The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics
Posted on 2017-06-29 - 05:00
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.
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Gopalakrishnan, Shyam; Samaniego Castruita, Jose; Sinding, Mikkel-Holger; Kuderna, Lukas; RäikkÜnen, Jannikke; Petersen, Bent; et al. (2017). The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics. figshare. Collection. https://doi.org/10.6084/m9.figshare.c.3815656.v1
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AUTHORS (13)
SG
Shyam Gopalakrishnan
JS
Jose Samaniego Castruita
MS
Mikkel-Holger Sinding
LK
Lukas Kuderna
JR
Jannikke RäikkÜnen
BP
Bent Petersen
TS
Thomas Sicheritz-Ponten
GL
Greger Larson
LO
Ludovic Orlando
TM
Tomas Marques-Bonet
AH
Anders Hansen
LD
Love DalĂŠn
MG
M. Gilbert