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 of 10.45, 7.82, 3.11 and 2.24 million SNPs and small Indels were identified within wolf and dog genomes, 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. The genes related to olfactory and immune systems were enriched in the set of structural variants (SVs) identified in this work. Annotation of genomic variations showed that in general the proportion of genomic variations in the intron and intergenic regions in wolf genome is higher than that in dog genome while their proportion in the coding sequences and 3'-UTR in dog genome is higher than that in wolf genome. Generally, genes engaged in digestion and metabolism and neurological process had an important role in the process of dog domestication. Conclusions By providing the first Iranian dog and wolf variome map, our findings contribute to understanding the genetic architecture of the dog domestication.

Genome Sequencing a Gray Wolf from Peninsular India Provides New Insights into the Evolution and Hybridization of Gray Wolves

“…S7-S9, Supplementary Material online), as well as between IW01 and three more recently reported Iranian wolves (supplementary fig. S10, Supplementary Material online) (Amiri Ghanatsaman et al 2020). Admixture among these lineages is expected, given the lack of reproductive barriers and any major geographic barriers separating these populations.…”

Genome resequencing data for Iranian local dogs and wolves

“…We firstly carried out genome sequencing of six Iranian local canids including two hunting dogs (Saluki breed), a mastiff dog (Qahderijani ecotype) and three wolves (Table 1 ). We used these data for identifying effective genomic variants in dogs and wolves [ 14 ].…”

“…The mapping output files were preprocessed using SAMtools [ 16 ], the Picard tools ( http://broadinstitute.github.io/picard/ ) and GATK tools [ 17 ]. We used variome detection pipeline for this data using CNVnator [ 18 ], BreakDancer [ 19 ], DELLY [ 20 ] and Bedtools [ 21 ] programs [ 14 ]. Finally, we compared the effect of variome between the dog and wolf genomes using Sorting Intolerant from Tolerant (SIFT) algorithm [ 19 ], Ensembl annotation [ 22 ] and DAVID [ 23 ] tool [ 14 ].…”

“…We used variome detection pipeline for this data using CNVnator [ 18 ], BreakDancer [ 19 ], DELLY [ 20 ] and Bedtools [ 21 ] programs [ 14 ]. Finally, we compared the effect of variome between the dog and wolf genomes using Sorting Intolerant from Tolerant (SIFT) algorithm [ 19 ], Ensembl annotation [ 22 ] and DAVID [ 23 ] tool [ 14 ]. The data presented herein together with our previously mitochondrial DNA sequence on Iranian dogs [ 11 ] will provide useful resources to understand genetic structure of the Iranian dogs and testing hypotheses on the dog origin and domestication issues.…”