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. 2017 Jun 29;18(1):495.
doi: 10.1186/s12864-017-3883-3.

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

Shyam Gopalakrishnan  1 , Jose A Samaniego Castruita  1 , Mikkel-Holger S Sinding  1   2 , Lukas F K Kuderna  3   4 , Jannikke Räikkönen  5 , Bent Petersen  6 , Thomas Sicheritz-Ponten  6 , Greger Larson  7 , Ludovic Orlando  1 , Tomas Marques-Bonet  3   4   8 , Anders J Hansen  1 , Love Dalén  9 , M Thomas P Gilbert  10   11   12
Affiliations

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

Shyam Gopalakrishnan et al. BMC Genomics. .

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.

Keywords: Canis lupus; Evolutionary genomics; Genome; Wolf.

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Not applicable.

Competing interests

The authors declare that they have no competing interests.

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Figures

Fig. 1
Fig. 1
Principal components analysis comparing the first two PCs when using the wolf or the dog reference genome. The left panel shows the principal components analysis when using the variants obtained from mapping to the dog genome, and the right panel shows the same when using variants obtained from mapping to the wolf genome
Fig. 2
Fig. 2
Effective population sizes estimated using PSMC. The left panel shows the effective population sizes for dogs in the Wang dataset, estimated using the data mapped to both the reference genomes. The right panel shows the population size estimates for the wolves in the Wang dataset, when using the data mapped to both the reference genomes
Fig. 3
Fig. 3
Admixture plot showing the estimated ancestry components. The plots on the left, panel a, show the estimates obtained when the dog reference genome is used, whereas the figures on the right, panel b, were obtained using the wolf reference genome
See this image and copyright information in PMC

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