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.
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 |