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Chumová Z, Havlíčková E, Zeisek V, Šemberová K, Mandáková T, Euston-Brown D, Trávníček P. Deciphering Pteronia's evolution in the Cape Floristic Region: A comprehensive study disputes polyploid deficiency and affirms diploid radiation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:2236-2254. [PMID: 38981008 DOI: 10.1111/tpj.16914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/04/2024] [Accepted: 06/22/2024] [Indexed: 07/11/2024]
Abstract
The Greater Cape Floristic Region (GCFR) is renowned for its exceptional biodiversity, accommodating over 11 000 plant species, notable degree of endemism, and substantial diversification within limited plant lineages, a phenomenon ascribed to historical radiation events. While both abiotic and biotic factors contribute to this diversification, comprehensive genomic alterations, recognized as pivotal in the diversification of angiosperms, are perceived as uncommon. This investigation focuses on the genus Pteronia, a prominent representative of the Asteraceae family in the GCFR. Employing NGS-based HybSeq and RADSeq methodologies, flow cytometry, karyology, and ecological modeling, we scrutinize the intricacies of its polyploid evolution. Phylogenetic reconstructions using 951 low-copy nuclear genes confirm Pteronia as a well-supported, distinct clade within the tribe Astereae. The ingroup displays a structure indicative of rapid radiation likely antedating polyploid establishment, with the two main groups demarcated by their presence or absence in the fynbos biome. Genome size analysis encompasses 1293 individuals across 347 populations, elucidating significant variation ranging from 6.1 to 34.2 pg (2C-value). Pteronia demonstrates substantially large genome sizes within Astereae and phanerophytes. Polyploidy is identified in 31% of the studied species, with four discerned ploidy levels (2x, 4x, 6x, 8x). Cytotypes exhibit marked distinctions in environmental traits, influencing their distribution across biomes and augmenting their niche differentiation. These revelations challenge the presumed scarcity of polyploidy in the Cape flora, underscoring the imperative need for detailed population studies. The intricate evolutionary history of Pteronia, characterized by recent polyploidy and genome size variation, contributes substantially to the comprehension of diversification patterns within the GCFR biodiversity hotspot.
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Affiliation(s)
- Zuzana Chumová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
| | - Eliška Havlíčková
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Prague, CZ-12800, Czech Republic
| | - Vojtěch Zeisek
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Prague, CZ-12800, Czech Republic
| | - Kristýna Šemberová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
| | - Terezie Mandáková
- Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, CZ-625 00, Czech Republic
| | | | - Pavel Trávníček
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
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Gaynor ML, Landis JB, O'Connor TK, Laport RG, Doyle JJ, Soltis DE, Ponciano JM, Soltis PS. nQuack: An R package for predicting ploidal level from sequence data using site-based heterozygosity. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11606. [PMID: 39184199 PMCID: PMC11342224 DOI: 10.1002/aps3.11606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/01/2024] [Accepted: 05/28/2024] [Indexed: 08/27/2024]
Abstract
Premise Traditional methods of ploidal-level estimation are tedious; using DNA sequence data for cytotype estimation is an ideal alternative. Multiple statistical approaches to leverage sequence data for ploidy inference based on site-based heterozygosity have been developed. However, these approaches may require high-coverage sequence data, use inappropriate probability distributions, or have additional statistical shortcomings that limit inference abilities. We introduce nQuack, an open-source R package that addresses the main shortcomings of current methods. Methods and Results nQuack performs model selection for improved ploidy predictions. Here, we implement expectation maximization algorithms with normal, beta, and beta-binomial distributions. Using extensive computer simulations that account for variability in sequencing depth, as well as real data sets, we demonstrate the utility and limitations of nQuack. Conclusions Inferring ploidy based on site-based heterozygosity alone is difficult. Even though nQuack is more accurate than similar methods, we suggest caution when relying on any site-based heterozygosity method to infer ploidy.
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Affiliation(s)
- Michelle L. Gaynor
- Florida Museum of Natural HistoryUniversity of FloridaGainesville32611FloridaUSA
- Department of BiologyUniversity of FloridaGainesville32611FloridaUSA
| | - Jacob B. Landis
- School of Integrative Plant ScienceCornell UniversityIthaca14850New YorkUSA
| | - Timothy K. O'Connor
- Department of Ecology and EvolutionUniversity of ChicagoChicago60637IllinoisUSA
| | | | - Jeff J. Doyle
- School of Integrative Plant ScienceCornell UniversityIthaca14850New YorkUSA
| | - Douglas E. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesville32611FloridaUSA
- Department of BiologyUniversity of FloridaGainesville32611FloridaUSA
| | | | - Pamela S. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesville32611FloridaUSA
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Rosero J, Pereira Dos Santos Silva A, Alves Dos Santos SC, Shigueki Yasui G. Dried storage of sperm at supra-zero temperatures: An alternative for flow cytometric analysis under field conditions. Cryobiology 2024; 115:104899. [PMID: 38663664 DOI: 10.1016/j.cryobiol.2024.104899] [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: 01/09/2024] [Revised: 04/15/2024] [Accepted: 04/22/2024] [Indexed: 04/29/2024]
Abstract
In biotechnological processes such as chromosomal manipulation studies, semen has become a reference in the ploidy verification of the evaluated material. However, the use of fresh samples is limited to the use at field conditions because the analysis is performed under laboratory conditions. Thus, this study aimed to develop a simpler procedure for storing dry semen at 28 °C to reduce cold storage costs. For this, semen samples were evaluated according to established quality semen parameters, a protocol for dry, and 3 sterilization treatments of dry semen were applied to the store. The integrity of the DNA was evaluated every two months, using fresh semen, dry semen (untreated), and particles 3C to compare the peaks by flow cytometry. The results indicated that all samples evaluated before and after drying showed no significant difference in the DNA content. UV-treated semen showed a 1C peak in the histogram up to 180 days of storage and a non-significant difference (P > 0.05) from fresh control in the number of DNA particles up to 120 days and untreated only showed a 1C peak up to 120 days. The developed method may become an interesting procedure to serve as a reference peak for practical flow cytometric analysis, not only in the field of fish biology but also in biomedical and agricultural sciences. Furthermore, dried semen can become a tool for the preservation of genetic material and is a promising low-cost storage technique for biobanking.
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Affiliation(s)
- Jenyffer Rosero
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil; Laboratory of Fish Biotechnology, National Center for Research and Conservation of Continental Aquatic Biodiversity, Chico Mendes Institute of Biodiversity Conservation, Pirassununga, São Paulo, Brazil.
| | - Amanda Pereira Dos Santos Silva
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil; Laboratory of Fish Biotechnology, National Center for Research and Conservation of Continental Aquatic Biodiversity, Chico Mendes Institute of Biodiversity Conservation, Pirassununga, São Paulo, Brazil
| | | | - George Shigueki Yasui
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil; Laboratory of Fish Biotechnology, National Center for Research and Conservation of Continental Aquatic Biodiversity, Chico Mendes Institute of Biodiversity Conservation, Pirassununga, São Paulo, Brazil
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Chumová Z, Monier Z, Šemberová K, Havlíčková E, Euston-Brown D, Muasya AM, Bergh NG, Trávníček P. Diploid and tetraploid cytotypes of the flagship Cape species Dicerothamnus rhinocerotis (Asteraceae): variation in distribution, ecological niche, morphology and genetics. ANNALS OF BOTANY 2024; 133:851-870. [PMID: 37410810 PMCID: PMC11082512 DOI: 10.1093/aob/mcad084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 07/04/2023] [Indexed: 07/08/2023]
Abstract
BACKGROUND AND AIMS The Greater Cape Floristic Region is one of the world's biodiversity hotspots and is considered poor in polyploids. To test this assumption, ploidy variation was investigated in a widespread Cape shrub, Dicerothamnus rhinocerotis (renosterbos, Asteraceae). The aim was to elucidate the cytotype distribution and population composition across the species range, and to assess differences in morphology, environmental niches and genetics. METHODS Ploidy level and genome size were determined via flow cytometry and cytotype assignment was confirmed by chromosome counting. Restriction site-associated DNA sequencing (RADseq) analyses were used to infer genetic relationships. Cytotype climatic and environmental niches were compared using a range of environmental layers and a soil model, while morphological differences were examined using multivariate methods. KEY RESULTS The survey of 171 populations and 2370 individuals showed that the species comprises diploid and tetraploid cytotypes, no intermediates and only 16.8 % of mixed populations. Mean 2C values were 1.80-2.06 pg for diploids and 3.48-3.80 pg for tetraploids, with very similar monoploid genome sizes. Intra-cytotype variation showed a significant positive correlation with altitude and longitude in both cytotypes and with latitude in diploids. Although niches of both cytotypes were highly equivalent and similar, their optima and breadth were shifted due to differences mainly in isothermality and available water capacity. Morphometric analyses showed significant differences in the leaves and corolla traits, the number of florets per capitulum, and cypsela dimensions between the two cytotypes. Genetic analyses revealed four groups, three of them including both cytotypes. CONCLUSIONS Dicerothamnus rhinocerotis includes two distinct cytotypes that are genetically similar. While tetraploids arise several times independently within different genetic groups, morphological and ecological differences are evident between cytotypes. Our results open up new avenues for questions regarding the importance of ploidy in the megadiverse Cape flora, and exemplify the need for population-based studies focused on ploidy variation.
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Affiliation(s)
- Zuzana Chumová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, 252 43, Czech Republic
| | - Zafar Monier
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Cape Town, 7707, South Africa
| | - Kristýna Šemberová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, 252 43, Czech Republic
| | - Eliška Havlíčková
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, 252 43, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Prague, 120 00, Czech Republic
| | | | - A Muthama Muasya
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Cape Town, 7707, South Africa
| | - Nicola G Bergh
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Cape Town, 7707, South Africa
- The Compton Herbarium, Kirstenbosch National Botanical Gardens, Cape Town, 7735, South Africa
| | - Pavel Trávníček
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, 252 43, Czech Republic
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Hrabovský M, Kubalová S, Mičieta K, Ščevková J. Environmental impacts on intraspecific variation in Ambrosia artemisiifolia genome size in Slovakia, Central Europe. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:33960-33974. [PMID: 38693457 PMCID: PMC11136817 DOI: 10.1007/s11356-024-33410-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 04/16/2024] [Indexed: 05/03/2024]
Abstract
The quantity of DNA in angiosperms exhibits variation attributed to many external influences, such as environmental factors, geographical features, or stress factors, which exert constant selection pressure on organisms. Since invasive species possess adaptive capabilities to acclimate to novel environmental conditions, ragweed (Ambrosia artemisiifolia L.) was chosen as a subject for investigating their influence on genome size variation. Slovakia has diverse climatic conditions, suitable for testing the hypothesis that air temperature and precipitation, the main limiting factors of ragweed occurrence, would also have an impact on its genome size. Our results using flow cytometry confirmed this hypothesis and also found a significant association with geographical features such as latitude, altitude, and longitude. We can conclude that plants growing in colder environments farther from oceanic influences exhibit smaller DNA amounts, while optimal growth conditions result in a greater variability in genome size, reflecting the diminished effect of selection pressure.
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Affiliation(s)
- Michal Hrabovský
- Department of Botany, Faculty of Natural Sciences, Comenius University, Révová 39, 811 02, Bratislava, Slovakia.
| | - Silvia Kubalová
- Department of Botany, Faculty of Natural Sciences, Comenius University, Révová 39, 811 02, Bratislava, Slovakia
| | - Karol Mičieta
- Department of Botany, Faculty of Natural Sciences, Comenius University, Révová 39, 811 02, Bratislava, Slovakia
| | - Jana Ščevková
- Department of Botany, Faculty of Natural Sciences, Comenius University, Révová 39, 811 02, Bratislava, Slovakia
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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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Burian M, Podgórska A, Kryzheuskaya K, Gieczewska K, Sliwinska E, Szal B. Ammonium treatment inhibits cell cycle activity and induces nuclei endopolyploidization in Arabidopsis thaliana. PLANTA 2024; 259:94. [PMID: 38509428 DOI: 10.1007/s00425-024-04372-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
MAIN CONCLUSION This study determined the effect of ammonium supply on the cell division process and showed that ammonium-dependent elevated reactive oxygen species production could mediate the downregulation of the cell cycle-related gene expression. Plants grown under high-ammonium conditions show stunted growth and other toxicity symptoms, including oxidative stress. However, how ammonium regulates the development of plants remains unknown. Growth is defined as an increase in cell volume or proliferation. In the present study, ammonium-related changes in cell cycle activity were analyzed in seedlings, apical buds, and young leaves of Arabidopsis thaliana plants. In all experimental ammonium treatments, the genes responsible for regulating cell cycle progression, such as cyclin-dependent kinases and cyclins, were downregulated in the studied tissues. Thus, ammonium nutrition could be considered to reduce cell proliferation; however, the cause of this phenomenon may be secondary. Reactive oxygen species (ROS), which are produced in large amounts in response to ammonium nutrition, can act as intermediates in this process. Indeed, high ROS levels resulting from H2O2 treatment or reduced ROS production in rbohc mutants, similar to ammonium-triggered ROS, correlated with altered cell cycle-related gene expression. It can be concluded that the characteristic ammonium growth suppression may be executed by enhanced ROS metabolism to inhibit cell cycle activity. This study provides a base for future research in determining the mechanism behind ammonium-induced dwarfism in plants, and strategies to mitigate such stress.
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Affiliation(s)
- Maria Burian
- Department of Plant Bioenergetics, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Anna Podgórska
- Department of Plant Bioenergetics, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Katsiaryna Kryzheuskaya
- Department of Plant Bioenergetics, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Katarzyna Gieczewska
- Department of Plant Anatomy and Cytology, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, Bydgoszcz University of Science and Technology, Kaliskiego 7, 85-796, Bydgoszcz, Poland
| | - Bożena Szal
- Department of Plant Bioenergetics, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland.
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Guenzi-Tiberi P, Istace B, Alsos IG, Coissac E, Lavergne S, Aury JM, Denoeud F. LocoGSE, a sequence-based genome size estimator for plants. FRONTIERS IN PLANT SCIENCE 2024; 15:1328966. [PMID: 38550287 PMCID: PMC10972871 DOI: 10.3389/fpls.2024.1328966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/22/2024] [Indexed: 06/21/2024]
Abstract
Extensive research has focused on exploring the range of genome sizes in eukaryotes, with a particular emphasis on land plants, where significant variability has been observed. Accurate estimation of genome size is essential for various research purposes, but existing sequence-based methods have limitations, particularly for low-coverage datasets. In this study, we introduce LocoGSE, a novel genome size estimator designed specifically for low-coverage datasets generated by genome skimming approaches. LocoGSE relies on mapping the reads on single copy consensus proteins without the need for a reference genome assembly. We calibrated LocoGSE using 430 low-coverage Angiosperm genome skimming datasets and compared its performance against other estimators. Our results demonstrate that LocoGSE accurately predicts monoploid genome size even at very low depth of coverage (<1X) and on highly heterozygous samples. Additionally, LocoGSE provides stable estimates across individuals with varying ploidy levels. LocoGSE fills a gap in sequence-based plant genome size estimation by offering a user-friendly and reliable tool that does not rely on high coverage or reference assemblies. We anticipate that LocoGSE will facilitate plant genome size analysis and contribute to evolutionary and ecological studies in the field. Furthermore, at the cost of an initial calibration, LocoGSE can be used in other lineages.
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Affiliation(s)
- Pierre Guenzi-Tiberi
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Benjamin Istace
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Inger Greve Alsos
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway
| | - Eric Coissac
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA (Laboratoire d’Ecologie Alpine), Grenoble, France
| | - Sébastien Lavergne
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA (Laboratoire d’Ecologie Alpine), Grenoble, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
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Jyoti TP, Chandel S, Singh R. Flow cytometry: Aspects and application in plant and biological science. JOURNAL OF BIOPHOTONICS 2024; 17:e202300423. [PMID: 38010848 DOI: 10.1002/jbio.202300423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 10/28/2023] [Indexed: 11/29/2023]
Abstract
Flow cytometry is a potent method that enables the quick and concurrent investigation of several characteristics of single cells in solution. Photodiodes or photomultiplier tubes are employed to detect the dispersed and fluorescent light signals that are produced by the laser beam as it passes through the cells. Photodetectors transform the light signals produced by the laser into electrical impulses. A computer then analyses these electrical impulses to identify and measure the various cell populations depending on their fluorescence or light scattering characteristics. Based on their fluorescence or light scattering properties, cell populations can be examined and/or isolated. This review covers the basic principle, components, working and specific biological applications of flow cytometry, including studies on plant, cell and molecular biology and methods employed for data processing and interpretation as well as the potential future relevance of this methodology in light of retrospective analysis and recent advancements in flow cytometry.
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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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Kozlowski G, Fragnière Y, Clément B, Gilg O, Sittler B, Lang J, Eidesen PB, Lang SI, Wasowicz P, Meade C. Genome Size in the Arenaria ciliata Species Complex (Caryophyllaceae), with Special Focus on Northern Europe and the Arctic. PLANTS (BASEL, SWITZERLAND) 2024; 13:635. [PMID: 38475481 DOI: 10.3390/plants13050635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024]
Abstract
The main aim of the present study has been the completion of genome size data for the diverse arctic-alpine A. ciliata species complex, with special focus on the unexplored arctic taxon A. pseudofrigida, the north-European A. norvegica, and A. gothica from Gotland (Sweden). Altogether, 46 individuals of these three Nordic taxa have been sampled from seven different regions and their genome size estimated using flow cytometry. Three other alpine taxa in the A. ciliata complex (A. multicaulis, A. ciliata subsp. ciliata, and A. ciliata subsp. bernensis) were also collected and analyzed for standardization purposes, comprising 20 individuals from six regions. A mean 2c value of 1.65 pg of DNA was recorded for A. pseudofrigida, 2.80 pg for A. norvegica, and 4.14 pg for A. gothica, as against the reconfirmed 2c value of 1.63 pg DNA for the type taxon A. ciliata subsp. ciliata. Our results presenting the first estimations of genome sizes for the newly sampled taxa, corroborate ploidy levels described in the available literature, with A. pseudofrigida being tetraploid (2n = 4x = 40), A. norvegica possessing predominantly 2n = 8x = 80, and A. gothica with 2n = 10x = 100. The present study also reconfirms genome size and ploidy level estimations published previously for the alpine members of this species complex. Reflecting a likely complex recent biogeographic history, the A. ciliata species group comprises a polyploid arctic-alpine species complex characterized by reticulate evolution, polyploidizations and hybridizations, probably associated with rapid latitudinal and altitudinal migrations in the Pleistocene-Holocene period.
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Affiliation(s)
- Gregor Kozlowski
- Department of Biology and Botanical Garden, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
- Natural History Museum Fribourg, Chemin du Musée 6, 1700 Fribourg, Switzerland
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
| | - Yann Fragnière
- Department of Biology and Botanical Garden, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Benoît Clément
- Department of Biology and Botanical Garden, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Olivier Gilg
- UMR 6249 Chrono-Environment, CNRS, Université de Bourgogne Franche-Comté, 25000 Besançon, France
- Groupe de Recherche en Ecologie Arctique (GREA), 16 rue de Vernot, 21440 Francheville, France
| | - Benoît Sittler
- Groupe de Recherche en Ecologie Arctique (GREA), 16 rue de Vernot, 21440 Francheville, France
- Nature Conservation and Landscape Ecology, University of Freiburg, Tannenbacherstrasse 4, 79106 Freiburg im Breisgau, Germany
| | - Johannes Lang
- Groupe de Recherche en Ecologie Arctique (GREA), 16 rue de Vernot, 21440 Francheville, France
- Arbeitsgruppe Wildtierforschung, Justus-Liebig-University Giessen, Frankfurter Strasse 114, 35392 Giessen, Germany
| | | | - Simone I Lang
- Department of Arctic Biology, The University Centre in Svalbard, P.O. Box 156, 9171 Longyearbyen, Norway
| | - Pawel Wasowicz
- Icelandic Institute of Natural History, Borgum við Norðurslóð, 600 Akureyri, Iceland
| | - Conor Meade
- Molecular Ecology & Biogeography Laboratory, Biology Department, Maynooth University, W23 F2H6 Maynooth, Ireland
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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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Pyšek P, Lučanová M, Dawson W, Essl F, Kreft H, Leitch IJ, Lenzner B, Meyerson LA, Pergl J, van Kleunen M, Weigelt P, Winter M, Guo WY. Small genome size and variation in ploidy levels support the naturalization of vascular plants but constrain their invasive spread. THE NEW PHYTOLOGIST 2023; 239:2389-2403. [PMID: 37438886 DOI: 10.1111/nph.19135] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 06/17/2023] [Indexed: 07/14/2023]
Abstract
Karyological characteristics are among the traits underpinning the invasion success of vascular plants. Using 11 049 species, we tested the effects of genome size and ploidy levels on plant naturalization (species forming self-sustaining populations where they are not native) and invasion (naturalized species spreading rapidly and having environmental impact). The probability that a species naturalized anywhere in the world decreased with increasing monoploid genome size (DNA content of a single chromosome set). Naturalized or invasive species with intermediate monoploid genomes were reported from many regions, but those with either small or large genomes occurred in fewer regions. By contrast, large holoploid genome sizes (DNA content of the unreplicated gametic nucleus) constrained naturalization but favoured invasion. We suggest that a small genome is an advantage during naturalization, being linked to traits favouring adaptation to local conditions, but for invasive spread, traits associated with a large holoploid genome, where the impact of polyploidy may act, facilitate long-distance dispersal and competition with other species.
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Affiliation(s)
- Petr Pyšek
- Department of Invasion Ecology, Institute of Botany, Czech Academy of Sciences, Průhonice, CZ-252 43, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, CZ-128 44, Czech Republic
| | - Magdalena Lučanová
- Department of Evolutionary Biology of Plants, Institute of Botany, Czech Academy of Sciences, Průhonice, CZ-252 43, Czech Republic
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-370 05, Czech Republic
| | - Wayne Dawson
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Franz Essl
- Division of Bioinvasions, Global Change & Macroecology, Department of Botany and Biodiversity Research, University of Vienna, Wien, 1030, Austria
| | - Holger Kreft
- Biodiversity, Macroecology & Biogeography, University of Göttingen, Büsgenweg 1, Göttingen, 37077, Germany
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Goettingen, Büsgenweg 1, Göttingen, D-37077, Germany
- Campus-Institute Data Science, Goldschmidtstraße 1, Göttingen, 37077, Germany
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Bernd Lenzner
- Division of Bioinvasions, Global Change & Macroecology, Department of Botany and Biodiversity Research, University of Vienna, Wien, 1030, Austria
| | - Laura A Meyerson
- University of Rhode Island, Natural Resources Science, 9 East Alumni Avenue, Kingston, 02881, RI, USA
| | - Jan Pergl
- Department of Invasion Ecology, Institute of Botany, Czech Academy of Sciences, Průhonice, CZ-252 43, Czech Republic
| | - Mark van Kleunen
- Ecology, Department of Biology, University of Konstanz, Universitätsstrasse 10, Constance, D-78464, Germany
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000, China
| | - Patrick Weigelt
- Biodiversity, Macroecology & Biogeography, University of Göttingen, Büsgenweg 1, Göttingen, 37077, Germany
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Goettingen, Büsgenweg 1, Göttingen, D-37077, Germany
- Campus-Institute Data Science, Goldschmidtstraße 1, Göttingen, 37077, Germany
| | - Marten Winter
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, Leipzig, 04103, Germany
| | - Wen-Yong Guo
- Research Centre for Global Change and Complex Ecosystems, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China
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13
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Fomicheva M, Domblides E. Mastering DNA Content Estimation by Flow Cytometry as an Efficient Tool for Plant Breeding and Biodiversity Research. Methods Protoc 2023; 6:mps6010018. [PMID: 36827505 PMCID: PMC9963313 DOI: 10.3390/mps6010018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Flow cytometry gives a unique opportunity to analyze thousands of individual cells for multiple parameters in a course of minutes. The most commonly used flow cytometry application in plant biology is estimation of nuclear DNA content. This becomes an indispensable tool in different areas of plant research, including breeding, taxonomy, plant development, evolutionary biology, populational studies and others. DNA content analysis can provide an insight into natural ploidy changes that reflect evolutionary processes, such as interspecific hybridization and polyploidization. It is also widely used for processing samples with biotechnologically induced ploidy changes, for instance, plants produced by doubled haploid technology. Absolute genome size data produced by cytometric analysis serve as useful taxon-specific markers since genome size vary between different taxa. It often allows the distinguishing of species within a genus or even different subspecies. Introducing flow cytometry method in the lab is extremely appealing, but new users face a significant challenge of learning instrument management, quality sample preparation and data processing. Not only is flow cytometry a complex method, but plant samples have unique features that make plants a demanding research subject. Without proper training, researchers risk damaging the expensive instrument or publishing poor quality data, artifacts or unreproducible results. We bring together information from our experience, key papers and online resources to provide step by step protocols and give a starting point for exploring the abundant cytometry literature.
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Šemberová K, Svitok M, Marhold K, Suda J, Schmickl RE. Morphological and environmental differentiation as prezygotic reproductive barriers between parapatric and allopatric Campanula rotundifolia agg. cytotypes. ANNALS OF BOTANY 2023; 131:71-86. [PMID: 34559179 PMCID: PMC9904352 DOI: 10.1093/aob/mcab123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 09/21/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Reproductive isolation and local establishment are necessary for plant speciation. Polyploidy, the possession of more than two complete chromosome sets, creates a strong postzygotic reproductive barrier between diploid and tetraploid cytotypes. However, this barrier weakens between polyploids (e.g. tetraploids and hexaploids). Reproductive isolation may be enhanced by cytotype morphological and environmental differentiation. Moreover, morphological adaptations to local conditions contribute to plant establishment. However, the relative contributions of ploidy level and the environment to morphology have generally been neglected. Thus, the extent of morphological variation driven by ploidy level and the environment was modelled for diploid, tetraploid and hexaploid cytotypes of Campanula rotundifolia agg. Cytotype distribution was updated, and morphological and environmental differentiation was tested in the presence and absence of natural contact zones. METHODS Cytotype distribution was assessed from 231 localities in Central Europe, including 48 localities with known chromosome counts, using flow cytometry. Differentiation in environmental niche and morphology was tested for cytotype pairs using discriminant analyses. A structural equation model was used to explore the synergies between cytotype, environment and morphology. KEY RESULTS Tremendous discrepancies were revealed between the reported and detected cytotype distribution. Neither mixed-ploidy populations nor interploidy hybrids were detected in the contact zones. Diploids had the broadest environmental niche, while hexaploids had the smallest and specialized niche. Hexaploids and spatially isolated cytotype pairs differed morphologically, including allopatric tetraploids. While leaf and shoot morphology were influenced by environmental conditions and polyploidy, flower morphology depended exclusively on the cytotype. CONCLUSIONS Reproductive isolation mechanisms vary between cytotypes. While diploids and polyploids are isolated postzygotically, the environmental niche shift is essential between higher polyploids. The impact of polyploidy and the environment on plant morphology implies the adaptive potential of polyploids, while the exclusive relationship between flower morphology and cytotype highlights the role of polyploidy in reproductive isolation.
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Affiliation(s)
| | - Marek Svitok
- Faculty of Ecology and Environmental Sciences, Technical University in Zvolen, T. G. Masaryka, Zvolen, Slovakia
- Faculty of Science, Department of Ecosystem Biology, University of South Bohemia, Branišovská, České Budějovice, Czech Republic
| | - Karol Marhold
- Faculty of Science, Department of Botany, Charles University, Benátská, Prague, Czech Republic
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta, Bratislava, Slovakia
| | | | - Roswitha E Schmickl
- Faculty of Science, Department of Botany, Charles University, Benátská, Prague, Czech Republic
- Czech Academy of Sciences, Institute of Botany, Department of Evolutionary Plant Biology, Zámek, Průhonice, Czech Republic
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15
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Viruel J, Hidalgo O, Pokorny L, Forest F, Gravendeel B, Wilkin P, Leitch IJ. A Bioinformatic Pipeline to Estimate Ploidy Level from Target Capture Sequence Data Obtained from Herbarium Specimens. Methods Mol Biol 2023; 2672:115-126. [PMID: 37335471 DOI: 10.1007/978-1-0716-3226-0_5] [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] [Indexed: 06/21/2023]
Abstract
Whole genome duplications (WGD) are frequent in many plant lineages; however, ploidy level variation is unknown in most species. The most widely used methods to estimate ploidy levels in plants are chromosome counts, which require living specimens, and flow cytometry estimates, which necessitate living or relatively recently collected samples. Newly described bioinformatic methods have been developed to estimate ploidy levels using high-throughput sequencing data, and these have been optimized in plants by calculating allelic ratio values from target capture data. This method relies on the maintenance of allelic ratios from the genome to the sequence data. For example, diploid organisms will generate allelic data in a 1:1 proportion, with an increasing number of possible allelic ratio combinations occurring in individuals with higher ploidy levels. In this chapter, we explain step-by-step this bioinformatic approach for the estimation of ploidy level.
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Affiliation(s)
| | - Oriane Hidalgo
- Royal Botanic Gardens, Kew, Richmond, UK
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, UK
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain
- Real Jardín Botánico (RJB-CSIC), Madrid, Spain
| | | | - Barbara Gravendeel
- Naturalis Biodiversity Center, Evolutionary Ecology, Leiden, Netherlands
- Radboud Institute for Biological and Environmental Sciences, Leiden University, Leiden, Netherlands
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16
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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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17
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Early warning and diagnostic visualization of Sclerotinia infected tomato based on hyperspectral imaging. Sci Rep 2022; 12:21140. [PMID: 36477460 PMCID: PMC9729219 DOI: 10.1038/s41598-022-23326-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/29/2022] [Indexed: 12/12/2022] Open
Abstract
This research explored the feasibility of early warning and diagnostic visualization of Sclerotinia infected tomato by using hyperspectral imaging technology. Healthy tomato plants and tomato plants with Sclerotinia sclerotiorum were cultivated, and hyperspectral images at 400-1000 nm were collected from healthy and infected tomato leaves at 1, 3, 5, and 7 days of incubation. After preprocessing the spectra with first derivative (FD), second derivative (SD), standard normal variant (SNV), and multiplicative scatter correction (MSC) partial least squares discriminant analysis (PLS-DA) and support vector machine (SVM) were used to construct tomato sclerotinia identification model and select the best preprocessing method. On this basis, two band screening methods, competitive adaptive reweighted sampling (CARS) and successive projections algorithm (SPA), were introduced to reduce data redundancy and improve the model's prediction accuracy. The results showed that the accuracy of the validation sets and operation speed of the CARS-PLS and CARS-SVM models were 87.88% and 1.8 s, and 87.95% and 1.78 s, respectively. The experiment was based on the SNV-CARS-SVM prediction model combined with image processing, spectral extraction, and visualization analysis methods to create diagnostic visualization software, which opens a new avenue to the implementation of online monitoring and early warning system for sclerotinia infected tomato.
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18
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Becker FW, Oberlander KC, Trávníček P, Dreyer LL. Inconsistent expression of the gigas effect in polyploid Oxalis. AMERICAN JOURNAL OF BOTANY 2022; 109:1607-1621. [PMID: 36193941 DOI: 10.1002/ajb2.16077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
PREMISE It is well-known that whole genome duplication (WGD) has played a significant role in the evolution of plants. The best-known phenotypic effect of WGD is the gigas effect, or the enlargement of polyploid plant traits. WGD is often linked with increased weediness, which could be a result of fitness advantages conferred by the gigas effect. As a result, the gigas effect could potentially explain polyploid persistence and abundance. We test whether a gigas effect is present in the polyploid-rich geophyte Oxalis, at both organ and cellular scales. METHODS We measured traits in conspecific diploid and polyploid accessions of 24 species across the genus. In addition, we measured the same and additional traits in 20 populations of the weedy and highly ploidy-variable species Oxalis purpurea L., including measures of clonality and selfing as a proxy for weediness. Ploidy level was determined using flow cytometry. RESULTS We found substantial variation and no consistent ploidy-related size difference, both between and within species, and across traits. Oxalis purpurea polyploids did, however, produce significantly more underground biomass and more bulbils than diploids, consistent with a potential role of WGD in the weediness of this species. CONCLUSIONS Our results suggest a more nuanced role for the gigas effect, at least in Oxalis. It may be temporary, short-lived, and inconsistently expressed and retained on evolutionary time scales, but in the short term can contribute to lineage success via increased vegetative reproduction.
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Affiliation(s)
- Frederik W Becker
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Kenneth C Oberlander
- H. G. W. J. Schweickerdt Herbarium, Department of Plant and Soil Sciences, Plant Sciences Complex, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Pavel Trávníček
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic, and Department of Botany, Charles University, Praha, Czech Republic
| | - Léanne L Dreyer
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
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Chumová Z, Belyayev A, Mandáková T, Zeisek V, Hodková E, Šemberová K, Euston-Brown D, Trávníček P. The relationship between transposable elements and ecological niches in the Greater Cape Floristic Region: A study on the genus Pteronia (Asteraceae). FRONTIERS IN PLANT SCIENCE 2022; 13:982852. [PMID: 36247607 PMCID: PMC9559566 DOI: 10.3389/fpls.2022.982852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Non-coding repetitive DNA (repeatome) is an active part of the nuclear genome, involved in its structure, evolution and function. It is dominated by transposable elements (TEs) and satellite DNA and is prone to the most rapid changes over time. The TEs activity presumably causes the global genome reorganization and may play an adaptive or regulatory role in response to environmental challenges. This assumption is applied here for the first time to plants from the Cape Floristic hotspot to determine whether changes in repetitive DNA are related to responses to a harsh, but extremely species-rich environment. The genus Pteronia (Asteraceae) serves as a suitable model group because it shows considerable variation in genome size at the diploid level and has high and nearly equal levels of endemism in the two main Cape biomes, Fynbos and Succulent Karoo. First, we constructed a phylogeny based on multiple low-copy genes that served as a phylogenetic framework for detecting quantitative and qualitative changes in the repeatome. Second, we performed a comparative analysis of the environments of two groups of Pteronia differing in their TEs bursts. Our results suggest that the environmental transition from the Succulent Karoo to the Fynbos is accompanied by TEs burst, which is likely also driving phylogenetic divergence. We thus hypothesize that analysis of rapidly evolving repeatome could serve as an important proxy for determining the molecular basis of lineage divergence in rapidly radiating groups.
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Affiliation(s)
- Zuzana Chumová
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Alexander Belyayev
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Faculty of Science, Masaryk University, Brno, Czechia
| | - Vojtěch Zeisek
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
| | - Eva Hodková
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
| | - Kristýna Šemberová
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
| | | | - Pavel Trávníček
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
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20
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Karyotype Analysis, Genomic and Fluorescence In Situ Hybridization (GISH and FISH) Reveal the Ploidy and Parental Origin of Chromosomes in Paeonia Itoh Hybrids. Int J Mol Sci 2022; 23:ijms231911406. [PMID: 36232706 PMCID: PMC9570356 DOI: 10.3390/ijms231911406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 12/03/2022] Open
Abstract
Itoh hybrids are intersectional hybrids in Paeonia L. with sect. Moutan and sect. Paeonia as paternal and maternal parents, respectively. Therefore, these hybrids have herbaceous stems with improved ornamental value introduced by the paternal parent. Although both of their parents are diploids, Itoh hybrids are triploids. Moreover, the parental origin of their chromosomes has not been extensively studied. This study systematically analyzed the genome size, ploidy, and karyotype of Itoh hybrids and compared them with their parental taxa. Although the monoploid genome size of Itoh hybrids was different, it was not significantly different from that of the parents. However, the size of varieties in the two parental taxa was significantly different from the wild species, probably due to genome rearrangements caused by artificial selection. Further karyotype analysis, correlation analysis, and hierarchical clustering could not identify the parental origin of chromosomes in Itoh hybrids. Verification through genomic and fluorescence in situ hybridization (GISH and FISH) suggested that for the three sets of chromosomes in Itoh hybrids, two were from the paternal parent, and one was from the maternal parent. One of the first two sets was from wild species, and the other from a cultivated variety. GISH could not label the chromosomes of cultivated peonies from the sect. Moutan, probably due to the huge and complex genomes compared with the wild species. Meanwhile, 5S rDNA-based FISH was first applied in Paeonia, which may be used for ploidy assessment. This work may give insights into the utilization of Itoh hybrid resources.
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21
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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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22
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Cytogenetic, Morphometric, and Ecological Characterization of Festuca indigesta Boiss. in the Southeast of Spain. PLANTS 2022; 11:plants11050693. [PMID: 35270163 PMCID: PMC8912771 DOI: 10.3390/plants11050693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/15/2022] [Accepted: 03/01/2022] [Indexed: 11/21/2022]
Abstract
Festuca indigesta subsp. indigesta (Poaceae) is endemic to the southeast of Spain, and until recently, it was considered that its range of distribution was restricted to the siliceous core of Sierra Nevada. However, it has been recently extended in the territory to others calcareous mountains. This study investigates the cytogenetic variability throughout the geographic range of this taxon, the possible edaphic preferences of each cytotype, and the morphological variation of cytotypes. Genome sizes and ploidy levels were estimated using flow cytometry and chromosome count. Soil samples were collected to test the nature of the substrate, i.e., pH, and calcium and magnesium contents. Finally, morphological characters were measured in herbarium specimens. This study provides the first genome size data for the species. Hidden cytogenetic diversity was detected in the taxon, comprising hexaploid (2n = 6x = 42), octoploid (2n = 8x = 56) and dodecaploid (2n = 12x = 84) individuals. No relationship between substrate nature and cytotype was observed. Morphological differences were detected for the size of floral parts and stomata among cytotypes, but these were blurred if the entire morphological variation range was considered. Our results suggest that each mountain range could act as a reservoir of morphologically cryptic genetic diversity regarding this taxon.
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23
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Sliwinska E. Investigations on Nuclear DNA Content and DNA Synthesis in Plants and Fungi Using Flow Cytometry and Fluorescence Microscopy. Genes (Basel) 2022; 13:genes13030417. [PMID: 35327971 PMCID: PMC8954512 DOI: 10.3390/genes13030417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 01/25/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, Bydgoszcz University of Science and Technology, Kaliskiego Ave. 7, 85-796 Bydgoszcz, Poland
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Trávníček P, Chumová Z, Záveská E, Hanzlíčková J, Kupková (Jankolová) L, Kučera J, Gbúrová Štubňová E, Rejlová L, Mandáková T, Ponert J. Integrative Study of Genotypic and Phenotypic Diversity in the Eurasian Orchid Genus Neotinea. FRONTIERS IN PLANT SCIENCE 2021; 12:734240. [PMID: 34745168 PMCID: PMC8570840 DOI: 10.3389/fpls.2021.734240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/20/2021] [Indexed: 05/04/2023]
Abstract
Knowledge of population variation across species' ranges is a prerequisite for correctly assessing the overall variability of any group of organisms and provides an invaluable basis for unraveling evolutionary history, optimizing taxonomy and devising effective conservation strategies. Here, we examine the genus Neotinea, which represents a relatively recently delimited monophyletic genus of orchids, for which a detailed study of its overall variability was lacking. We applied a suite of biosystematic methods, consisting of flow cytometry, multivariate and geometric morphometrics, and analysis of genomic SNP data, to identify phylogenetic lineages within the genus, to delineate phenotypic variation relevant to these lineages, and to identify potential cryptic taxa within lineages. We found clear differentiation into four major lineages corresponding to the groups usually recognized within the genus: Neotinea maculata as a distinct and separate taxon, the Neotinea lactea group comprising two Mediterranean taxa N. lactea and Neotinea conica, the Neotinea ustulata group comprising two phenologically distinct varieties, and the rather complex Neotinea tridentata group comprising two major lineages and various minor lineages of unclear taxonomic value. N. conica constitutes both a monophyletic group within N. lactea and a distinct phenotype within the genus and merits its proposed subspecies-level recognition. By contrast, the spring and summer flowering forms of N. ustulata (var. ustulata and var. aestivalis) were confirmed to be distinct only morphologically, not phylogenetically. The most complex pattern emerged in the N. tridentata group, which splits into two main clades, one containing lineages from the Balkans and eastern Mediterranean and the other consisting of plants from Central Europe and the central Mediterranean. These individual lineages differ in genome size and show moderate degrees of morphological divergence. The tetraploid Neotinea commutata is closely related to the N. tridentata group, but our evidence points to an auto- rather than an allopolyploid origin. Our broad methodological approach proved effective in recognizing cryptic lineages among the orchids, and we propose the joint analysis of flow cytometric data on genome size and endopolyploidy as a useful and beneficial marker for delineating orchid species with partial endoreplication.
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Affiliation(s)
- Pavel Trávníček
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
- *Correspondence: Pavel Trávníček,
| | - Zuzana Chumová
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
- Zuzana Chumová,
| | - Eliška Záveská
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
| | - Johana Hanzlíčková
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | | | - Jaromír Kučera
- Institute of Botany, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Eliška Gbúrová Štubňová
- Institute of Botany, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Bratislava, Slovakia
- Slovak National Museum, Bratislava, Slovakia
| | - Ludmila Rejlová
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jan Ponert
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czechia
- Prague Botanical Garden, Prague, Czechia
- Jan Ponert,
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