The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
J S Heslopharrison - One of the best experts on this subject based on the ideXlab platform.
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the Repetitive DNA landscape in avena poaceae chromosome and genome evolution defined by major repeat classes in whole genome sequence reads
BMC Plant Biology, 2019Co-Authors: Qing Liu, J S Heslopharrison, Trude Schwarzacher, Xiangying Zhou, Fengjiao ZhangAbstract:Repetitive DNA motifs – not coding genetic information and repeated millions to hundreds of times – make up the majority of many genomes. Here, we identify the nature, abundance and organization of all the Repetitive DNA families in oats (Avena sativa, 2n = 6x = 42, AACCDD), a recognized health-food, and its wild relatives. Whole-genome sequencing followed by k-mer and RepeatExplorer graph-based clustering analyses enabled assessment of Repetitive DNA composition in common oat and its wild relatives’ genomes. Fluorescence in situ hybridization (FISH)-based karyotypes are developed to understand chromosome and Repetitive sequence evolution of common oat. We show that some 200 repeated DNA motifs make up 70% of the Avena genome, with less than 20 families making up 20% of the total. Retroelements represent the major component, with Ty3/Gypsy elements representing more than 40% of all the DNA, nearly three times more abundant than Ty1/Copia elements. DNA transposons are about 5% of the total, while tandemly repeated, satellite DNA sequences fit into 55 families and represent about 2% of the genome. The Avena species are monophyletic, but both bioinformatic comparisons of repeats in the different genomes, and in situ hybridization to metaphase chromosomes from the hexaploid species, shows that some repeat families are specific to individual genomes, or the A and D genomes together. Notably, there are terminal regions of many chromosomes showing different repeat families from the rest of the chromosome, suggesting presence of translocations between the genomes. The relatively small number of repeat families shows there are evolutionary constraints on their nature and amplification, with mechanisms leading to homogenization, while repeat characterization is useful in providing genome markers and to assist with future assemblies of this large genome (c. 4100 Mb in the diploid). The frequency of inter-genomic translocations suggests optimum strategies to exploit genetic variation from diploid oats for improvement of the hexaploid may differ from those used widely in bread wheat.
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Repetitive DNA molecular cytogenetics and genome organization in the king scallop pecten maximus
Gene, 2007Co-Authors: Maria Assunta Biscotti, Ettore Olmo, Adriana Canapa, Marco Barucca, Chee How Teo, Trude Schwarzacher, Sven Dennerlein, Rica Richter, J S HeslopharrisonAbstract:We studied the structure, organization and relationship of Repetitive DNA sequences in the genome of the scallop, Pecten maximus, a bivalve that is important both commercially and in marine ecology. Recombinant DNA libraries were constructed after partial digestion of genomic DNA from scallop with PstI and ApaI restriction enzymes. Clones containing Repetitive DNA were selected by hybridisation to labelled DNA from scallop, oyster and mussel; colonies showing strong hybridisation only to scallop were selected for analysis and sequencing. Six non-homologous tandemly repeated sequences were identified in the sequences, and Southern hybridisation with all repeat families to genomic DNA digests showed characteristic ladders of hybridised bands. Three families had monomer lengths around 40 bp while three had repeats characteristic of the length wrapping around one (170 bp), or two (326 bp) nucleosomes. In situ hybridisation to interphase nuclei showed each family had characteristic numbers of clusters indicating contrasting arrangements. Two of the repeats had unusual repetitions of bases within their sequence, which may relate to the nature of microsatellites reported in bivalves. The study of these rapidly evolving sequences is valuable to understand an important source of genomic diversity, has the potential to provide useful markers for population studies and gives a route to identify mechanisms of DNA sequence evolution.
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Repetitive DNA elements as a major component of plant genomes
Annals of Botany, 1998Co-Authors: Sybille Kubis, Thomas Schmidt, J S HeslopharrisonAbstract:A major part of the nuclear genome of most plants is composed of different Repetitive DNA elements. Studying these sequence elements is essential for our understanding of the nature and consequences of genome size variation between different species, and for studying the large-scale organization and evolution of plant genomes. Sugar beet (Beta vulgaris L.) is an important crop and a suitable model for such investigations: with a genome size of 0-8 pg C (760 Mbp) it contains significant amounts of all major groups of Repetitive sequences among its nine chromosome pairs, but analysis is not complicated by polyploidy or the huge size of some genomes, and there are valuable genetic data, recombinant DNA libraries and wild relatives to complement studies of sequence contribution to genome size in sugar beet. A sophisticated understanding of the structure of the genome will provide valuable data about the major factors responsible for genome size variation, useful aids in the development of a molecular understanding of genome evolution, and perhaps indicate strategies for crop improvement. Using molecular and cytological approaches, we have characterized a range of differentially organized Repetitive DNA sequence elements from the genomes of cultivated and wild beet species, leading to an extensive model of the Repetitive DNA, its organization and evolution. © 1998 Annals of Botany Company
Diogo Cavalcanti Cabraldemello - One of the best experts on this subject based on the ideXlab platform.
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tracking the evolution of sex chromosome systems in melanoplinae grasshoppers through chromosomal mapping of Repetitive DNA sequences
BMC Evolutionary Biology, 2013Co-Authors: Octavio M Palaciosgimenez, Elio Rodrigo Daniel Castillo, Dardo A Marti, Diogo Cavalcanti CabraldemelloAbstract:Background The accumulation of Repetitive DNA during sex chromosome differentiation is a common feature of many eukaryotes and becomes more evident after recombination has been restricted or abolished. The accumulated Repetitive sequences include multigene families, microsatellites, satellite DNAs and mobile elements, all of which are important for the structural remodeling of heterochromatin. In grasshoppers, derived sex chromosome systems, such as neo-XY♂/XX♀ and neo-X1X2Y♂/X1X1X2X2♀, are frequently observed in the Melanoplinae subfamily. However, no studies concerning the evolution of sex chromosomes in Melanoplinae have addressed the role of the Repetitive DNA sequences. To further investigate the evolution of sex chromosomes in grasshoppers, we used classical cytogenetic and FISH analyses to examine the Repetitive DNA sequences in six phylogenetically related Melanoplinae species with X0♂/XX♀, neo-XY♂/XX♀ and neo-X1X2Y♂/X1X1X2X2♀ sex chromosome systems.
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tracking the evolution of sex chromosome systems in melanoplinae grasshoppers through chromosomal mapping of Repetitive DNA sequences
BMC Evolutionary Biology, 2013Co-Authors: Octavio M Palaciosgimenez, Elio Rodrigo Daniel Castillo, Dardo A Marti, Diogo Cavalcanti CabraldemelloAbstract:The accumulation of Repetitive DNA during sex chromosome differentiation is a common feature of many eukaryotes and becomes more evident after recombination has been restricted or abolished. The accumulated Repetitive sequences include multigene families, microsatellites, satellite DNAs and mobile elements, all of which are important for the structural remodeling of heterochromatin. In grasshoppers, derived sex chromosome systems, such as neo-XY♂/XX♀ and neo-X1X2Y♂/X1X1X2X2♀, are frequently observed in the Melanoplinae subfamily. However, no studies concerning the evolution of sex chromosomes in Melanoplinae have addressed the role of the Repetitive DNA sequences. To further investigate the evolution of sex chromosomes in grasshoppers, we used classical cytogenetic and FISH analyses to examine the Repetitive DNA sequences in six phylogenetically related Melanoplinae species with X0♂/XX♀, neo-XY♂/XX♀ and neo-X1X2Y♂/X1X1X2X2♀ sex chromosome systems. Our data indicate a non-spreading of heterochromatic blocks and pool of Repetitive DNAs (C 0 t-1 DNA) in the sex chromosomes; however, the spreading of multigene families among the neo-sex chromosomes of Eurotettix and Dichromatos was remarkable, particularly for 5S rDNA. In autosomes, FISH mapping of multigene families revealed distinct patterns of chromosomal organization at the intra- and intergenomic levels. These results suggest a common origin and subsequent differential accumulation of Repetitive DNAs in the sex chromosomes of Dichromatos and an independent origin of the sex chromosomes of the neo-XY and neo-X1X2Y systems. Our data indicate a possible role for Repetitive DNAs in the diversification of sex chromosome systems in grasshoppers.
Sybille Kubis - One of the best experts on this subject based on the ideXlab platform.
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Repetitive DNA elements as a major component of plant genomes
Annals of Botany, 1998Co-Authors: Sybille Kubis, Thomas Schmidt, J S HeslopharrisonAbstract:A major part of the nuclear genome of most plants is composed of different Repetitive DNA elements. Studying these sequence elements is essential for our understanding of the nature and consequences of genome size variation between different species, and for studying the large-scale organization and evolution of plant genomes. Sugar beet (Beta vulgaris L.) is an important crop and a suitable model for such investigations: with a genome size of 0-8 pg C (760 Mbp) it contains significant amounts of all major groups of Repetitive sequences among its nine chromosome pairs, but analysis is not complicated by polyploidy or the huge size of some genomes, and there are valuable genetic data, recombinant DNA libraries and wild relatives to complement studies of sequence contribution to genome size in sugar beet. A sophisticated understanding of the structure of the genome will provide valuable data about the major factors responsible for genome size variation, useful aids in the development of a molecular understanding of genome evolution, and perhaps indicate strategies for crop improvement. Using molecular and cytological approaches, we have characterized a range of differentially organized Repetitive DNA sequence elements from the genomes of cultivated and wild beet species, leading to an extensive model of the Repetitive DNA, its organization and evolution. © 1998 Annals of Botany Company
Octavio M Palaciosgimenez - One of the best experts on this subject based on the ideXlab platform.
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tracking the evolution of sex chromosome systems in melanoplinae grasshoppers through chromosomal mapping of Repetitive DNA sequences
BMC Evolutionary Biology, 2013Co-Authors: Octavio M Palaciosgimenez, Elio Rodrigo Daniel Castillo, Dardo A Marti, Diogo Cavalcanti CabraldemelloAbstract:Background The accumulation of Repetitive DNA during sex chromosome differentiation is a common feature of many eukaryotes and becomes more evident after recombination has been restricted or abolished. The accumulated Repetitive sequences include multigene families, microsatellites, satellite DNAs and mobile elements, all of which are important for the structural remodeling of heterochromatin. In grasshoppers, derived sex chromosome systems, such as neo-XY♂/XX♀ and neo-X1X2Y♂/X1X1X2X2♀, are frequently observed in the Melanoplinae subfamily. However, no studies concerning the evolution of sex chromosomes in Melanoplinae have addressed the role of the Repetitive DNA sequences. To further investigate the evolution of sex chromosomes in grasshoppers, we used classical cytogenetic and FISH analyses to examine the Repetitive DNA sequences in six phylogenetically related Melanoplinae species with X0♂/XX♀, neo-XY♂/XX♀ and neo-X1X2Y♂/X1X1X2X2♀ sex chromosome systems.
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tracking the evolution of sex chromosome systems in melanoplinae grasshoppers through chromosomal mapping of Repetitive DNA sequences
BMC Evolutionary Biology, 2013Co-Authors: Octavio M Palaciosgimenez, Elio Rodrigo Daniel Castillo, Dardo A Marti, Diogo Cavalcanti CabraldemelloAbstract:The accumulation of Repetitive DNA during sex chromosome differentiation is a common feature of many eukaryotes and becomes more evident after recombination has been restricted or abolished. The accumulated Repetitive sequences include multigene families, microsatellites, satellite DNAs and mobile elements, all of which are important for the structural remodeling of heterochromatin. In grasshoppers, derived sex chromosome systems, such as neo-XY♂/XX♀ and neo-X1X2Y♂/X1X1X2X2♀, are frequently observed in the Melanoplinae subfamily. However, no studies concerning the evolution of sex chromosomes in Melanoplinae have addressed the role of the Repetitive DNA sequences. To further investigate the evolution of sex chromosomes in grasshoppers, we used classical cytogenetic and FISH analyses to examine the Repetitive DNA sequences in six phylogenetically related Melanoplinae species with X0♂/XX♀, neo-XY♂/XX♀ and neo-X1X2Y♂/X1X1X2X2♀ sex chromosome systems. Our data indicate a non-spreading of heterochromatic blocks and pool of Repetitive DNAs (C 0 t-1 DNA) in the sex chromosomes; however, the spreading of multigene families among the neo-sex chromosomes of Eurotettix and Dichromatos was remarkable, particularly for 5S rDNA. In autosomes, FISH mapping of multigene families revealed distinct patterns of chromosomal organization at the intra- and intergenomic levels. These results suggest a common origin and subsequent differential accumulation of Repetitive DNAs in the sex chromosomes of Dichromatos and an independent origin of the sex chromosomes of the neo-XY and neo-X1X2Y systems. Our data indicate a possible role for Repetitive DNAs in the diversification of sex chromosome systems in grasshoppers.
J. S. Heslop-harrison - One of the best experts on this subject based on the ideXlab platform.
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The Repetitive DNA landscape in Avena (Poaceae): chromosome and genome evolution defined by major repeat classes in whole-genome sequence reads.
2019Co-Authors: Qing Liu, Xiangying Zhou, Fengjiao Zhang, T Schwarzacher, J. S. Heslop-harrisonAbstract:BACKGROUND: Repetitive DNA motifs - not coding genetic information and repeated millions to hundreds of times - make up the majority of many genomes. Here, we identify the nature, abundance and organization of all the Repetitive DNA families in oats (Avena sativa, 2n = 6x = 42, AACCDD), a recognized health-food, and its wild relatives. RESULTS: Whole-genome sequencing followed by k-mer and RepeatExplorer graph-based clustering analyses enabled assessment of Repetitive DNA composition in common oat and its wild relatives' genomes. Fluorescence in situ hybridization (FISH)-based karyotypes are developed to understand chromosome and Repetitive sequence evolution of common oat. We show that some 200 repeated DNA motifs make up 70% of the Avena genome, with less than 20 families making up 20% of the total. Retroelements represent the major component, with Ty3/Gypsy elements representing more than 40% of all the DNA, nearly three times more abundant than Ty1/Copia elements. DNA transposons are about 5% of the total, while tandemly repeated, satellite DNA sequences fit into 55 families and represent about 2% of the genome. The Avena species are monophyletic, but both bioinformatic comparisons of repeats in the different genomes, and in situ hybridization to metaphase chromosomes from the hexaploid species, shows that some repeat families are specific to individual genomes, or the A and D genomes together. Notably, there are terminal regions of many chromosomes showing different repeat families from the rest of the chromosome, suggesting presence of translocations between the genomes. CONCLUSIONS: The relatively small number of repeat families shows there are evolutionary constraints on their nature and amplification, with mechanisms leading to homogenization, while repeat characterization is useful in providing genome markers and to assist with future assemblies of this large genome (c. 4100 Mb in the diploid). The frequency of inter-genomic translocations suggests optimum strategies to exploit genetic variation from diploid oats for improvement of the hexaploid may differ from those used widely in bread wheat
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Centromeric Repetitive DNA sequences in the genus Brassica
Theoretical and Applied Genetics, 1995Co-Authors: G. E. Harrison, J. S. Heslop-harrisonAbstract:Representatives of two major Repetitive DNA sequence families from the diploid Brassica species B. campestris and B. oleracea were isolated, sequenced and localized to chromosomes by in situ hybridization. Both sequences were located near the centromeres of many chromosome pairs in both diploid species, but major sites of the two probes were all on different chromosome pairs. Such chromosome specificity is unusual for plant paracentromeric Repetitive DNA. Reduction of stringency of hybridization gave centromeric hybridization sites on more chromosomes, indicating that there are divergent sequences present on other chromosomes. In tetraploid species derived from the diploids, the number of hybridization sites was different from the sum of the diploid ancestors, and some chromosomes had both sequences, indicating relatively rapid homogenization and copy number evolution since the origin of the tetraploid species.
