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Articles, 26 registres trobats
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Articles 26 registres trobats  1 - 10següentfinal  anar al registre:
1.
13 p, 1.6 MB Different Families of Retrotransposons and DNA Transposons Are Actively Transcribed and May Have Transposed Recently in Physcomitrium (Physcomitrella) patens / Vendrell-Mir, Pol (Centre de Recerca en Agrigenòmica) ; López-Obando, Mauricio (Swedish University of Agricultural Sciences. Department of Plant Biology) ; Nogué, Fabien (Institut national de recherche pour l'agriculture, l'alimentation et l'environnement) ; Casacuberta i Suñer, Josep M (Centre de Recerca en Agrigenòmica)
Similarly to other plant genomes of similar size, more than half of the genome of P. patens is covered by Transposable Elements (TEs). However, the composition and distribution of P. patens TEs is quite peculiar, with Long Terminal Repeat (LTR)-retrotransposons, which form patches of TE-rich regions interleaved with gene-rich regions, accounting for the vast majority of the TE space. [...]
2020 - 10.3389/fpls.2020.01274
Frontiers in plant science, Vol. 11 (August 2020) , art. 1274  
2.
21 p, 653.7 KB Genomics of evolutionary novelty in hybrids and polyploids / Nieto Feliner, Gonzalo (Real Jardín Botánico. Departamento de Biodiversidad y Conservación) ; Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica) ; Wendel, Jonathan F. (Iowa State University. Department of Ecology, Evolution, and Organismal Biology (USA))
It has long been recognized that hybridization and polyploidy are prominent processes in plant evolution. Although classically recognized as significant in speciation and adaptation, recognition of the importance of interspecific gene flow has dramatically increased during the genomics era, concomitant with an unending flood of empirical examples, with or without genome doubling. [...]
2020 - 10.3389/fgene.2020.00792
Frontiers in genetics, Vol. 11 (July 2020) , art. 792  
3.
5 p, 629.0 KB Additional ORFs in plant LTR-retrotransposons / Vicient Sánchez, Carlos M. (Centre de Recerca en Agrigenòmica) ; Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica)
LTR-retrotransposons share a common genomic organization in which the 5' long terminal repeat (LTR) is followed by the gag and pol genes and terminates with the 3' LTR. Although GAG-POL-encoded proteins are considered sufficient to accomplish the LTR-retrotransposon transposition, a number of elements carrying additional open reading frames (aORF) have been described. [...]
2020 - 10.3389/fpls.2020.00555
Frontiers in plant science, Vol. 11 (May 2020) , art. 555  
4.
10 p, 1.1 MB An Improved Melon Reference Genome With Single-Molecule Sequencing Uncovers a Recent Burst of Transposable Elements With Potential Impact on Genes / Castanera, Raúl (Centre de Recerca en Agrigenòmica) ; Ruggieri, Valentino (Centre de Recerca en Agrigenòmica) ; Pujol, Marta (Centre de Recerca en Agrigenòmica) ; Garcia Mas, Jordi (Centre de Recerca en Agrigenòmica) ; Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica)
The published melon (Cucumis melo L. ) reference genome assembly (v3. 6. 1) has still 41. 6 Mb (Megabases) of sequences unassigned to pseudo-chromosomes and about 57 Mb of gaps. Although different approaches have been undertaken to improve the melon genome assembly in recent years, the high percentage of repeats (~40%) and limitations due to read length have made it difficult to resolve gaps and scaffold's misassignments to pseudomolecules, especially in the heterochromatic regions. [...]
2020 - 10.3389/fpls.2019.01815
Frontiers in plant science, Vol. 10 (January 2020) , art. 1815  
5.
7 p, 1.9 MB T-lex3 : An accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data / Bogaerts-Márquez, María (Universitat Pompeu Fabra. Institut de Biologia Evolutiva) ; Barron, Maite G. (Universitat Pompeu Fabra. Institut de Biologia Evolutiva) ; Fiston-Lavier, Anna-Sophie (Institut des Sciences de l'Evolution de Montpellier) ; Vendrell Mir, Pol (Centre de Recerca en Agrigenòmica) ; Castanera, Raúl (Centre de Recerca en Agrigenòmica) ; Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica) ; González, Josefa (Universitat Pompeu Fabra. Institut de Biologia Evolutiva)
Motivation: Transposable elements (TEs) constitute a significant proportion of the majority of genomes sequenced to date. TEs are responsible for a considerable fraction of the genetic variation within and among species. [...]
2020 - 10.1093/bioinformatics/btz727
Bioinformatics, Vol. 36, Issue 4 (February 2020) , p. 1191-1197  
6.
19 p, 3.5 MB A benchmark of transposon insertion detection tools using real data / Vendrell Mir, Pol (Centre de Recerca en Agrigenòmica) ; Barteri, Fabio (Centre de Recerca en Agrigenòmica) ; Merenciano, Miriam (Universitat Pompeu Fabra. Institut de Biologia Evolutiva) ; González, Josefa (Universitat Pompeu Fabra. Institut de Biologia Evolutiva) ; Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica) ; Castanera, Raúl (Centre de Recerca en Agrigenòmica)
Background: Transposable elements (TEs) are an important source of genomic variability in eukaryotic genomes. Their activity impacts genome architecture and gene expression and can lead to drastic phenotypic changes. [...]
2019 - 10.1186/s13100-019-0197-9
Mobile DNA, Vol. 10 (December 2019) , art. 53  
7.
4 p, 557.8 KB Evolution of plant phenotypes, from genomes to traits / Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica) ; Jackson, Scott (University of Georgia (Tbilisi, Geòrgia). Center for Applied Genetic Technologies) ; Panaud, Olivier (Université de Perpignan. Laboratoire Génome et Développement des Plantes) ; Purugganan, Michael (New York University. Center for Genomics and Systems Biology) ; Wendel, Jonathan (Iowa State University. Department of Ecology, Evolution and Organismal Biology)
2016 - 10.1534/g3.115.025502
G3, Vol. 6, issue 4 (April 2016) , p. 775-778  
8.
12 p, 1.3 MB Genome engineering and plant breeding : impact on trait discovery and development / Nogué, Fabien (INRA Centre de Versailles) ; Mara, Kostlend (INRA Centre de Versailles) ; Collonnier, Cécile (INRA Centre de Versailles) ; Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica)
Key message: New tools for the precise modification of crops genes are now available for the engineering of new ideotypes. A future challenge in this emerging field of genome engineering is to develop efficient methods for allele mining. [...]
2016 - 10.1007/s00299-016-1993-z
Plant cell reports, Vol. 35, Issue 7 (July 2016) , p. 1475-1486  
9.
9 p, 588.8 KB A call for benchmarking transposable element annotation methods / Hoen, Douglas R. (McGill University. Department of Biology) ; Hickey, Glenn (McGill Centre for Bioinformatics) ; Bourque, Guillaume (McGill University) ; Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica) ; Cordaux, Richard (Université de Poitiers) ; Feschotte, Cédric (University of Utah. Department of Human Genetics) ; Fiston-Lavier, Anna-Sophie (Institut des Sciences de l'Evolution de Montpellier) ; Hua-Van, Aurélie (Université Paris-Saclay) ; Hubley, Robert (Institute for Systems Biology) ; Kapusta, Aurélie (University of Utah. Department of Human Genetics) ; Lerat, Emmanuelle (Université Claude Bernard) ; Maumus, Florian (INRA de Versailles-Grignon) ; Pollock, David D. (University of Colorado) ; Quesneville, Hadi (INRA de Versailles-Grignon) ; Smit, Arian (Institute for Systems Biology) ; Wheeler, Travis J. (University of Montana. Department of Computer Science) ; Bureau, Thomas E. (McGill University. Department of Biology) ; Blanchette, Mathieu (McGill Centre for Bioinformatics)
DNA derived from transposable elements (TEs) constitutes large parts of the genomes of complex eukaryotes, with major impacts not only on genomic research but also on how organisms evolve and function. [...]
2015 - 10.1186/s13100-015-0044-6
Mobile DNA, Vol. 6 (August 2015) , art. 13  
10.
13 p, 2.2 MB The Tnt1 retrotransposon escapes silencing in tobacco, its natural host / Hernández-Pinzón, Inmaculada (Centre de Recerca en Agrigenòmica) ; Cifuentes, Marta (Centre de Recerca en Agrigenòmica) ; Hénaff, Elizabeth (Centre de Recerca en Agrigenòmica) ; Santiago, Néstor (Centre de Recerca en Agrigenòmica) ; Espinás, M. Lluïsa (Institut de Biologia Molecular de Barcelona) ; Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica)
Retrotransposons' high capacity for mutagenesis is a threat that genomes need to control tightly. Transcriptional gene silencing is a general and highly effective control of retrotransposon expression. [...]
2012 - 10.1371/journal.pone.0033816
PloS one, Vol. 7, Issue 3 (March 2012) , art. e33816  

Articles : 26 registres trobats   1 - 10següentfinal  anar al registre:
Documents de recerca 2 registres trobats  
1.
252 p, 7.5 MB Impact of transposable elements in the evolution of plant genomes / Vives i Cobo, Cristina ; Casacuberta i Suñer, Josep M., 1962-, dir. ; Tolrà Pérez, Roser, dir. (Universitat Autònoma de Barcelona. Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia) ; Universitat Autònoma de Barcelona. Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia
Los transposones son elementos genéticos que tienen la capacidad de modificar su posición en el genoma. Como consecuencia, tienen un impacto en la evolución de los genomas inactivando o alterando los genes del huésped y proporcionando nuevas funciones génicas. [...]
Els transposons són elements genètics que tenen la capacitat de modificar la seva posició dins el genoma. Com a conseqüència, tenen un impacte en l'evolució del genomes inactivant o alterant els gens de l'hoste i proporcionant noves funcions gèniques. [...]
Transposable elements are genetic elements that have the capacity to modify their position within the genome. As a consequence, they impact the evolution of genomes by inactivating or altering host genes and by providing new gene functions. [...]

[Barcelona] : Universitat Autònoma de Barcelona, 2017.  
2.
81 p, 4.4 MB Control de la transposición e impacto de los elementos transponibles en genomas vegetales : : análisis del retrotransposón Tnt1 de tabaco y del MITE Emigrant de Arabidopsis / Santiago Gonzalvo, Néstor ; Casacuberta i Suñer, Josep M., 1962-, dir.
El trabajo presentado en esta tesis se centra en el estudio del impacto de los elementos transponibles sobre los genes y genomas vegetales y en los mecanismos de control de la transposición en estos genomas. [...]
The work presented in this doctorate thesis focuses on the analysis of plant transposable elements. Here is described the study of the impact these sequences have had on plant genes and genomes and, on the other hand, on the control of the proliferation of the transposable elements within genomes. [...]

Bellaterra : Universitat Autònoma de Barcelona, 2006
2 documents

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