Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication

Abstract

Background: Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and three dogs from Iran which covers the eastern part of the Fertile Crescent located in Southwest Asia where the independent domestication of most of the plants and animals has been documented and also high haplotype sharing between wolves and dog breeds has been reported.

Results: Higher diversity was found within the wolf genome compared with the dog genome. A total number of 12.45 million SNPs were detected in all individuals (10.45 and 7.82 million SNPs were identified for all the studied wolves and dogs, respectively) and a total number of 3.49 million small Indels were detected in all individuals (3.11 and 2.24 million small Indels were identified for all the studied wolves and dogs, respectively). A total of 10,571 copy number variation regions (CNVRs) were detected across the 6 individual genomes, covering 154.65 Mb, or 6.41%, of the reference genome (canFam3.1). Further analysis showed that the distribution of deleterious variants in the dog genome is higher than the wolf genome. Also, genomic annotation results from intron and intergenic regions showed that the proportion of variations in the wolf genome is higher than that in the dog genome, while the proportion of the coding sequences and 3'-UTR in the dog genome is higher than that in the wolf genome. The genes related to the olfactory and immune systems were enriched in the set of the structural variants (SVs) identified in this work.

Conclusions: Our results showed more deleterious mutations and coding sequence variants in the domestic dog genome than those in wolf genome. By providing the first Iranian dog and wolf variome map, our findings contribute to understanding the genetic architecture of the dog domestication.

Keywords: Copy number variant; Fertile crescent; Single nucleotide variant; Structural variant.

Fig. 1

The proportion of SNPs present in each genomic regions, including intergenic, introns, exon, transcript, upstream, downstream, three prime untranslated regions (3′-UTR) and five prime untranslated

Fig. 2

The length and distribution of CNVRs. a a total of 6702 (63.39%) and 494 (4.67%) out of all CNVRs had sizes ranging from 1.049 to 10 kb and longer than 50 kb in size, respectively. b 4466 (42.25%) CNVRs are shared in at least two individuals and 6105 (57.75%) CNVRs present in only one individual

Fig. 3

Graphical visualization of predicted SVs for dog and wolf. Starting from outside of the circle, the following features are shown: chromosome ideograms, heatmap plot of copy number variation with color according to the CNV value computed by CNVnator, genomic locations of tandem duplications, genomic locations of inversions and genomic locations of intra and inter- chromosomal links

Fig. 4

The proportion of deleterious mutations in wolf and dog chromosomes