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12 p, 2.6 MB |
Transposable element polymorphisms improve prediction of complex agronomic traits in rice
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Vourlaki, Ioanna-Theoni (Centre de Recerca en Agrigenòmica) ;
Ramos-Onsins, Sebastián E. (Centre de Recerca en Agrigenòmica) ;
Casacuberta i Suñer, Josep M 1962- (Centre de Recerca en Agrigenòmica) ;
Perez-Enciso, Miguel (Universitat Autònoma de Barcelona. Departament de Patologia i de Producció Animals) ;
Castanera, Raúl (Centre de Recerca en Agrigenòmica)
Key message: Transposon insertion polymorphisms can improve prediction of complex agronomic traits in rice compared to using SNPs only, especially when accessions to be predicted are less related to the training set. [...]
2022 -  10.1007/s00122-022-04180-2
Theoretical and Applied Genetics, Vol. 135, Issue 9 (September 2022) , p. 3211-3222
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15 p, 2.4 MB |
A blueprint for gene function analysis through Base Editing in the model plant Physcomitrium (Physcomitrella) patens
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Guyon-Debast, Anouchka (Institut Jean-Pierre Bourgin) ;
Alboresi, Alessandro (University of Padova) ;
Terret, Zoé (Institut national de recherche pour l'agriculture, l'alimentation et l'environnement) ;
Charlot, Florence (Institut Jean-Pierre Bourgin) ;
Berthier, Floriane (Institut Jean-Pierre Bourgin) ;
Vendrell-Mir, Pol (Centre de Recerca en Agrigenòmica) ;
Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica) ;
Veillet, Florian (Institut de Génétique, Environnement et Protection des Plantes) ;
Morosinotto, Tomas (University of Padova) ;
Gallois, Jean-Luc (Institut national de recherche pour l'agriculture, l'alimentation et l'environnement) ;
Nogué, Fabien (Institut national de recherche pour l'agriculture, l'alimentation et l'environnement)
CRISPR-Cas9 has proven to be highly valuable for genome editing in plants, including the model plant Physcomitrium patens. However, the fact that most of the editing events produced using the native Cas9 nuclease correspond to small insertions and deletions is a limitation. [...]
2021 - 10.1111/nph.17171
New phytologist, Vol. 230, Issue 3 (May 2021) , p. 1258-1272
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46 p, 19.9 MB |
Amplification dynamics of miniature inverted-repeat transposable elements and their impact on rice trait variability
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Castanera, Raúl (Centre de Recerca en Agrigenòmica) ;
Vendrell-Mir, Pol (Centre de Recerca en Agrigenòmica) ;
Bardil, Amélie (Centre de Recerca en Agrigenòmica) ;
Carpentier, Marie-Christine (Université de Perpignan. Laboratoire Génome et Développement des Plantes) ;
Panaud, Olivier (Université de Perpignan. Laboratoire Génome et Développement des Plantes) ;
Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica)
Transposable elements (TEs) are a rich source of genetic variability. Among TEs, miniature inverted-repeat TEs (MITEs) are of particular interest as they are present in high copy numbers in plant genomes and are closely associated with genes. [...]
2021 - 10.1111/tpj.15277
The Plant Journal, Vol. 107, Issue 1 (July 2021) , p. 118-135
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13 p, 1.6 MB |
Different Families of Retrotransposons and DNA Transposons Are Actively Transcribed and May Have Transposed Recently in Physcomitrium (Physcomitrella) patens
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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. 1962- (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
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21 p, 653.7 KB |
Genomics of evolutionary novelty in hybrids and polyploids
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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
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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
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Castanera, Raúl (Centre de Recerca en Agrigenòmica) ;
Ruggieri, Valentino (Centre de Recerca en Agrigenòmica) ;
Pujol Abajo, 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
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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
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Bogaerts-Márquez, María (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Barrón Aduriz, Maite Garazi (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
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 (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))
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
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