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19 p, 6.2 MB |
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx
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Abascal, Federico (Centro Nacional de Investigaciones Oncológicas) ;
Corvelo, André (Centre Nacional d'Anàlisi Genòmica) ;
Cruz, Fernando (Centre Nacional d'Anàlisi Genòmica) ;
Villanueva-Cañas, J. L. (Institut Hospital del Mar d'Investigacions Mèdiques) ;
Vlasova, Anna (Centre de Regulació Genòmica) ;
Marcet-Houben, Marina (Centre de Regulació Genòmica) ;
Martínez-Cruz, B. (Estación Biológica de Doñana) ;
Cheng, J. Y. (Aarhus University. Bioinformatics Research Centre) ;
Prieto, P. (Centre de Regulació Genòmica) ;
Quesada, V. (Universidad de Oviedo. Instituto Universitario de Oncología) ;
Quilez, J. (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Li, G. (Texas A;M University. Department of Veterinary Integrative Biosciences) ;
García, Francisca (Universitat Autònoma de Barcelona. Servei de Cultius Cel·lulars, Producció d'Anticossos i Citometria) ;
Rubio-Camarillo, M. (Centro Nacional de Investigaciones Oncológicas) ;
Frias, Leonor (Centre Nacional d'Anàlisi Genòmica) ;
Ribeca, Paolo (Centre Nacional d'Anàlisi Genòmica) ;
Capella-Gutiérrez, Salvador (Centre de Regulació Genòmica) ;
Rodríguez, J. M. (Centro Nacional de Investigaciones Oncológicas) ;
Câmara, F. (Centre de Regulació Genòmica) ;
Lowy, Ernesto (Centre de Regulació Genòmica) ;
Cozzuto, Luca (Centre de Regulació Genòmica) ;
Erb, I. (Centre de Regulació Genòmica) ;
Tress, M. L. (Centro Nacional de Investigaciones Oncológicas) ;
Rodriguez-Ales, J. L. (Centre de Regulació Genòmica) ;
Ruiz-Orera, J. (Institut Hospital del Mar d'Investigacions Mèdiques) ;
Reverter, F. (Centre de Regulació Genòmica) ;
Casas-Marce, M. (Estación Biológica de Doñana) ;
Soriano, L. (Estación Biológica de Doñana) ;
Arango, Javier R (Universidad de Oviedo. Departamento de Bioquímica y Biología Molecular) ;
Derdak, Sophia (Centre Nacional d'Anàlisi Genòmica) ;
Galán, Beatriz (Centro de Investigaciones Biológicas (Madrid)) ;
Blanc, Julie (Centre Nacional d'Anàlisi Genòmica) ;
Gut, Marta (Centre Nacional d'Anàlisi Genòmica) ;
Lorente-Galdos, Belen (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Andrés Nieto, Marta (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
López-Otín, C. (Universidad de Oviedo. Departamento de Bioquímica y Biología Molecular) ;
Valencia, A. (Centro Nacional de Investigaciones Oncológicas) ;
Gut, I. (Centre Nacional d'Anàlisi Genòmica) ;
García, J. L. (Centro de Investigaciones Biológicas (Madrid)) ;
Guigó, R. (Centre de Regulació Genòmica) ;
Murphy, W. J. (Texas A;M University. Department of Veterinary Integrative Biosciences) ;
Ruiz-Herrera Moreno, Aurora (Universitat Autònoma de Barcelona. Departament de Biologia Cel·lular, de Fisiologia i d'Immunologia) ;
Marques-Bonet, Tomas. 1975- (Centre Nacional d'Anàlisi Genòmica) ;
Roma, Guglielmo (Centre de Regulació Genòmica) ;
Notredame, C. (Centre de Regulació Genòmica) ;
Mailund, Thomas (Aarhus University. Bioinformatics Research Centre) ;
Albà, M. Mar (Institut Hospital del Mar d'Investigacions Mèdiques) ;
Gabaldón, Toni (Centre de Regulació Genòmica) ;
Alioto, Tyler Scott (Centre Nacional d'Anàlisi Genòmica) ;
Godoy, J. A. (Estación Biológica de Doñana)
Background: Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. [...]
2016 -  10.1186/s13059-016-1090-1
Genome biology, Vol. 17 (2016) , art. 251
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13 p, 561.5 KB |
Gene fusions derived by transcriptional readthrough are driven by segmental duplication in human
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McCartney, Ann M. (Dublin City University. Bioinformatics and Molecular Evolution Group) ;
Hyland, Edel M. (Queens University Belfast. Institute for Global Food Security) ;
Cormican, Paul (Animal and Grassland Research and Innovation Centre (Irlanda)) ;
Moran, Raymond J. (Dublin City University. Bioinformatics and Molecular Evolution Group) ;
Webb, Andrew E. (Dublin City University. Bioinformatics and Molecular Evolution Group) ;
Lee, Kate D. (Massey University (New Zealand)) ;
Hernandez Rodriguez, Jessica (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Prado-Martinez, Javier (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Creevey, Christopher J. (Aberystwyth University. Institute of Biological, Environmental and Rural Sciences) ;
Aspden, Julie L. (University of Leeds. School of Molecular and Cellular Biology) ;
McInerney, James O. (University of Nottingham. School of Life Sciences) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
O'Connell, Mary J. (University of Nottingham. School of Life Sciences)
Gene fusion occurs when two or more individual genes with independent open reading frames becoming juxtaposed under the same open reading frame creating a new fused gene. A small number of gene fusions described in detail have been associated with novel functions, for example, the hominid-specific PIPSL gene, TNFSF12, and the TWE-PRIL gene family. [...]
2019 - 10.1093/gbe/evz163
Genome biology and evolution, Vol. 11, Issue 9 (September 2019) , p. 2678-2690
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17.
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19 p, 3.0 MB |
Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development
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Pajoro, Alice (Wageningen University. Laboratory of Molecular Biology) ;
Madrigal, Pedro fl. 1586-1594 (Polish Academy of Sciences. Institute of Plant Genetics) ;
Muiño, Jose M. (Max-Planck Institute for Molecular Genetics. Department of Computational Molecular Biology) ;
Matus, José Tomás (Centre de Recerca en Agrigenòmica) ;
Jin, Jian (Centre de Recerca en Agrigenòmica) ;
Mecchia, Martin A. (Instituto de Biología Molecular y Celular de Rosario) ;
Debernardi, Juan M. (Instituto de Biología Molecular y Celular de Rosario) ;
Palatnik, Javier F. (Instituto de Biología Molecular y Celular de Rosario) ;
Balazadeh, Salma (University of Potsdam. Institute of Biochemistry and Biology) ;
Arif, Muhammad (University of Potsdam. Institute of Biochemistry and Biology) ;
Ó'Maoiléidigh, Diarmuid S. (Trinity College Dublin. Smurfit Institute of Genetics) ;
Wellmer, Frank (Trinity College Dublin. Smurfit Institute of Genetics) ;
Krajewski, Pawel (Polish Academy of Sciences. Institute of Plant Genetics) ;
Riechmann, José Luis (Institució Catalana de Recerca i Estudis Avançats) ;
Angenent, Gerco C. (Business Unit Bioscience. Plant Research International) ;
Kaufmann, Kerstin (University of Potsdam. Institute of Biochemistry and Biology)
Background: Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programs. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. [...]
2014 - 10.1186/gb-2014-15-3-r41
Genome biology, Vol. 15 (March 2014) , p. R41
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14 p, 627.9 KB |
Genetic variation in pan species is shaped by demographic history and harbors lineage-specific functions
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Han, Sojung, 1984- (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Andrés, Aida M. (UCL Genetics Institute) ;
Marques-Bonet, Tomas, 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Kuhlwilm, Martin (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Universitat Autònoma de Barcelona
Chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) are the closest living relatives of humans, but the two species show distinct behavioral and physiological differences, particularly regarding female reproduction. [...]
2019 - 10.1093/gbe/evz047
Genome biology and evolution, Vol. 11, Issue 4 (April 2019) , p. 1178-1191
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12 p, 1.9 MB |
Diurnal regulation of SDG2 and JMJ14 by circadian clock oscillators orchestrates histone modification rhythms in Arabidopsis
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Song, Qingxin (Nanjing Agricultural University) ;
Huang, Tien-Yu (University of Texas at Austin. Department of Integrative Biology) ;
Yu, Helen H. (University of Texas at Austin. Department of Integrative Biology) ;
Ando, Atsumi (University of Texas at Austin. Department of Integrative Biology) ;
Mas, Paloma (Centre de Recerca en Agrigenòmica) ;
Ha, Misook (Samsung Advanced Institute of Technology) ;
Chen, Z. Jeffrey (Nanjing Agricultural University)
Background: Circadian rhythms modulate growth and development in all organisms through interlocking transcriptional-translational feedback loops. The transcriptional loop involves chromatin modifications of central circadian oscillators in mammals and plants. [...]
2019 - 10.1186/s13059-019-1777-1
Genome biology, Vol. 20 (August 2019) , art. 170
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24 p, 2.4 MB |
Delegating sex : differential gene expression in stolonizing syllids uncovers the hormonal control of reproduction
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Álvarez-Campos, Patricia (Universidad Autónoma de Madrid. Departamento de Biología (Zoología)) ;
Kenny, Nathan J. (The Natural History Museum of London. Department of Life Sciences) ;
Verdes, Aida (Universidad Autónoma de Madrid. Departamento de Biología (Zoología)) ;
Fernández García, Rosa (Centre de Recerca en Agrigenòmica) ;
Novo, Marta (Universidad Complutense de Madrid. Departamento de Biodiversidad, Ecología y Evolución) ;
Giribet, Gonzalo (Harvard University. Museum of Comparative Zoology) ;
Riesgo, Ana (City University of New York. The Graduate Center. Department of Biology)
Stolonization in syllid annelids is a unique mode of reproduction among animals. During the breeding season, a structure resembling the adult but containing only gametes, called stolon, is formed generally at the posterior end of the animal. [...]
2019 - 10.1093/gbe/evy265
Genome biology and evolution, Vol. 11, issue 1 (Jan. 2019) , p. 295-318
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21.
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12 p, 836.9 KB |
The evolutionary consequences of transposon-related pericentromer expansion in melon
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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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22.
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13 p, 1.7 MB |
Genomes reveal marked differences in the adaptive evolution between orangutan species
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Mattle-Greminger, Maja P. (University of Zurich. Department of Anthropology) ;
Bilgin Sonay, Tugce (University of Zurich. Department of Anthropology) ;
Nater, Alexander (University of Zurich. Department of Anthropology) ;
Pybus, Marc (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Desai, Tariq (University of Cambridge. Department of Genetics) ;
Valles, Guillem de (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Casals, Ferran (Universitat Pompeu Fabra. Servei de Genòmica) ;
Scally, Aylwyn (University of Cambridge. Department of Genetics) ;
Bertranpetit, Jaume (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Marques-Bonet, Tomas, 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
van Schaik, Carel P. (University of Zurich. Department of Anthropology) ;
Anisimova, Maria (Zurich University of Applied Sciences ZHAW) ;
Krützen, Michael (University of Zurich. Department of Anthropology)
Background: Integrating demography and adaptive evolution is pivotal to understanding the evolutionary history and conservation of great apes. However, little is known about the adaptive evolution of our closest relatives, in particular if and to what extent adaptions to environmental differences have occurred. [...]
2018 - 10.1186/s13059-018-1562-6
Genome biology, Vol. 19 (Novembre 2018) , art. 193
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11 p, 563.4 KB |
Plant lineage-specific amplification of transcription factor binding motifs by miniature inverted-repeat transposable elements (MITEs)
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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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