data related to the effects of air pollution on pollen grains from different plant species. Several studies carried out either on in situ harvested pollen or on pollen exposed in different places more or less polluted are presented and discussed. The different experimental procedures used to monitor the impact of pollution on pollen grains and on various produced external or internal subparticles are listed. Physicochemical and biological effects of artificial pollution (gaseous and particulate) on pollen from different plants, in different laboratory conditions, are considered. The effects of polluted pollen grains, subparticles, and derived aeroallergens in animal models, in in vitro cell culture, on healthy human and allergic patients are described. Combined effects of atmospheric pollutants and pollen grains-derived biological material on allergic population are specifically discussed. Within the notion of "polluen," some methodological biases are underlined and research tracks in this field are proposed.
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Affiliation(s)
- Hélène Sénéchal
- Allergy & Environment Team, Biochemistry Department, Armand Trousseau Children Hospital (AP-HP), 26 avenue du Dr. Arnold Netter, 75571 Paris, France
| | - Nicolas Visez
- Physical Chemistry of Combustion and Atmosphere Processes (PC2A), UMR CNRS 8522, University of Lille, 59655 Villeneuve d'Ascq, France
| | - Denis Charpin
- Pneumo-Allergology Department, North Hospital, 265 chemin des Bourrely, 13915 Marseille 20, France
| | - Youcef Shahali
- Allergy & Environment Team, Biochemistry Department, Armand Trousseau Children Hospital (AP-HP), 26 avenue du Dr. Arnold Netter, 75571 Paris, France
- Persiflore, 18 avenue du Parc, 91220 Le Plessis-Pâté, France
| | | | - Jean-Philippe Biolley
- SEVE Team, Ecology and Biology of Interactions (EBI), UMR-CNRS-UP 7267, University of Poitiers, 3 rue Jacques Fort, 86073 Poitiers, France
| | | | - Rémy Couderc
- Biochemistry Department, Armand Trousseau Children Hospital (AP-HP), 26 avenue du Dr. Arnold Netter, 75571 Paris 12, France
| | - Ohri Yamada
- French Agency for Food, Environmental and Occupational Health Safety, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort, France
| | - Audrey Malrat-Domenge
- French Agency for Food, Environmental and Occupational Health Safety, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort, France
| | - Nhân Pham-Thi
- Allergology Department, Pasteur Institute, 25-28 rue du Dr. Roux, 75724 Paris 15, France
| | - Pascal Poncet
- Allergy & Environment Team, Biochemistry Department, Armand Trousseau Children Hospital (AP-HP), 26 avenue du Dr. Arnold Netter, 75571 Paris, France
- Infections & Epidemiology Department, Pasteur Institute, 25-28 rue du Dr. Roux, 75724 Paris 15, France
| | - Jean-Pierre Sutra
- Allergy & Environment Team, Biochemistry Department, Armand Trousseau Children Hospital (AP-HP), 26 avenue du Dr. Arnold Netter, 75571 Paris, France
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Petrovská B, Jeřábková H, Chamrád I, Vrána J, Lenobel R, Uřinovská J, Šebela M, Doležel J. Proteomic Analysis of Barley Cell Nuclei Purified by Flow Sorting. Cytogenet Genome Res 2014; 143:78-86. [DOI: 10.1159/000365311] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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