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Articles 30 records found  beginprevious15 - 24next  jump to record: Search took 0.01 seconds. 
15.
14 p, 521.7 KB Genome-wide analysis of the "cut-and-paste" transposons of grapevine / Benjak, Andrej (Centre de Recerca en Agrigenòmica) ; Forneck, Astrid (University of Natural Resources and Applied Life Sciences. Institute of Horticulture and Viticulture (AUSTRIA)) ; Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica)
Background: The grapevine is a widely cultivated crop and a high number of different varieties have been selected since its domestication in the Neolithic period. Although sexual crossing has been a major driver of grapevine evolution, its vegetative propagation enhanced the impact of somatic mutations and has been important for grapevine diversity. [...]
2008 - 10.1371/journal.pone.0003107
PloS one, Vol. 3, Issue 9 (September 2008) , p. e3107  
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16.
9 p, 1.4 MB The proteins encoded by the pogo-like Lemi1 element bind the TIRs and subterminal repeated motifs of the Arabidopsis Emigrant MITE : Consequences for the transposition mechanism of MITEs / Loot, Céline (Institut de Recerca i Tecnologia Agroalimentàries) ; Santiago, Néstor (Institut de Recerca i Tecnologia Agroalimentàries) ; Sanz, Alicia (Institut de Recerca i Tecnologia Agroalimentàries) ; Casacuberta i Suñer, Josep M. 1962- (Institut de Recerca i Tecnologia Agroalimentàries)
MITEs (miniature inverted-repeated transposable elements) are a particular class of defective DNA transposons usually present within genomes as high copy number populations of highly homogeneous elements. [...]
2006 - 10.1093/nar/gkl688
Nucleic acids research, Vol. 34, Issue 18 (October 2006) , p. 5238-5246  
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17.
50 p, 962.3 KB Transposons played a major role in the diversification between the closely related almond and peach genomes : Results from the almond genome sequence / Alioto, Tyler Scott (Centre de Regulació Genòmica) ; Alexiou, Konstantinos G. (Centre de Recerca en Agrigenòmica) ; Bardil, Amélie (Centre de Recerca en Agrigenòmica) ; Barteri, Fabio (Centre de Recerca en Agrigenòmica) ; Castanera, Raúl (Centre de Recerca en Agrigenòmica) ; Cruz, Fernando (Centre de Regulació Genòmica) ; Dhingra, Amit (Washington State University. Department of Horticulture) ; Duval, Henri (Institut National de la Recherche Agronomique (França)) ; Fernández i Martí, Angel (University of California) ; Frias, Leonor (Centre de Regulació Genòmica) ; Galán, Beatriz (Consejo Superior de Investigaciones Científicas) ; García, José Luis (Consejo Superior de Investigaciones Científicas) ; Howad, Werner (Centre de Recerca en Agrigenòmica) ; Gómez-Garrido, Jessica (Centre de Regulació Genòmica) ; Gut, Marta (Centre de Regulació Genòmica) ; Julca, Irene (Centre de Regulació Genòmica) ; Morata, Jordi (Centre de Recerca en Agrigenòmica) ; Puigdomènech, Pere, 1948- (Centre de Recerca en Agrigenòmica) ; Ribeca, Paolo (Centre de Regulació Genòmica) ; Rubio Cabetas, María José (Centro de Investigación y Tecnología Agroalimentaria de Aragón) ; Vlasova, Anna (Centre de Regulació Genòmica) ; Wirthensohn, Michelle (The University of Adelaide. School of Agriculture, Food and Wine) ; Garcia-Mas, Jordi (Centre de Recerca en Agrigenòmica) ; Gabaldón, Toni (Centre de Regulació Genòmica) ; Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica) ; Arús i Gorina, Pere (Centre de Recerca en Agrigenòmica)
We sequenced the genome of the highly heterozygous almond Prunus dulcis cv. Texas combining short and long-read sequencing. We obtained a genome assembly totaling 227. 6 Mb of the estimated 238 Mb almond genome size, of which 91% is anchored to eight pseudomolecules corresponding to its haploid chromosome complement, and annotated 27,969 protein-coding genes and 6,747 non-coding transcripts. [...]
2020 - 10.1111/tpj.14538
The Plant journal, Vol. 101, Issue 2 (January 2020) , p. 455-472  
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18.
18 p, 287.1 KB On the importance to acknowledge transposable elements in epigenomic analyses / Lerat, Emmanuelle (Université de Lyon. Laboratoire de Biométrie et Biologie Evolutive) ; Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica) ; Chaparro, Cristian (University of Perpignan Via Domitia) ; Vieira, Cristina (Université de Lyon. Laboratoire de Biométrie et Biologie Evolutive)
Eukaryotic genomes comprise a large proportion of repeated sequences, an important fraction of which are transposable elements (TEs). TEs are mobile elements that have a significant impact on genome evolution and on gene functioning. [...]
2019 - 10.3390/genes10040258
Genes, Vol. 10, Issue 4 (April 2019) , art. 258  
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19.
38 p, 5.4 MB Differences in firing efficiency, chromatin and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins / Sequeira-Mendes, Joana (Centro de Biología Molecular Severo Ochoa) ; Vergara, Zaida (Centro de Biología Molecular Severo Ochoa) ; Peiró, Ramón (Centro de Biología Molecular Severo Ochoa) ; Morata, Jordi (Centre de Recerca en Agrigenòmica) ; Aragüez, Irene (Centro de Biología Molecular Severo Ochoa) ; Costas, Celina (Centro de Biología Molecular Severo Ochoa) ; Méndez Giráldez, Raúl (Centro de Biología Molecular Severo Ochoa) ; Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica) ; Bastolla, Ugo (Centro de Biología Molecular Severo Ochoa) ; Gutiérrez, Crisanto (Centro de Biología Molecular Severo Ochoa)
Eukaryotic genome replication depends on thousands of DNA replication origins (ORIs). A major challenge is to learn ORI biology in multicellular organisms in the context of growing organs to understand their developmental plasticity. [...]
2019 - 10.1101/gr.240986.118
Genome research, Vol. 29, Issue 5 (May 2019) , p. 784-797  
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20.
7 p, 145.7 KB Genetic alterations that do or do not occur naturally : consequences for genome edited organisms in the context of regulatory oversight / Custers, René (Vlaams Instituut voor Biotechnologie) ; Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica) ; Eriksson, Dennis (Sveriges Lantbruksuniversitet) ; Sági, László (Magyar Tudományos Akadémiát. Mezőgazdasági Kutatóközpont) ; Schiemann, Joachim (Julius Kühn-Institut. Federal Research Centre for Cultivated Plants)
The ability to successfully exploit genome edited organisms for the benefit of food security and the environment will essentially be determined by the extent to which these organisms fall under specific regulatory provisions. [...]
2019 - 10.3389/fbioe.2018.00213
Frontiers in Bioengineering and Biotechnology, Vol. 6 (Jan. 2019) , art. 213  
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21.
9 p, 1.8 MB An improved assembly and annotation of the melon (Cucumis melo L.) reference genome / Ruggieri, Valentino (Centre de Recerca en Agrigenòmica) ; Alexiou, Konstantinos G. (Institut de Recerca i Tecnologia Agroalimentàries) ; Morata, Jordi (Centre de Recerca en Agrigenòmica) ; Argyris, Jason (Centre de Recerca en Agrigenòmica) ; Pujol Abajo, Marta (Institut de Recerca i Tecnologia Agroalimentàries) ; Yano, Ryoichi (University of Tsukuba. Faculty of Life and Environmental Sciences) ; Nonaka, Satoko (University of Tsukuba. Faculty of Life and Environmental Sciences) ; Ezura, Hiroshi (University of Tsukuba. Faculty of Life and Environmental Sciences) ; Latrasse, David (University of Evry. Institute of Plant Sciences Paris-Saclay (IPS2)) ; Boualem, Adnane (University of Evry. Institute of Plant Sciences Paris-Saclay (IPS2)) ; Benhamed, Moussa (University of Evry. Institute of Plant Sciences Paris-Saclay (IPS2)) ; Bendahmane, Abdelhafid (University of Evry. Institute of Plant Sciences Paris-Saclay (IPS2)) ; Aiese Cigliano, Riccardo (Sequentia Biotech SL) ; Sanseverino, Walter (Sequentia Biotech SL) ; Puigdomènech, Pere, 1948- (Centre de Recerca en Agrigenòmica) ; Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica) ; Garcia-Mas, Jordi (Centre de Recerca en Agrigenòmica)
We report an improved assembly (v3. 6. 1) of the melon (Cucumis melo L. ) genome and a new genome annotation (v4. 0). The optical mapping approach allowed correcting the order and the orientation of 21 previous scaffolds and permitted to correctly define the gap-size extension along the 12 pseudomolecules. [...]
2018 - 10.1038/s41598-018-26416-2
Scientific reports, Vol. 8 (May 2018) , art. 8088  
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22.
12 p, 836.9 KB The evolutionary consequences of transposon-related pericentromer expansion in melon / Morata, Jordi (Centre de Recerca en Agrigenòmica) ; Tormo, Marc (Centre de Recerca en Agrigenòmica) ; Alexiou, Konstantinos G. (Institut de Recerca i Tecnologia Agroalimentàries) ; Vives, Cristina (Centre de Recerca en Agrigenòmica) ; Ramos-Onsins, Sebastian (Centre de Recerca en Agrigenòmica) ; Garcia-Mas, Jordi (Centre de Recerca en Agrigenòmica) ; Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica)
Transposable elements (TEs) are a major driver of plant genome evolution. A part frombeing a rich source of new genes and regulatory sequences, TEs can also affect plant genome evolution by modifying genome size and shaping chromosome structure. [...]
2018 - 10.1093/gbe/evy115
Genome biology and evolution, Vol. 10, Núm. 6 (June 2018) , p. 1584-1595  
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23.
60 p, 1.6 MB The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution / Lang, Daniel (Helmholtz Center Munich. Plant Genome and Systems Biology) ; Ullrich, Kristian K. (University of Marburg. Faculty of Biology) ; Murat, Florent (Institut national de la recherche agronomique. UMR 1095 Genetics. Diversity and Ecophysiology of Cereals) ; Fuchs, Jorg (Leibniz Institute of Plant Genetics and Crop Plant Research) ; Jenkins, Jerry (HudsonAlpha Institute for Biotechnology) ; Haas, Fabian B. (University of Marburg. Faculty of Biology) ; Piednoel, M. (Max Planck Institute for Plant Breeding Research) ; Gundlach, H. (Helmholtz Center Munich. Plant Genome and Systems Biology) ; Van Bel, M. (VIB-UGent Center for Plant Systems Biology) ; Meyberg, R. (University of Marburg. Faculty of Biology) ; Vives, Cristina (Centre de Recerca en Agrigenòmica) ; Morata, Jordi (Centre de Recerca en Agrigenòmica) ; Symeonidi, Aikaterini (University of Marburg. Faculty of Biology) ; Hiss, Manuel (University of Marburg. Faculty of Biology) ; Muchero, Wellington (Oak Ridge National Laboratory. Biosciences Division) ; Kamisugi, Yasuko (University of Leeds. Centre for Plant Sciences) ; Saleh, Omar (University of Freiburg. Faculty of Biology) ; Blanc, Guillaume (Aix-Marseille Université. Structural and Genomic Information Laboratory) ; Decker, Eva L. (University of Freiburg. Faculty of Biology) ; van Gessel, Nico (University of Freiburg. Faculty of Biology) ; Grimwood, Jane (HudsonAlpha Institute for Biotechnology) ; Hayes, Richard D. (DOE Joint Genome Institute) ; Graham, Sean W. (University of British Columbia. Department of Botany) ; Gunter, Lee E. (Oak Ridge National Laboratory. Biosciences Division) ; McDaniel, Stuart F. (University of Florida. Department of Biology) ; Hoernstein, Sebastian N. W. (University of Freiburg. Faculty of Biology) ; Larsson, Anders (Uppsala University. Evolutionary Biology Centre) ; Li, Fay-Wei (Boyce Thompson Institute) ; Perroud, Pierre-François (University of Marburg. Faculty of Biology) ; Phillips, Jeremy (DOE Joint Genome Institute) ; Ranjan, Priya (Oak Ridge National Laboratory) ; Rokshar, Daniel S. (DOE Joint Genome Institute) ; Rothfels, Carl J. (University of California. Department of Integrative Biology) ; Schneider, Lucas (University of Marburg. Faculty of Biology) ; Shu, Shengqiang (DOE Joint Genome Institute) ; Stevenson, Dennis W. (New York Botanical Garden) ; Thümmler, Fritz (Vertis Biotechnologie AG) ; Tillich, Michael (Max Planck Institute of Molecular Plant Physiology) ; Villarreal Aguilar, Juan C. (Université Laval. Department of Biology) ; Widiez, Thomas (University of Geneva. Department of Plant Biology) ; Wong, Gane Ka-Shu (University of Alberta. Department of Biological Sciences) ; Wymore, Ann (Oak Ridge National Laboratory) ; Zhang, Yong (Shenzhen Huahan Gene Life Technology Co. Ltd) ; Zimmer, Aandreas D. (University of Freiburg. Faculty of Biology) ; Quatrano, Ralph S. (Washington University. Department of Biology) ; Mayer, Klaus F. X. (Technical University Munich) ; Goodstein, David (DOE Joint Genome Institute) ; Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica) ; Vandepoele, Klaas (Ghent University. Department of Plant Biotechnology and Bioinformatics) ; Reski, Ralph (University of Freiburg. Faculty of Biology) ; Cuming, Andrew C. (University of Leeds. Faculty of Biological Sciences) ; Tuskan, Gerald A. (Oak Ridge National Laboratory. Biosciences Division) ; Maumus, Florian (Institut National de la Recherche Agronomique (França)) ; Salse, Jerome (Institut national de la recherche agronomique. UMR 1095 Genetics. Diversity and Ecophysiology of Cereals) ; Schmutz, Jeremy (DOE Joint Genome Institute) ; Rensing, Stefan A. (University of Freiburg. BIOSS Centre for Biological Signalling Studies)
The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. [...]
2018 - 10.1111/tpj.13801
The Plant journal, Vol. 93, issue 3 (Feb. 2018) , p. 515-533  
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24.
11 p, 563.4 KB Plant lineage-specific amplification of transcription factor binding motifs by miniature inverted-repeat transposable elements (MITEs) / Morata, Jordi (Centre de Recerca en Agrigenòmica) ; Marín Nieto, Fátima (Centre de Recerca en Agrigenòmica) ; Payet, Jordi ; Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica)
Transposable elements are one of the main drivers of plant genome evolution. Transposon insertions can modify the gene coding capacity or the regulation of their expression, the latter being a more subtle effect, and therefore particularly useful for evolution. [...]
2018 - 10.1093/gbe/evy073
Genome biology and evolution, Vol. 10, issue 5 (May 2018) , p. 1210-1220  
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