TY - JOUR
T1 - The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics
AU - Gopalakrishnan, Shyam
AU - Samaniego Castruita, Jose Alfredo
AU - Sinding, Mikkel Holger Strander
AU - Kuderna, Lukas F. K.
AU - Räikkönen, Jannikke
AU - Petersen, Bent
AU - Sicheritz-Pontén, Thomas
AU - Larson, Greger
AU - Orlando, Ludovic Antoine Alexandre
AU - Marques-Bonet, Tomas
AU - Hansen, Anders Johannes
AU - Dalén, Love
AU - Gilbert, Tom
PY - 2017
Y1 - 2017
N2 - 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.
AB - 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.
KW - Canis lupus
KW - Evolutionary genomics
KW - Genome
KW - Wolf
U2 - 10.1186/s12864-017-3883-3
DO - 10.1186/s12864-017-3883-3
M3 - Journal article
C2 - 28662691
AN - SCOPUS:85021348818
SN - 1471-2164
VL - 18
JO - BMC Genomics
JF - BMC Genomics
M1 - 495
ER -