Artículo

Vlasova, A.; Capella-Gutiérrez, S.; Rendón-Anaya, M.; Hernández-Oñate, M.; Minoche, A.E.; Erb, I.; Câmara, F.; Prieto-Barja, P.; Corvelo, A.; Sanseverino, W.; Westergaard, G.; Dohm, J.C.; Pappas, G.J., Jr.; Saburido-Alvarez, S.; Kedra, D.; Gonzalez, I.; Cozzuto, L.; Gómez-Garrido, J. (...) Guigó, R. "Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes" (2016) Genome Biology. 17(1)
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Abstract:

Background: Legumes are the third largest family of angiosperms and the second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million year old whole genome duplication shared by most crop legumes. Results: We report the genome and the transcription atlas of coding and non-coding genes of a Mesoamerican genotype of common bean (Phaseolus vulgaris L., BAT93). Using a comprehensive phylogenomics analysis, we assessed the past and recent evolution of common bean, and traced the diversification of patterns of gene expression following duplication. We find that successive rounds of gene duplications in legumes have shaped tissue and developmental expression, leading to increased levels of specialization in larger gene families. We also find that many long non-coding RNAs are preferentially expressed in germ-line-related tissues (pods and seeds), suggesting that they play a significant role in fruit development. Our results also suggest that most bean-specific gene family expansions, including resistance gene clusters, predate the split of the Mesoamerican and Andean gene pools. Conclusions: The genome and transcriptome data herein generated for a Mesoamerican genotype represent a counterpart to the genomic resources already available for the Andean gene pool. Altogether, this information will allow the genetic dissection of the characters involved in the domestication and adaptation of the crop, and their further implementation in breeding strategies for this important crop. © 2016 Vlasova et al.

Registro:

Documento: Artículo
Título:Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes
Autor:Vlasova, A.; Capella-Gutiérrez, S.; Rendón-Anaya, M.; Hernández-Oñate, M.; Minoche, A.E.; Erb, I.; Câmara, F.; Prieto-Barja, P.; Corvelo, A.; Sanseverino, W.; Westergaard, G.; Dohm, J.C.; Pappas, G.J., Jr.; Saburido-Alvarez, S.; Kedra, D.; Gonzalez, I.; Cozzuto, L.; Gómez-Garrido, J.; Aguilar-Morón, M.A.; Andreu, N.; Aguilar, O.M.; Garcia-Mas, J.; Zehnsdorf, M.; Vázquez, M.P.; Delgado-Salinas, A.; Delaye, L.; Lowy, E.; Mentaberry, A.; Vianello-Brondani, R.P.; García, J.L.; Alioto, T.; Sánchez, F.; Himmelbauer, H.; Santalla, M.; Notredame, C.; Gabaldón, T.; Herrera-Estrella, A.; Guigó, R.
Filiación:Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona, 08003, Spain
Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona, 08003, Spain
Yeast and Basidiomycete Research Group, CBS Fungal Biodiversity Centre, Uppsalalaan 8, Utrecht, 3584 LT, Netherlands
Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, Irapuato Guanajuato, CP 36821, Mexico
Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia
New York Genome Center, 101 Avenue of the Americas, New York, NY 10013, United States
IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra Barcelona Catalonia, 08193, Spain
Instituto de Agrobiotecnología Rosario (INDEAR), Rosario Santa Fe, 2000, Argentina
Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, Vienna, 1190, Austria
University of Brasilia, Biological Science Institute, Department of Cellular Biology, Brasília DF, 70790-160, Brazil
Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona Catalonia, 08003, Spain
CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona, 08003, Spain
Instituto de Biotecnología y Biología Molecular (IBBM), UNLP-CONICET, La Plata, 1900, Argentina
Universidad Nacional Autónoma de México, Departamento de Botánica, Instituto de Biología, Mexico City, 04510, Mexico
Unidad Irapuato, Cinvestav, Departamento de Ingeniería Genética, Irapuato Guanajuato, 36821, Mexico
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge, CB10 1SD, United Kingdom
Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), C1428EGA, Buenos Aires, Argentina
EMBRAPA Rice and Beans, Biotechnology Laboratory, Santo Antônio de Goiás GO, 75375-000, Brazil
Environmental Biology Department, Centro de Investigaciones Biológicas, (CSIC), Madrid, 28040, Spain
Universidad Nacional Autónoma de México, Depto. de Biología Molecular de Plantas, Instituto Biotecnología, Cuernavaca Morelos, 62210, Mexico
Mision Biológica de Galicia (MBG)-National Spanish Research Council (CSIC), Pontevedra, 36080, Spain
Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, Barcelona, 08010, Spain
IMIM (Hospital del Mar Medical Research Institute), Barcelona, 08003, Spain
Palabras clave:BAT93; Common bean; Gene duplication; LncRNAs; Tissue expression; Transcriptome; long untranslated RNA; transcriptome; microsatellite DNA; plant DNA; transcriptome; Article; controlled study; fruit development; gene duplication; gene expression; genetic transcription; genetic variability; genome analysis; genotype; nonhuman; Phaseolus vulgaris; phylogenomics; plant evolution; plant genome; plant seed; pod; transcriptomics; DNA sequence; gene duplication; gene expression profiling; genetics; human; Phaseolus; phylogeny; DNA, Plant; Gene Duplication; Gene Expression Profiling; Genome, Plant; Genotype; Humans; Microsatellite Repeats; Phaseolus; Phylogeny; Seeds; Sequence Analysis, DNA; Transcriptome
Año:2016
Volumen:17
Número:1
DOI: http://dx.doi.org/10.1186/s13059-016-0883-6
Título revista:Genome Biology
Título revista abreviado:Genome Biol.
ISSN:14747596
CODEN:GNBLF
CAS:DNA, Plant
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_14747596_v17_n1_p_Vlasova

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Citas:

---------- APA ----------
Vlasova, A., Capella-Gutiérrez, S., Rendón-Anaya, M., Hernández-Oñate, M., Minoche, A.E., Erb, I., Câmara, F.,..., Guigó, R. (2016) . Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes. Genome Biology, 17(1).
http://dx.doi.org/10.1186/s13059-016-0883-6
---------- CHICAGO ----------
Vlasova, A., Capella-Gutiérrez, S., Rendón-Anaya, M., Hernández-Oñate, M., Minoche, A.E., Erb, I., et al. "Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes" . Genome Biology 17, no. 1 (2016).
http://dx.doi.org/10.1186/s13059-016-0883-6
---------- MLA ----------
Vlasova, A., Capella-Gutiérrez, S., Rendón-Anaya, M., Hernández-Oñate, M., Minoche, A.E., Erb, I., et al. "Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes" . Genome Biology, vol. 17, no. 1, 2016.
http://dx.doi.org/10.1186/s13059-016-0883-6
---------- VANCOUVER ----------
Vlasova, A., Capella-Gutiérrez, S., Rendón-Anaya, M., Hernández-Oñate, M., Minoche, A.E., Erb, I., et al. Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes. Genome Biol. 2016;17(1).
http://dx.doi.org/10.1186/s13059-016-0883-6