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20 p, 3.6 MB |
Improved high-quality genome assembly and annotation of pineapple (Ananas comosus) cultivar md2 revealed extensive haplotype diversity and diversified frs/frf gene family
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Yow, Ashley (North Carolina State University. Department of Horticultural Science) ;
Bostan, Hamed (North Carolina State University. Plants for Human Health Institute) ;
Castanera, Raúl (Centre de Recerca en Agrigenòmica) ;
Ruggieri, Valentino (Biomeets Consulting (Barcelona)) ;
Mengist, Mengist F. (North Carolina State University. Plants for Human Health Institute) ;
Curaba, Julien (North Carolina State University. Plants for Human Health Institute) ;
Young, Roberto (Standard Fruit de Honduras. Research Department of Dole) ;
Gillitt, Nicholas (David H. Murdock Research Institute) ;
Iorizzo, Massimo (North Carolina State University. Plants for Human Health Institute)
Pineapple (Ananas comosus (L. ) Merr. ) is the second most important tropical fruit crop globally, and 'MD2' is the most important cultivated variety. A high-quality genome is important for molecular-based breeding, but available pineapple genomes still have some quality limitations. [...]
2022 - 10.3390/genes13010052
Genes, Vol. 13, Issue 1 (January 2022) , art. 52
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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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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, 1.7 MB |
Distribution, characteristics, and regulatory potential of long noncoding RNAs in brown-rot fungi
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Borgognone, Alessandra (Sequentia Biotech) ;
Sanseverino, Walter (Sequentia Biotech) ;
Aiese Cigliano, Riccardo (Sequentia Biotech) ;
Castanera, Raúl (Centre de Recerca en Agrigenòmica)
Long noncoding RNAs have been thoroughly studied in plants, animals, and yeasts, where they play important roles as regulators of transcription. Nevertheless, almost nothing is known about their presence and characteristics in filamentous fungi, especially in basidiomycetes. [...]
2019 - 10.1155/2019/9702342
International journal of genomics, Vol. 2019 (May 2019) , art. 9702342
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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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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
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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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