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Krawczyk K, Paukszto Ł, Maździarz M, Sawicki J. The low level of plastome differentiation observed in some lineages of Poales hinders molecular species identification. FRONTIERS IN PLANT SCIENCE 2023; 14:1275377. [PMID: 38143577 PMCID: PMC10739336 DOI: 10.3389/fpls.2023.1275377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/23/2023] [Indexed: 12/26/2023]
Abstract
Chloroplast genomes are a source of information successfully used in various fields of plant genetics, including molecular species identification. However, recent studies indicate an extremely low level of interspecific variability in the plastomes of some taxonomic groups of plants, including the genus Stipa L., which is a representative of the grass family. In this study we aimed to analyze the level of chloroplast genome diversity within particular genera as well as the effectiveness of identifying plant species in the Poaceae family and the other representatives of Poales order. Analysis of complete plastid genome alignments created for 96 genera comprising 793 species and 1707 specimens obtained from the GenBank database allowed defining and categorizing molecular diagnostic characters distinguishing the analyzed species from the other representatives of the genus. The results also demonstrate which species do not have any species-specific mutations, thereby they cannot be identified on the basis of differences between the complete chloroplast genomes. Our research showed a huge diversity of the analyzed species in terms of the number of molecular diagnostic characters and indicated which genera pose a particular challenge in terms of molecular species identification. The results show that a very low level of genetic diversity between plastomes is not uncommon in Poales. This is the first extensive research on super-barcoding that tests this method on a large data set and illustrates its effectiveness against the background of phylogenetic relationships.
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Affiliation(s)
- Katarzyna Krawczyk
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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Said M, Kubaláková M, Karafiátová M, Molnár I, Doležel J, Vrána J. Dissecting the Complex Genome of Crested Wheatgrass by Chromosome Flow Sorting. THE PLANT GENOME 2019; 12:180096. [PMID: 31290923 DOI: 10.3835/plantgenome2018.12.0096] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Wheatgrass (Agropyron sp.) is a potential source of beneficial traits for wheat improvement. Among them, crested wheatgrass [A. cristatum (L.) Gaertn.] comprises a complex of diploid, tetraploid, and hexaploid forms with the basic genome P, with some accessions carrying supernumerary B chromosomes (Bs). In this work, we applied flow cytometry to dissect the complex genome of crested wheatgrass into individual chromosomes to facilitate its analysis. Flow karyotypes obtained after the analysis of 4',6-diamidino-2-phenylindole (DAPI)-stained mitotic chromosomes of diploid and tetraploid accessions consisted of three peaks, each corresponding to a group of two or three chromosomes. To improve the resolution, bivariate flow karyotyping after fluorescent labeling of chromosomes with fluorescein isothiocyanate (FITC)-conjugated probe (GAA) microsatellite was applied and allowed discrimination and sorting of P genome chromosomes from wheat-crested wheatgrass addition lines. Chromosomes 1P-6P and seven telomeric chromosomes could be sorted at purities ranging from 81.7 to 98.2% in disomics and from 44.8 to 87.3% in telosomics. Chromosome 7P was sorted at purities reaching 50.0 and 39.5% in diploid and tetraploid crested wheatgrass, respectively. In addition to the whole complement chromosomes (A), Bs could be easily discriminated and sorted from a diploid accession at 95.4% purity. The sorted chromosomes will streamline genome analysis of crested wheatgrass, facilitating gene cloning and development of molecular tools to support alien introgression into wheat.
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Datta AK, Mandal A, Das D, Gupta S, Saha A, Paul R, Sengupta S. B chromosomes in angiosperm—a review. CYTOL GENET+ 2016. [DOI: 10.3103/s0095452716010035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Grandont L, Jenczewski E, Lloyd A. Meiosis and its deviations in polyploid plants. Cytogenet Genome Res 2013; 140:171-84. [PMID: 23817089 DOI: 10.1159/000351730] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Meiosis is a fundamental process in all sexual organisms that ensures fertility and genome stability and creates genetic diversity. For each of these outcomes, the exclusive formation of crossovers between homologous chromosomes is needed. This is more difficult to achieve in polyploid species which have more than 2 sets of chromosomes able to recombine. In this review, we describe how meiosis and meiotic recombination 'deviate' in polyploid plants compared to diploids, and give an overview of current knowledge on how they are regulated. See also the sister article focusing on animals by Stenberg and Saura in this themed issue.
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Affiliation(s)
- L Grandont
- INRA - Institut Jean Pierre Bourgin, Station de Génétique et Amélioration des Plantes, Versailles, France
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Leflon M, Grandont L, Eber F, Huteau V, Coriton O, Chelysheva L, Jenczewski E, Chèvre AM. Crossovers get a boost in Brassica allotriploid and allotetraploid hybrids. THE PLANT CELL 2010; 22:2253-64. [PMID: 20622148 PMCID: PMC2929096 DOI: 10.1105/tpc.110.075986] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 06/08/2010] [Accepted: 06/18/2010] [Indexed: 05/18/2023]
Abstract
Meiotic crossovers are necessary to generate balanced gametes and to increase genetic diversity. Even if crossover number is usually constrained, recent results suggest that manipulating karyotype composition could be a new way to increase crossover frequency in plants. In this study, we explored this hypothesis by analyzing the extent of crossover variation in a set of related diploid AA, allotriploid AAC, and allotetraploid AACC Brassica hybrids. We first used cytogenetic methods to describe the meiotic behavior of the different hybrids. We then combined a cytogenetic estimation of class I crossovers in the entire genome by immunolocalization of a key protein, MutL Homolog1, which forms distinct foci on meiotic chromosomes, with genetic analyses to specifically compare crossover rates between one pair of chromosomes in the different hybrids. Our results showed that the number of crossovers in the allotriploid AAC hybrid was higher than in the diploid AA hybrid. Accordingly, the allotetraploid AACC hybrid showed an intermediate behavior. We demonstrated that this increase was related to hybrid karyotype composition (diploid versus allotriploid versus allotetraploid) and that interference was maintained in the AAC hybrids. These results could provide another efficient way to manipulate recombination in traditional breeding and genetic studies.
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Affiliation(s)
- Martine Leflon
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 118, Amélioration des Plantes et Biotechnologies Végétales, BP 35327, F-35653 Le Rheu cedex, France
| | - Laurie Grandont
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique–AgroParisTech, Bâtiment 7, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, 78026 Versailles cedex, France
| | - Frédérique Eber
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 118, Amélioration des Plantes et Biotechnologies Végétales, BP 35327, F-35653 Le Rheu cedex, France
| | - Virginie Huteau
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 118, Amélioration des Plantes et Biotechnologies Végétales, BP 35327, F-35653 Le Rheu cedex, France
| | - Olivier Coriton
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 118, Amélioration des Plantes et Biotechnologies Végétales, BP 35327, F-35653 Le Rheu cedex, France
| | - Liudmila Chelysheva
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique–AgroParisTech, Bâtiment 7, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, 78026 Versailles cedex, France
| | - Eric Jenczewski
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique–AgroParisTech, Bâtiment 7, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, 78026 Versailles cedex, France
| | - Anne-Marie Chèvre
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 118, Amélioration des Plantes et Biotechnologies Végétales, BP 35327, F-35653 Le Rheu cedex, France
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Abstract
This review of supernumerary B chromosome systems in flowering plants deals mainly with work published in the last 15 yr, hut also includes older material which has not hitherto been presented systematically. The term B chromosome (B) is defined, and there is an introductory overview dealing with general characteristics and the significance of Bs as a widespread chromosome polymorphism. Detailed sections are then presented covering the occurrence of Bs in different taxa, their structure and molecular organization, their irregular modes of inheritance, their phenotypic effects, population dynamics and origin. Particular attention is paid to the research growth points in molecular analysis of the structure and genome organization of Bs, and to transmission genotypes in the context of their adaptive versus their selfish properties. Where appropriate, reference is also made to likely future lines of research, and also to the usefulness of B chromosomes in genetic analysis and as model systems to study general phenomena of genome organization and evolution, nuclear physiology and architecture, chromosome polymorphism and selfish DNA. CONTENTS Summary 411 I. Introduction 411 II. Occurrence 411 III. Structure and organization 415 IV. Inheritance 422 V. Phenotypic effects 426 VI. Populations 429 VII. Applications 430 VIII. Origin 430 Acknowiedgements 430 References 431.
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Affiliation(s)
- R Neil Jones
- Institute of Biological Sciences, University of Walt's Aberystwyth, Sir George Stapledon Building, Penglais, Aberystwyth SY23 3DD, UK
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Jenkins G, Jimenez G. Genetic control of synapsis and recombination in Lolium amphidiploids. Chromosoma 1995; 104:164-8. [PMID: 8529455 DOI: 10.1007/bf00352180] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Homologous bivalent formation in amphidiploids of Lolium is promoted during meiosis by diploidising genes carried by A-chromosomes, and by supernumerary B-chromosomes. The site and mode of action of these diploidising factors were investigated by comparing the relative frequencies of pairing configurations at meiotic prophase and metaphase I in several different hybrid genotypes. The results indicate that diploidising genes act predominantly by increasing the stringency of synapsis at early stages of meiotic prophase. By contrast, B-chromosomes appear to promote bivalent formation by ensuring that homoeologously paired chromosome segments within multivalents do not crossover. The results show that the additive effects of diploidising genes and B-chromosomes are to a certain extent separable in terms of their mode of action and timing during meiosis.
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Affiliation(s)
- G Jenkins
- Institute of Biological Sciences, Sir George Stapledon Building, University of Wales, Aberystwyth, Dyfed, SY23 3DD, UK
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Cytogenetics of Polyploids and Their Diploid Progenitors. ACTA ACUST UNITED AC 1991. [DOI: 10.1016/b978-0-444-88259-2.50012-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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10
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The fate of multivalents during meiotic prophase in the hybrid Gibasis consobrina x G. karwinskyana Rafin. (Commelinaceae). Genetica 1990. [DOI: 10.1007/bf00124639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Jenkins G, White J. Elimination of synaptonemal complex irregularities in a Lolium hybrid. Heredity (Edinb) 1990. [DOI: 10.1038/hdy.1990.6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Jones M, Rees H, Jenkins G. Synaptonemal complex formation in Avena polyploids. Heredity (Edinb) 1989. [DOI: 10.1038/hdy.1989.94] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Synaptonemal complex formation among supernumerary B chromosomes: an electron microscopic study on spermatocytes of Chinese raccoon dogs. Chromosoma 1988. [DOI: 10.1007/bf00327376] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Synaptonemal complex pairing and metaphase I association in a telo-substituted telotrisomic of rye (Secale cereale L.). Chromosoma 1988. [DOI: 10.1007/bf00331798] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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The effect of chromosome 5B on synapsis and chiasma formation in wheat, triticum aestivum cv. Chinese Spring. ACTA ACUST UNITED AC 1988. [DOI: 10.1007/bf02907179] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Heslop-Harrison JS, Smith JB, Bennett MD. The absence of the somatic association of centromeres of homologous chromosomes in grass mitotic metaphases. Chromosoma 1988. [DOI: 10.1007/bf00331044] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Gillies CB. The effect of Ph gene alleles on synaptonemal complex formation in Triticum aestivum × T. kotschyi hybrids. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1987; 74:430-438. [PMID: 24241796 DOI: 10.1007/bf00289817] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/1987] [Accepted: 04/24/1987] [Indexed: 06/02/2023]
Abstract
Chromosome pairing at zygotene-pachytene was studied in Triticum aestivum × T. kotschyi hybrids (2n=5x=35, genomic constitution ABDC(U)S(v)) by electron microscopy of synaptonemal complexes in spread microsporocyte nuclei. Hybrids carrying either the Ph allele or the ph allele, which differ markedly in metaphase I pairing, are both capable of greater than 90% pachytene pairing, although pairing in the Ph hybrids appeared slower or less synchronised. In both genotypes branched synaptonemal complexes were formed by intra-and interchromosomal pairing. The Ph gene control on homoeologous pairing does not act on the ability to pair into synaptonemal complexes. It may act on the rate of pairing or the time of crossing over.
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Affiliation(s)
- C B Gillies
- School of Biological Sciences A. 12, University of Sydney, 2006, Sydney, NSW, Australia
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Jenkins G, Scanlon MJ. Chromosome pairing in a Lolium temulentum X Lolium perenne diploid hybrid with a low chiasma frequency. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1987; 73:516-522. [PMID: 24241107 DOI: 10.1007/bf00289188] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/1986] [Accepted: 10/14/1986] [Indexed: 06/02/2023]
Abstract
Despite an average difference of about 50% in DNA amount, homoeologous chromosomes pair effectively at first metaphase in the diploid interspecific hybrid between Lolium temulentum and Lolium perenne. However, in the presence of accessory B chromosomes and "diploidising genes" pairing at metaphase I is severely reduced. Reconstruction of serial electron micrographs through pollen mother cell nuclei show that synaptonemal complexes are formed at pachytene between not only homoeologous but also non-homologous chromosome segments resulting in multivalent formation. These associations are largely ineffective in terms of chiasma formation and degenerate at late pachytene. It is highly probable that the pairing determinants exercise their control on chromosome pairing largely by prohibiting the siting of crossovers in homoeologously paired chromosome segments.
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Affiliation(s)
- G Jenkins
- Department of Agricultural Botany, School of Agricultural Sciences, U.C.W., SY23 3DD, Penglais, Aberystwyth, Dyfed, UK
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Ingram R, Noltie HJ. The control of chiasma frequeney within a polyploid series in the genus Senecio (Compositae). Genetica 1987. [DOI: 10.1007/bf00126976] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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