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The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics

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dc.contributor.author Gopalakrishnan, Shyam
dc.contributor.author Samaniego Castruita, Jose A.
dc.contributor.author Strander Sinding, Mikkel Holger
dc.contributor.author Kuderna, Lukas F.K.
dc.contributor.author Petersen, Bent
dc.contributor.author Sicheritz-Ponten, Thomas
dc.contributor.author Larson, Greger
dc.contributor.author Orlando, Ludovic
dc.contributor.author Marquès i Bonet, Tomàs, 1975-
dc.contributor.author Hansen, Anders J.
dc.contributor.author Dalén, Love
dc.contributor.author Gilbert, M Thomas
dc.date.accessioned 2017-11-14T16:22:40Z
dc.date.available 2017-11-14T16:22:40Z
dc.date.issued 2017
dc.identifier.citation Gopalakrishnan S, Samaniego Castruita JA, Sinding MS, Kuderna LFK, Räikkönen J, Petersen B et al. The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics. BMC Genomics. 2017; 18(1):495. DOI: 10.1186/s12864-017-3883-3
dc.identifier.issn 1471-2164
dc.identifier.uri http://hdl.handle.net/10230/33223
dc.description.abstract Background: An increasing number of studies are addressing the evolutionary genomics of dog domestication, principally through resequencing dog, wolf and related canid genomes. There is, however, only one de novo assembled canid genome currently available against which to map such data - that of a boxer dog (Canis lupus familiaris). We generated the first de novo wolf genome (Canis lupus lupus) as an additional choice of reference, and explored what implications may arise when previously published dog and wolf resequencing data are remapped to this reference. Results: Reassuringly, we find that regardless of the reference genome choice, most evolutionary genomic analyses yield qualitatively similar results, including those exploring the structure between the wolves and dogs using admixture and principal component analysis. However, we do observe differences in the genomic coverage of re-mapped samples, the number of variants discovered, and heterozygosity estimates of the samples. Conclusion: In conclusion, the choice of reference is dictated by the aims of the study being undertaken; if the study focuses on the differences between the different dog breeds or the fine structure among dogs, then using the boxer reference genome is appropriate, but if the aim of the study is to look at the variation within wolves and their relationships to dogs, then there are clear benefits to using the de novo assembled wolf reference genome.
dc.description.sponsorship Carlsbergfondet grant CF14–0995 and Marie Curie grant 655732-Wherewolf to SG, Danish National Research Foundation grant DNRF94, Lundbeckfonden grant R52–5062 and ERC Consolidator Grant (681396-Extinction Genomics) (to MTPG) and the Swedish Research Council (to LD). LFKK is supported by an FPI fellowship associated to BFU2014–55090-P (FEDER). TMB is supported by MINECO BFU2014–55090-P (FEDER), Fundacio Zoo Barcelona and Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya. GL was supported by a European Research Council grant (ERC-2013-StG-337574-UNDEAD) and Natural Environmental Research Council grants (NE/K005243/1 and NE/K003259/1).
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher BioMed Central
dc.relation.ispartof BMC Genomics. 2017; 18(1):495
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.uri http://creativecommons.org/licenses/by/4.0/
dc.title The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1186/s12864-017-3883-3
dc.subject.keyword Canis lupus
dc.subject.keyword Evolutionary genomics
dc.subject.keyword Genome
dc.subject.keyword Wolf
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/681396
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/655732
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/337574
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2014–55090-P
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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