Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes

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• dc.contributor.author Vlasova, Annaca
• dc.contributor.author Capella Gutiérrez, Salvador Jesús, 1985-ca
• dc.contributor.author Erb, Ionasca
• dc.contributor.author Cámara, Franciscoca
• dc.contributor.author Prieto Barja, Pablo, 1986-ca
• dc.contributor.author Kedra, Darekca
• dc.contributor.author González Navarrete, Irene, 1983-ca
• dc.contributor.author Cozzuto, Lucaca
• dc.contributor.author Gómez Garrido, Jèssicaca
• dc.contributor.author Aguilar Morón, María Asunciónca
• dc.contributor.author Andreu Somavilla, Núriaca
• dc.contributor.author Zehnsdorf, Maikca
• dc.contributor.author Alioto, Tylerca
• dc.contributor.author Notredame, Cedricca
• dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-ca
• dc.contributor.author Guigó Serra, Rodericca
• dc.date.accessioned 2016-02-25T13:41:46Z
• dc.date.available 2016-02-25T13:41:46Z
• dc.date.issued 2016
• dc.description.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.ca
• dc.description.sponsorship This work was supported by Ibero-American Programme for Science, Technology and Development - CYTED (PhasIbeAm project); Spanish Government - Ministry of Economy and Competitiveness (EUI2009-04052, BIO2011-26205); Brazilian Government — National Council for Scientific and Technological Development - CNPq/Prosul (490725/2010-4) and Brazilian Agricultural Research Corporation - Embrapa (MP2-0212000050000); Ministerio de Ciencia, Tecnología e Innovación Productiva de la República Argentina; the European Molecular Biology Laboratory; Consejo Nacional de Ciencia y Tecnología - Conacyt, Mexico (J010-214-2009) for financial support to undertake parts of research presented in this study. We acknowledge support of the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’, SEV-2012-0208 and Instituto Nacional de Bioinformatica (INB, Project PT13/0001/0021, ISCIII — Subdirección General de Evaluación y Fomento de la Investigación/FEDER “Una Manera de hacer Europa”).
• dc.format.mimetype application/pdfca
• dc.identifier.citation Vlasova A, Capella-Gutiérrez S, Rendón-Anaya M, Hernández-Oñate M, Minoche AE, 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. 2016;17:32. DOI: 10.1186/s13059-016-0883-6ca
• dc.identifier.doi http://dx.doi.org/10.1186/s13059-016-0883-6
• dc.identifier.issn 0927-6467
• dc.identifier.uri http://hdl.handle.net/10230/25947
• dc.language.iso engca
• dc.publisher BioMed Centralca
• dc.relation.ispartof Genome Biology. 2016;17:32
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BIO2011-26205
• dc.rights © 2016 Vlasova et al.Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise statedca
• dc.rights.accessRights info:eu-repo/semantics/openAccessca
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/ca
• dc.subject.keyword Common bean
• dc.subject.keyword BAT93
• dc.subject.keyword Gene duplication
• dc.subject.keyword Tissue expression
• dc.subject.keyword Transcriptome
• dc.subject.keyword lncRNAs
• dc.subject.other Genètica vegetalca
• dc.subject.other Transcripció genèticaca
• dc.title Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genesca
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersionca