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Dias S, Souza RC, Vasconcelos EV, Vasconcelos S, da Silva Oliveira AR, do Vale Martins L, de Oliveira Bustamante F, da Costa VA, Souza G, da Costa AF, Benko-Iseppon AM, Knytl M, Brasileiro-Vidal AC. Cytomolecular diversity among Vigna Savi (Leguminosae) subgenera. PROTOPLASMA 2024:10.1007/s00709-024-01944-z. [PMID: 38467939 DOI: 10.1007/s00709-024-01944-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 03/04/2024] [Indexed: 03/13/2024]
Abstract
The genus Vigna (Leguminosae) comprises about 150 species grouped into five subgenera. The present study aimed to improve the understanding of karyotype diversity and evolution in Vigna, using new and previously published data through different cytogenetic and DNA content approaches. In the Vigna subgenera, we observed a random distribution of rDNA patterns. The 35S rDNA varied in position, from terminal to proximal, and in number, ranging from one (V. aconitifolia, V. subg. Ceratotropis) to seven pairs (V. unguiculata subsp. unguiculata, V. subg. Vigna). On the other hand, the number of 5S rDNA was conserved (one or two pairs), except for V. radiata (V. subg. Ceratotropis), which had three pairs. Genome size was relatively conserved within the genus, ranging from 1C = 0.43 to 0.70 pg in V. oblongifolia and V. unguiculata subsp. unguiculata, respectively, both belonging to V. subg. Vigna. However, we observed a positive correlation between DNA content and the number of 35S rDNA sites. In addition, data from chromosome-specific BAC-FISH suggest that the ancestral 35S rDNA locus is conserved on chromosome 6 within Vigna. Considering the rapid diversification in the number and position of rDNA sites, such conservation is surprising and suggests that additional sites may have spread out from this ancestral locus.
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Affiliation(s)
- Sibelle Dias
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Rosilda Cintra Souza
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Laboratório de Imunopatologia Keizo Asami, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | | | | | | | - Lívia do Vale Martins
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Campus Amilcar Ferreira Sobral, Universidade Federal Do Piauí, Floriano, PI, Brazil
| | - Fernanda de Oliveira Bustamante
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Universidade Do Estado de Minas Gerais - Unidade Divinópolis, Divinópolis, MG, Brazil
| | - Victor Alves da Costa
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Gustavo Souza
- Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | | | - Ana Maria Benko-Iseppon
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Martin Knytl
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S4K1, Canada
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 12843, Czech Republic
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Escudero M, Marques A, Lucek K, Hipp AL. Genomic hotspots of chromosome rearrangements explain conserved synteny despite high rates of chromosome evolution in a holocentric lineage. Mol Ecol 2023. [PMID: 37486041 DOI: 10.1111/mec.17086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/26/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
Holocentric organisms, unlike typical monocentric organisms, have kinetochore activity distributed along almost the whole length of the chromosome. Because of this, chromosome rearrangements through fission and fusion are more likely to become fixed in holocentric species, which may account for the extraordinary rates of chromosome evolution that many holocentric lineages exhibit. Long blocks of genome synteny have been reported in animals with holocentric chromosomes despite high rates of chromosome rearrangements. Nothing is known from plants, however, despite the fact that holocentricity appears to have played a key role in the diversification of one of the largest angiosperm genera, Carex (Cyperaceae). In the current study, we compared genomes of Carex species and a distantly related Cyperaceae species to characterize conserved and rearranged genome regions. Our analyses span divergence times ranging between 2 and 50 million years. We also compared a C. scoparia chromosome-level genome assembly with a linkage map of the same species to study rearrangements at a population level and suppression of recombination patterns. We found longer genome synteny blocks than expected under a null model of random rearrangement breakpoints, even between very distantly related species. We also found repetitive DNA to be non-randomly associated with holocentromeres and rearranged regions of the genome. The evidence of conserved synteny in sedges despite high rates of chromosome fission and fusion suggests that conserved genomic hotspots of chromosome evolution related to repetitive DNA shape the evolution of recombination, gene order and crossability in sedges. This finding may help explain why sedges are able to maintain species cohesion even in the face of high interspecific chromosome rearrangements.
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Affiliation(s)
- Marcial Escudero
- Department of Plant Biology and Ecology, University of Seville, Sevilla, Spain
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Kay Lucek
- Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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3
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Song S, Liu H, Miao L, He L, Xie W, Lan H, Yu C, Yan W, Wu Y, Wen XP, Xu Q, Deng X, Chen C. Molecular cytogenetic map visualizes the heterozygotic genome and identifies translocation chromosomes in Citrus sinensis. J Genet Genomics 2023:S1673-8527(22)00283-1. [PMID: 36608932 DOI: 10.1016/j.jgg.2022.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 01/05/2023]
Abstract
Citrus sinensis is the most cultivated and economically valuable Citrus species in the world, whose genome has been assembled by three generation sequencings. However, chromosome recognition remains a problem due to the small size of chromosomes, and difficulty in differentiating between pseudo and real chromosomes because of a highly heterozygous genome. Here, we employ fluorescence in situ hybridization (FISH) with 9 chromosome painting probes, 30 oligo pools, and 8 repetitive sequences to visualize 18 chromosomes. Then, we develop an approach to identify each chromosome in one cell through single experiment of oligo-FISH and Chromoycin A3 (CMA) staining. By this approach, we construct a high-resolution molecular cytogenetic map containing the physical positions of CMA banding and 38 sequences of FISH including centromere regions, which enable us to visualize significant differences between homologous chromosomes. Based on the map, we locate several highly repetitive sequences on chromosomes and estimate sizes and copy numbers of each site. In particular, we discover the translocation regions of chromosomes 4 and 9 in C. sinensis "Valencia." The high-resolution molecular cytogenetic map will help improve understanding of sweet orange genome assembly and also provide a fundamental reference for investigating chromosome evolution and chromosome engineering for genetic improvement in Citrus.
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Affiliation(s)
- Shipeng Song
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Hui Liu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Luke Miao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Li He
- National-local Joint Engineering Laboratory of Citrus Breeding and Cultivation/Horticulture Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, China
| | - Wenzhao Xie
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; National Key Laboratory of Crop Genetics and Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Hong Lan
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; Hubei Province Engineering Research Center of Legume Plants, College of Life Science, Jianghan University, Wuhan, Hubei 430056, China
| | - Changxiu Yu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Wenkai Yan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yufeng Wu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xiao-Peng Wen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering, College of Life Science, Guizhou University, Guiyang, Guizhou 550025, China
| | - Qiang Xu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Xiuxin Deng
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Chunli Chen
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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Yucel G, Betekhtin A, Cabi E, Tuna M, Hasterok R, Kolano B. The Chromosome Number and rDNA Loci Evolution in Onobrychis (Fabaceae). Int J Mol Sci 2022; 23:ijms231911033. [PMID: 36232345 PMCID: PMC9570107 DOI: 10.3390/ijms231911033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 02/02/2023] Open
Abstract
The evolution of chromosome number and ribosomal DNA (rDNA) loci number and localisation were studied in Onobrychis Mill. Diploid and tetraploid species, as well as two basic chromosome numbers, x = 7 and x = 8, were observed among analysed taxa. The chromosomal distribution of rDNA loci was presented here for the first time using fluorescence in situ hybridisation (FISH) with 5S and 35S rDNA probes. Onobrychis species showed a high polymorphism in the number and localisation of rDNA loci among diploids, whereas the rDNA loci pattern was very similar in polyploids. Phylogenetic relationships among the species, inferred from nrITS sequences, were used as a framework to reconstruct the patterns of basic chromosome number and rDNA loci evolution. Analysis of the evolution of the basic chromosome numbers allowed the inference of x = 8 as the ancestral number and the descending dysploidy and polyploidisation as the major mechanisms of the chromosome number evolution. Analyses of chromosomal patterns of rRNA gene loci in a phylogenetic context resulted in the reconstruction of one locus of 5S rDNA and one locus of 35S rDNA in the interstitial chromosomal position as the ancestral state in this genus.
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Affiliation(s)
- Gulru Yucel
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032 Katowice, Poland
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun 55200, Turkey
- Department of Biology, Institute of Natural and Applied Sciences, Tekirdag Namik Kemal University, Tekirdag 59030, Turkey
| | - Alexander Betekhtin
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032 Katowice, Poland
| | - Evren Cabi
- Department of Biology, Faculty of Arts and Sciences, Tekirdag Namik Kemal University, Tekirdag 59030, Turkey
| | - Metin Tuna
- Department of Field Crops, Faculty of Agriculture, Tekirdag Namik Kemal University, Tekirdag 59030, Turkey
| | - Robert Hasterok
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032 Katowice, Poland
| | - Bozena Kolano
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032 Katowice, Poland
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Molecular and Cytogenetic Analysis of rDNA Evolution in Crepis Sensu Lato. Int J Mol Sci 2022; 23:ijms23073643. [PMID: 35409003 PMCID: PMC8998684 DOI: 10.3390/ijms23073643] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 01/27/2023] Open
Abstract
Although Crepis was the first model plant group in which chromosomal changes were considered to play an important role in speciation, their chromosome structure and evolution have been barely investigated using molecular cytogenetic methods. The aim of the study was to provide a better understanding of the patterns and directions of Crepis chromosome evolution, using comparative analyses of rDNA loci number and localisation. The chromosome base number and chromosomal organisation of 5S and 35S rDNA loci were analysed in the phylogenetic background for 39 species of Crepis, which represent the evolutionary lineages of Crepis sensu stricto and Lagoseris, including Lapsana communis. The phylogenetic relationships among all the species were inferred from nrITS and newly obtained 5S rDNA NTS sequences. Despite high variations in rDNA loci chromosomal organisation, most species had a chromosome with both rDNA loci within the same (usually short) chromosomal arm. The comparative analyses revealed several independent rDNA loci number gains and loci repositioning that accompanied diversification and speciation in Crepis. Some of the changes in rDNA loci patterns were reconstructed for the same evolutionary lineages as descending dysploidy.
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Maravilla AJ, Rosato M, Rosselló JA. Interstitial Telomeric-like Repeats (ITR) in Seed Plants as Assessed by Molecular Cytogenetic Techniques: A Review. PLANTS (BASEL, SWITZERLAND) 2021; 10:2541. [PMID: 34834904 PMCID: PMC8621592 DOI: 10.3390/plants10112541] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 05/12/2023]
Abstract
The discovery of telomeric repeats in interstitial regions of plant chromosomes (ITRs) through molecular cytogenetic techniques was achieved several decades ago. However, the information is scattered and has not been critically evaluated from an evolutionary perspective. Based on the analysis of currently available data, it is shown that ITRs are widespread in major evolutionary lineages sampled. However, their presence has been detected in only 45.6% of the analysed families, 26.7% of the sampled genera, and in 23.8% of the studied species. The number of ITR sites greatly varies among congeneric species and higher taxonomic units, and range from one to 72 signals. ITR signals mostly occurs as homozygous loci in most species, however, odd numbers of ITR sites reflecting a hemizygous state have been reported in both gymnosperm and angiosperm groups. Overall, the presence of ITRs appears to be poor predictors of phylogenetic and taxonomic relatedness at most hierarchical levels. The presence of ITRs and the number of sites are not significantly associated to the number of chromosomes. The longitudinal distribution of ITR sites along the chromosome arms indicates that more than half of the ITR presences are between proximal and terminal locations (49.5%), followed by proximal (29.0%) and centromeric (21.5%) arm regions. Intraspecific variation concerning ITR site number, chromosomal locations, and the differential presence on homologous chromosome pairs has been reported in unrelated groups, even at the population level. This hypervariability and dynamism may have likely been overlooked in many lineages due to the very low sample sizes often used in cytogenetic studies.
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Affiliation(s)
| | | | - Josep A. Rosselló
- Jardín Botánico, ICBiBE, Universitat de València, c/Quart 80, E-46008 València, Spain; (A.J.M.); (M.R.)
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Bednářová M, Karafiátová M, Hřibová E, Bartoš J. B Chromosomes in Genus Sorghum (Poaceae). PLANTS (BASEL, SWITZERLAND) 2021; 10:505. [PMID: 33803087 PMCID: PMC8001295 DOI: 10.3390/plants10030505] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 12/30/2022]
Abstract
B chromosomes (Bs) are supernumerary dispensable genomic elements that have been reported in several thousand eukaryotic species. Since their discovery, Bs have been subjected to countless studies aiming at the clarification of their origin, composition, and influence on the carriers. Despite these efforts, we still have very limited knowledge of the processes that led to the emergence of Bs, the mechanisms of their transmission, and the effects of Bs on the hosts. In the last decade, sophisticated molecular methods, including next-generation sequencing, have provided powerful tool to help answer some of these questions, but not many species have received much attention yet. In this review, we summarize the currently available information about Bs in the genus Sorghum, which has so far been on the periphery of scientific interest. We present an overview of the occurrence and characteristics of Bs in various Sorghum species, discuss the possible mechanisms involved in their maintenance and elimination, and outline hypotheses of the origin of Bs in this genus.
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Affiliation(s)
| | | | | | - Jan Bartoš
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic; (M.B.); (M.K.); (E.H.)
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8
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Xia QM, Miao LK, Xie KD, Yin ZP, Wu XM, Chen CL, Grosser JW, Guo WW. Localization and characterization of Citrus centromeres by combining half-tetrad analysis and CenH3-associated sequence profiling. PLANT CELL REPORTS 2020; 39:1609-1622. [PMID: 32897396 DOI: 10.1007/s00299-020-02587-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
The physical locations of citrus centromere are revealed by combining genetic and immunological assays for the first time and nine citrus centromere-specific markers for cytogenetics are mined. Centromere localization is challenging, because highly redundant repetitive sequences in centromeric regions make sequence assembly difficult. Although several citrus genomes have been released, the centromeric regions and their characteristics remain to be elucidated. Here, we mapped citrus centromeres through half-tetrad analysis (HTA) that included the genotyping of 54 tetraploid hybrids derived from 2n megagametophytes of Nadorcott tangor with 212 single nucleotide polymorphism (SNP) markers. The sizes of centromeric regions, which estimated based on the heterozygosity restitution rate pattern along the chromosomes, ranged from 1.12 to 18.19 Mb. We also profiled the binding sequences with the centromere-specific histone variant CenH3 by chromatin immunoprecipitation sequencing (ChIP-seq). Based on the positions of the top ten CenH3-enriched contigs, the sizes of centromeric regions were estimated to range from 0.01 to 7.60 Mb and were either adjacent to or included in the centromeric regions identified by HTA. We used DNA probes from two repeats selected from the centromeric regions and seven CenH3-binding centromeric repeats to verify centromeric locations by fluorescence in situ hybridization (FISH). Centromere localization in citrus will contribute to the mining of centromeric/pericentromeric markers, thus to facilitate the rapid identification of mechanisms underlying 2n gamete formation and serve the polyploidy breeding.
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Affiliation(s)
- Qiang-Ming Xia
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lu-Ke Miao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kai-Dong Xie
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Zhao-Ping Yin
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiao-Meng Wu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chun-Li Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jude W Grosser
- Citrus Research and Education Center, University of Florida, 700 Experiment Station Road, Lake Alfred, FL, 33850, USA
| | - Wen-Wu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
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9
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Pessoa E, Sader M, Pedrosa-Harand A, Alves M. A natural hybrid, an autopolyploid, or a new species? An integrative case study of a distinctive Costus species (Costaceae) from the Atlantic Forest of Brazil. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1729890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Edlley Pessoa
- Laboratório de Estudos Integrados de Plantas, Departamento de Botânica e Ecologia, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, 78060-900, Brazil
| | - Mariela Sader
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, 50670-901, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, 50670-901, Brazil
| | - Marccus Alves
- Laboratório de Morfo-Taxonomia Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco, Recife, Pernambuco, 50670-901, Brazil
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Deng H, Tang G, Xu N, Gao Z, Lin L, Liang D, Xia H, Deng Q, Wang J, Cai Z, Liang G, Lv X. Integrated Karyotypes of Diploid and Tetraploid Carrizo Citrange ( Citrus sinensis L. Osbeck × Poncirus trifoliata L. Raf.) as Determined by Sequential Multicolor Fluorescence in situ Hybridization With Tandemly Repeated DNA Sequences. FRONTIERS IN PLANT SCIENCE 2020; 11:569. [PMID: 32536930 PMCID: PMC7267054 DOI: 10.3389/fpls.2020.00569] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/16/2020] [Indexed: 05/20/2023]
Abstract
Carrizo citrange [Citrus sinensis (L.) Osbeck × Poncirus trifoliata (L.) Raf., CC] is one of the most widely used rootstocks in citriculture worldwide, but its cytogenetic study has been hampered by its inherent small size, morphological similarity to mitotic chromosomes, and lack of accessible cytological landmarks. In our previous study, a spontaneously occurring tetraploid CC seedling was discovered. The main goals of this study were to elucidate the chromosome constitution and construct the karyotypes of diploid CC rootstock and its corresponding spontaneously occurring tetraploid. To accomplish these, the chromosomal characteristics were investigated by sequential multicolor fluorescence in situ hybridization (FISH) with eight properly labeled repetitive DNA sequences, including a centromere-like repeat, four satellite repeats, two rDNAs, and an oligonucleotide of telomeric (TTTAGGG) n repeat. The results nicely demonstrated that these repetitive DNAs are reliable cytogenetic markers that collectively facilitate simultaneous and unequivocal identification of homologous chromosome pairs. Based on chromosome size and morphology together with FISH patterns of repetitive DNAs, an integrated karyotype of CC rootstock was constructed, consisting of 2n = 2x = 12m (1sat) + 6sm with karyotype asymmetry degree being divided into 2B category. Cytogenetically speaking, the variable and asymmetric distribution patterns of these repetitive DNAs were fully confirmed the hybrid nature of CC rootstock. In addition, comparative distribution patterns and chromosomal localizations of these repetitive DNAs convincingly showed that this tetraploid CC material arose from somatic chromosome doubling of diploid CC rootstock. This study revealed, for the first time, the integrated karyotype and chromosomal characteristics of this important citrus rootstock as well as its spontaneously occurring tetraploid plant. Furthermore, this study is a good prospective model for study species with morphologically indistinguishable small chromosomes.
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Affiliation(s)
- Honghong Deng
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Guohao Tang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Nuo Xu
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Zhijian Gao
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Lijin Lin
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Dong Liang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Hui Xia
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Qunxian Deng
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Jin Wang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Zexi Cai
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Guolu Liang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- *Correspondence: Guolu Liang,
| | - Xiulan Lv
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
- Xiulan Lv,
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Kus A, Szymanowska-Pułka J, Kwasniewska J, Hasterok R. Detecting Brachypodium distachyon Chromosomes Bd4 and Bd5 in MH- and X-Ray-Induced Micronuclei Using mcFISH. Int J Mol Sci 2019; 20:ijms20112848. [PMID: 31212692 PMCID: PMC6612364 DOI: 10.3390/ijms20112848] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 05/22/2019] [Accepted: 06/08/2019] [Indexed: 12/18/2022] Open
Abstract
Micronuclei are biomarkers of genotoxic effects and chromosomal instability. They are formed when chromosome fragments or whole chromosomes fail to disjoin into daughter nuclei. We present qualitative and quantitative analyses of the involvement of specific chromosome regions of chromosomes Bd4 and Bd5 in the formation of micronuclei of Brachypodium distachyon root tip cells following maleic hydrazide (MH) treatment and X-radiation. This is visualised by cytomolecular approaches using bacterial artificial chromosome (BAC)-based multicolour fluorescence in situ hybridisation (mcFISH) in combination with 5S and 25S rDNA probes. The results showed that the long arm of submetacentric chromosome Bd4 forms micronuclei at twice the frequency of its short arm, suggesting that the former is more prone to double-strand breaks (DSBs). In contrast, no difference was observed in the frequency of micronuclei derived from the long and short arms of submetacentric chromosome Bd5. Interestingly, the proximal region of the short arm of Bd5 is more prone to DSBs than its distal part. This demonstrates that 5S rDNA and 35S rDNA loci are not "hot spots" for DNA breaks after the application of these mutagens.
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Affiliation(s)
- Arita Kus
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, 28 Jagiellonska Street, 40-032 Katowice, Poland.
| | - Joanna Szymanowska-Pułka
- Department of Biophysics and Morphogenesis of Plants, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, 28 Jagiellonska Street, 40-032 Katowice, Poland.
| | - Jolanta Kwasniewska
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, 28 Jagiellonska Street, 40-032 Katowice, Poland.
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, 28 Jagiellonska Street, 40-032 Katowice, Poland.
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Deng H, Cai Z, Xiang S, Guo Q, Huang W, Liang G. Karyotype Analysis of Diploid and Spontaneously Occurring Tetraploid Blood Orange [ Citrus sinensis (L.) Osbeck] Using Multicolor FISH With Repetitive DNA Sequences as Probes. FRONTIERS IN PLANT SCIENCE 2019; 10:331. [PMID: 30967887 PMCID: PMC6440391 DOI: 10.3389/fpls.2019.00331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/04/2019] [Indexed: 05/17/2023]
Abstract
Blood orange [Citrus sinensis (L.) Osbeck] has been increasingly appreciated by consumers worldwide owing to its brilliant red color, abundant anthocyanin and other health-promoting compounds. However, there is still relatively little known about its cytogenetic characteristics, probably because of the small size and similar morphology of metaphase chromosomes and the paucity of chromosomal landmarks. In our previous study, a naturally occurring tetraploid blood orange plant was obtained via seedling screening. Before this tetraploid germplasm can be manipulated into a citrus triploid seedless breeding program, it is of great importance to determine its chromosome characterization and composition. In the present study, an integrated karyotype of blood orange was constructed using sequential multicolor fluorescence in situ hybridization (FISH) with four satellite repeats, two ribosomal DNAs (rDNAs), a centromere-like repeat and an oligonucleotide of telomere repeat (TTTAGGG)3 as probes. Satellite repeats were preferentially located at the terminal regions of the chromosomes of blood orange. Individual somatic chromosome pairs of blood orange were unambiguously identified by repetitive DNA-based multicolor FISH. These probes proved to be effective chromosomal landmarks. The karyotype was formulated as 2n = 2x = 18 = 16m+2sm (1sat) with the karyotype asymmetry degree belonging to 2B. The chromosomal distribution pattern of these repetitive DNAs in this spontaneously occurring tetraploid was identical to that of the diploid, but the tetraploid carried twice the number of hybridization sites as the diploid, indicating a possible pathway involving the spontaneous duplication of chromosome sets in nucellar cells. Our work may facilitate the molecular cytogenetic study of blood orange and provide chromosomal characterization for the future utilization of this tetraploid germplasm in the service of seedless breeding programs.
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Affiliation(s)
- Honghong Deng
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Zexi Cai
- College of Agronomy and Biotechnology, National Maize Improvement Center, China Agricultural University, Beijing, China
| | - Suqiong Xiang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Qigao Guo
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Wei Huang
- College of Agronomy and Biotechnology, National Maize Improvement Center, China Agricultural University, Beijing, China
| | - Guolu Liang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
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Deng H, Xiang S, Guo Q, Jin W, Cai Z, Liang G. Molecular cytogenetic analysis of genome-specific repetitive elements in Citrus clementina Hort. Ex Tan. and its taxonomic implications. BMC PLANT BIOLOGY 2019; 19:77. [PMID: 30770721 PMCID: PMC6377768 DOI: 10.1186/s12870-019-1676-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 02/07/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND Clementine mandarin (Citrus clementina Hort. ex Tan.) is one of the most famous and widely grown citrus cultivars worldwide. Variations in relation to the composition and distribution of repetitive DNA sequences that dominate greatly in eukaryote genomes are considered to be species-, genome-, or even chromosome-specific. Repetitive DNA-based fluorescence in situ hybridization (FISH) is a powerful tool for molecular cytogenetic study. However, to date few studies have involved in the repetitive elements and cytogenetic karyotype of Clementine. RESULTS A graph-based similarity sequence read clustering methodology was performed to analyze the repetitive DNA families in the Clementine genome. The bioinformatics analysis showed that repetitive DNAs constitute 41.95% of the Clementine genome, and the majority of repetitive elements are retrotransposons and satellite DNAs. Sequential multicolor FISH using a probe mix that contained CL17, four satellite DNAs, two rDNAs and an oligonucleotide of (TTTAGGG)3 was performed with Clementine somatic metaphase chromosomes. An integrated karyotype of Clementine was established based on unequivocal and reproducible chromosome discriminations. The distribution patterns of these probes in several Citrus, Poncirus and Fortunella species were summarized through extensive FISH analyses. Polymorphism and heterozygosity were commonly observed in the three genera. Some asymmetrical FISH loci in Clementine were in agreement with its hybrid origin. CONCLUSIONS The composition and abundance of repetitive elements in the Clementine genome were reanalyzed. Multicolor FISH-based karyotyping provided direct visual proof of the heterozygous nature of Clementine chromosomes with conspicuous asymmetrical FISH hybridization signals. We detected some similar and variable distribution patterns of repetitive DNAs in Citrus, Poncirus, and Fortunella, which revealed notable conservation among these genera, as well as obvious polymorphism and heterozygosity, indicating the potential utility of these repetitive element markers for the study of taxonomic, phylogenetic and evolutionary relationships in the future.
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Affiliation(s)
- Honghong Deng
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715 China
| | - Suqiong Xiang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715 China
| | - Qigao Guo
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715 China
| | - Weiwei Jin
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Zexi Cai
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Guolu Liang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715 China
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Rocha LC, Ferreira MTM, Cunha IMF, Mittelmann A, Techio VH. 45S rDNA sites in meiosis of Lolium multiflorum Lam.: variability, non-homologous associations and lack of fragility. PROTOPLASMA 2019; 256:227-235. [PMID: 30069603 DOI: 10.1007/s00709-018-1292-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 07/23/2018] [Indexed: 05/27/2023]
Abstract
In this study, we evaluated the behavior of 45S ribosomal DNA (rDNA) sites during the meiosis of Lolium multiflorum. The reason to study it in this species is that 45S rDNA sites are usually visualized as gaps in mitotic metaphase chromosomes and were initially denominated fragile sites (FSs). In different species, FSs were related to rearrangements that alter the karyotype and affect the chromosome pairing in meiosis. However, our findings show that the chromosome pairing in L. multiflorum is regular and, as in mitosis, the number of sites is variable. In diakinesis with five sites, one of the bivalents was in hemizygous state while, in diakinesis with seven sites, one of the bivalents had three conspicuous signals, two in syntheny in one of the homologous. Only four cells had gaps in the region of the 45S rDNA. Owing to the lower number of signals observed at the initial stages of meiosis, it is assumed that they are involved both in homologous and non-homologous associations and that they might assist the chromosome pairing. Regarding segregation, only meiocytes with five and six 45S rDNA signals were observed, and they were characterized by the segregation of 2/3 signals in the poles of anaphases I up to metaphases II; 2/2 and 3/3 in anaphases II and telophases II; and also 2/2 and 4/4 in the nuclei of tetrads, unlike the number of 45S signals expected. The numerical non-equivalence of sites among nuclei at later stages of meiosis is explained by the presence of chromosomes with hemizygous sites.
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Affiliation(s)
- Laiane Corsini Rocha
- Department of Biology, Federal University of Lavras-UFLA, Lavras, Minas Gerais State, Brazil
| | | | | | - Andréa Mittelmann
- Embrapa Gado de Leite/Embrapa Clima Temperado, Pelotas, Rio Grande do Sul State, Brazil
| | - Vânia Helena Techio
- Department of Biology, Federal University of Lavras-UFLA, Lavras, Minas Gerais State, Brazil.
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Karyotype heterogeneity in Philodendron s.l. (Araceae) revealed by chromosome mapping of rDNA loci. PLoS One 2018; 13:e0207318. [PMID: 30440003 PMCID: PMC6237374 DOI: 10.1371/journal.pone.0207318] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/29/2018] [Indexed: 12/18/2022] Open
Abstract
Philodendron s.l. (Araceae) has been recently focus of taxonomic and phylogenetic studies, but karyotypic data are limited to chromosome numbers and a few published genome sizes. In this work, karyotypes of 34 species of Philodendron s.l. (29 species of Philodendron and five of Thaumatophyllum), ranging from 2n = 28 to 36 chromosomes, were analyzed by fluorescence in situ hybridization (FISH) with rDNA and telomeric probes, aiming to understand the evolution of the karyotype diversity of the group. Philodendron presented a high number variation of 35S rDNA, ranging from two to 16 sites, which were mostly in the terminal region of the short arms, with nine species presenting heteromorphisms. In the case of Thaumatophyllum species, we observed a considerably lower variation, which ranged from two to four terminal sites. The distribution of the 5S rDNA clusters was more conserved, with two sites for most species, being preferably located interstitially in the long chromosome arms. For the telomeric probe, while exclusively terminal sites were observed for P. giganteum (2n = 30) chromosomes, P. callosum (2n = 28) presented an interstitial distribution associated with satellite DNA. rDNA sites of the analyzed species of Philodendron s.l. species were randomly distributed considering the phylogenetic context, probably due to rapid evolution and great diversity of these genomes. The observed heteromorphisms suggest the accumulation of repetitive DNA in the genomes of some species and the occurrence of chromosomal rearrangements along the karyotype evolution of the group.
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Relationship between epigenetic marks and the behavior of 45S rDNA sites in chromosomes and interphase nuclei of Lolium-Festuca complex. Mol Biol Rep 2018; 45:1663-1679. [PMID: 30121822 DOI: 10.1007/s11033-018-4310-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 08/14/2018] [Indexed: 10/28/2022]
Abstract
The grasses of the Lolium-Festuca complex show a prominent role in world agricultural scenario. Several studies have demonstrated that the plasticity of 45S rDNA sites has been recently associated with the possible fragility of the loci. Often, these fragile sites were observed as extended sites and gaps in metaphases. This organization can be evaluated in relation to their transcriptional activity/accessibility through epigenetic changes. Thus, this study aimed to investigate the relationship of the 5-methylcytosine and histone H3 lysine-9 dimethylation in different conformations of 45S rDNA sites in interphase nuclei and in metaphase chromosomes of L. perenne, L. multiflorum and F. arundinacea. The FISH technique using 45S rDNA probes was performed sequentially after the immunolocalization. The sites showed predominantly the following characteristics in the interphase nuclei: intra- and perinucleolar position, decondensed or partially condensed and hypomethylated and hyper/hypomethylated status. Extranucleolar sites were mainly hypermethylated for both epigenetic marks. The 45S rDNA sites with gaps identified in metaphases were always hypomethylated, which justifies it decondensed and transcriptional state. The frequency of sites with hypermethylated gaps was very low. The structural differences observed in these sites are directly related to the assessed epigenetic marks, justifying the different conformations throughout the cell cycle.
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Majka J, Zwierzykowski Z, Majka M, Kosmala A. Karyotype reshufflings of Festuca pratensis × Lolium perenne hybrids. PROTOPLASMA 2018; 255:451-458. [PMID: 28884345 PMCID: PMC5830480 DOI: 10.1007/s00709-017-1161-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/28/2017] [Indexed: 06/07/2023]
Abstract
Many different processes have an impact on the shape of plant karyotype. Recently, cytogenetic examination of Lolium species has revealed the occurrence of spontaneous fragile sites (FSs) associated with 35S rDNA regions. The FSs are defined as the chromosomal regions that are sensitive to forming gaps or breaks on chromosomes. The shape of karyotype can also be determined by interstitial telomeric sequences (ITSs), what was recognized for the first time in this paper in chromosomes of Festuca pratensis × Lolium perenne hybrids. Both FSs and ITSs can contribute to genome instabilities and chromosome rearrangements. To evaluate whether these cytogenetic phenomena have an impact on karyotype reshuffling observed in Festuca × Lolium hybrids, we examined F1 F. pratensis × L. perenne plants and generated F2-F9 progeny by fluorescent in situ hybridization (FISH) using rDNA sequences, telomere and centromere probes, as well as by genomic in situ hybridization (GISH). Analyses using a combination of FISH and GISH revealed that intergenomic rearrangements did not correspond to FSs but overlapped with ITSs for several analyzed genotypes. It suggests that internal telomeric repeats can affect the shape of F. pratensis × L. perenne karyotypes. However, other factors that are involved in rearrangements and have a more crucial impact could exist, but they are still unknown.
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Affiliation(s)
- Joanna Majka
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
| | - Zbigniew Zwierzykowski
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Maciej Majka
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Arkadiusz Kosmala
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
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High and uneven levels of 45S rDNA site-number variation across wild populations of a diploid plant genus (Anacyclus, Asteraceae). PLoS One 2017; 12:e0187131. [PMID: 29088249 PMCID: PMC5663423 DOI: 10.1371/journal.pone.0187131] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/13/2017] [Indexed: 12/13/2022] Open
Abstract
The nuclear genome harbours hundreds to several thousand copies of ribosomal DNA. Despite their essential role in cellular ribogenesis few studies have addressed intrapopulation, interpopulation and interspecific levels of rDNA variability in wild plants. Some studies have assessed the extent of rDNA variation at the sequence and copy-number level with large sampling in several species. However, comparable studies on rDNA site number variation in plants, assessed with extensive hierarchical sampling at several levels (individuals, populations, species) are lacking. In exploring the possible causes for ribosomal loci dynamism, we have used the diploid genus Anacyclus (Asteraceae) as a suitable system to examine the evolution of ribosomal loci. To this end, the number and chromosomal position of 45S rDNA sites have been determined in 196 individuals from 47 populations in all Anacyclus species using FISH. The 45S rDNA site-number has been assessed in a significant sample of seed plants, which usually exhibit rather consistent features, except for polyploid plants. In contrast, the level of rDNA site-number variation detected in Anacyclus is outstanding in the context of angiosperms particularly regarding populations of the same species. The number of 45S rDNA sites ranged from four to 11, accounting for 14 karyological ribosomal phenotypes. Our results are not even across species and geographical areas, and show that there is no clear association between the number of 45S rDNA loci and the life cycle in Anacyclus. A single rDNA phenotype was detected in several species, but a more complex pattern that included intra-specific and intra-population polymorphisms was recorded in A. homogamos, A. clavatus and A. valentinus, three weedy species showing large and overlapping distribution ranges. It is likely that part of the cytogenetic changes and inferred dynamism found in these species have been triggered by genomic rearrangements resulting from contemporary hybridisation.
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