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

BMC Genomics

Research Article

Jose A. Samaniego Castruita¹  Shyam Gopalakrishnan¹  Anders J. Hansen¹  Ludovic Orlando¹  Mikkel-Holger S. Sinding²  M. Thomas P. Gilbert³  Thomas Sicheritz-Ponten⁴  Bent Petersen⁴  Love Dalén⁵  Jannikke Räikkönen⁶  Lukas F. K. Kuderna⁷  Tomas Marques-Bonet⁸  Greger Larson⁹ 

[1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark;Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark;Natural History Museum, University of Oslo, N-0318, Oslo, Norway;Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark;Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia;NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway;Department of Bio and Health Informatics, Technical University of Denmark, 2800, Kongens Lyngby, Denmark;Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405, Stockholm, Sweden;Department of Environmental Research and Monitoring, Swedish Museum of Natural History, Box 50007, 10405, Stockholm, Sweden;Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003, Barcelona, Spain;CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain;Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003, Barcelona, Spain;CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain;Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain;Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, OX1 3QY, Oxford, UK;

关键词: Canis lupus;    Evolutionary genomics;    Genome;    Wolf;   

DOI  :  10.1186/s12864-017-3883-3

 received in 2016-12-12, accepted in 2017-06-20,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundAn 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.ResultsReassuringly, 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.ConclusionIn 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.

【 授权许可】

CC BY   
© The Author(s). 2017