Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing

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  • dc.contributor.author Serres Armero, Aitor, 1992-ca
  • dc.contributor.author Povolotskaya, Inna, 1986-ca
  • dc.contributor.author Quilez Oliete, Javierca
  • dc.contributor.author Ramírez, Oscarca
  • dc.contributor.author Santpere Baró, Gabriel, 1981-ca
  • dc.contributor.author Kuderna, Lukas, 1989-ca
  • dc.contributor.author Hernández Rodríguez, Jéssica, 1983-ca
  • dc.contributor.author Fernández Callejo, Marcosca
  • dc.contributor.author Gómez Sánchez, Danielca
  • dc.contributor.author Freedman, Adam H.ca
  • dc.contributor.author Fan, Zhenxinca
  • dc.contributor.author Novembre, Johnca
  • dc.contributor.author Navarro i Cuartiellas, Arcadi, 1969-ca
  • dc.contributor.author Boyko, Adamca
  • dc.contributor.author Wayne, Robert K.ca
  • dc.contributor.author Vilà, Carlesca
  • dc.contributor.author Lorente-Galdós, Belén, 1981-ca
  • dc.contributor.author Marquès i Bonet, Tomàs, 1975-ca
  • dc.date.accessioned 2018-02-26T15:13:58Z
  • dc.date.available 2018-02-26T15:13:58Z
  • dc.date.issued 2017
  • dc.description.abstract BACKGROUND: Whole genome re-sequencing data from dogs and wolves are now commonly used to study how natural and artificial selection have shaped the patterns of genetic diversity. Single nucleotide polymorphisms, microsatellites and variants in mitochondrial DNA have been interrogated for links to specific phenotypes or signals of domestication. However, copy number variation (CNV), despite its increasingly recognized importance as a contributor to phenotypic diversity, has not been extensively explored in canids. RESULTS: Here, we develop a new accurate probabilistic framework to create fine-scale genomic maps of segmental duplications (SDs), compare patterns of CNV across groups and investigate their role in the evolution of the domestic dog by using information from 34 canine genomes. Our analyses show that duplicated regions are enriched in genes and hence likely possess functional importance. We identify 86 loci with large CNV differences between dogs and wolves, enriched in genes responsible for sensory perception, immune response, metabolic processes, etc. In striking contrast to the observed loss of nucleotide diversity in domestic dogs following the population bottlenecks that occurred during domestication and breed creation, we find a similar proportion of CNV loci in dogs and wolves, suggesting that other dynamics are acting to particularly select for CNVs with potentially functional impacts. CONCLUSIONS: This work is the first comparison of genome wide CNV patterns in domestic and wild canids using whole-genome sequencing data and our findings contribute to study the impact of novel kinds of genetic changes on the evolution of the domestic dog.
  • dc.description.sponsorship TMB is supported by MINECO BFU2014-55090-P (FEDER), U01 MH106874 grant, Howard Hughes International Early Career, Obra Social "La Caixa" and Secretaria d'Universitats i Recerca del Departament d'Economia i Coneixement de la Generalitat de Catalunya. ISP is supported with a Juan de la Cierva - Formación FJCI-2015-24,275 fellowship. JHR is supported by the Spanish Ministry of Education under FPI grant (BES-2013-064333). BLG is supported with a Beatriu de Pinós (BP-DGR 2014) fellowship.
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Serres-Armero A, Povolotskaya IS, Quilez J, Ramirez O, Santpere G, Kuderna LFK et al. Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing. BMC Genomics. 2017 Dec 19;18(1):977. DOI: 10.1186/s12864-017-4318-x
  • dc.identifier.doi http://dx.doi.org/10.1186/s12864-017-4318-x
  • dc.identifier.issn 1471-2164
  • dc.identifier.uri http://hdl.handle.net/10230/34004
  • dc.language.iso eng
  • dc.publisher BioMed Centralca
  • dc.relation.ispartof BMC Genomics. 2017 Dec 19;18(1):977
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2014-55090-P
  • dc.rights © The Author(s). 2017 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 stated.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.subject.keyword Copy number variation
  • dc.subject.keyword Dog genomics
  • dc.subject.keyword Evolution
  • dc.subject.keyword Domestication
  • dc.title Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencingca
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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