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

- Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication.
- Background: Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication.
- 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..
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- Full list of author information is available at the end of the article.
- The dog (Canis familiaris) was likely the first domesti- cated animal and the only one humans’ friend in the past [21, 71].
- In the Southwest Asia, major–scale farming extended within the so- named Fertile Crescent (FC) where the independent do- mestication of plants and animals had led to shifting from gathering and hunting to sedentary farming follow- ing expansion of the first complex societies [23, 78]..
- Mostly, agricultural developments happened in the east- ern horn of FC especially Elam (covering a region of southern Iraq and Iran), joining Mesopotamia and Iran- ian plateau [5].
- There- fore, one of the most theories about the geographical origin of the domestic dog has been that they originated in Southwest Asia, presumably in the FC [21].
- One of the sequenced dogs, Qahderijani, is a mastiff ecotype dog originating in Qahderijan, Iran, which is located in FC belt (surround- ing areas of FC).
- Saluki is also considered as one of the long-marathon runner dog breeds in the world, as its incredible endurance enables it to run for several miles..
- In our analysis of the Iranian dog and wolf sequences, we applied assembly version canFam3.1 as a reference sequence [43].
- The potentially breed-specific CNVRs were defined and the functional relation of the SV and CNVR-covering genes was further evaluated by GO enrichment analysis..
- Genome-wide analysis indicates more genetic diversity in the dog genome than that in the wolf genome.
- The genomic annotation results from different variation types proposed increasing the percentage of genomic varia- tions in the coding and the regulatory regions than that in the intron and intergenic regions during domestica- tion, which is substantial contributor to the currently detected differences between dog and wolf.
- Our results indicate that most of the SNPs are located in the intergenic (53.57%) and intron (31.99%) regions (Additional file 1:.
- The results showed that the Indels of 1 bp in length across the 6 individual genomes had the highest frequency and the de- letions of the same size were more frequent than the in- sertions.
- According to our annotation results (Additional file 1: Table S8), most of the Indels are located in inter- genic and intron regions .
- GO analysis catego- rized genes related to small Indels in the three main classes (molecular function, biological process and cellular component) (Additional file 1: Table S9).
- For all of the autosomal CNVs categorized as gain, the mean copy number value of six individuals was 3.57 and the maximum copy num- ber assessment was 174.472 on chromosome 7 (chr7) of wolf.
- The results showed that the number of gains in the three dog genomes was higher than those in the three wolf genomes (Additional file 1: Table S13).
- Deletion:duplication ratio in the total CNVRs was 1.96.
- a Only enriched in the Saluki dog breed.
- A number of CNVR events were less than 10 Kb while of the CNVRs were longer than 50 kb in size (Table 2 and Fig.
- 6%) and 3′-UTR (6% vs 0) region in the dog genome was greatly higher than that in the wolf genome, but the percentage of CNVs in the intergenic regions (22% vs.
- 14%) in wolf genome was greatly higher than that in the dog genome (Additional file 1: Figs.
- A total of 8595 genes were retrieved, including 6703 of the CNVs.
- All the terms related to olfactory system are over-represented (P-value <0.01) in the wolf compared with those in the dog (Additional file 1: Table S14 and Table 1).
- The term “Starch and sucrose metabol- ism (P-value, 0.01)” is enriched in the dog CNV gains (Table 1).
- “ATP binding (P-value, 3.46E- 04)” and “calcium ion binding (P-value, 0.001)” are enriched among the CNV gains in the Saluki breed (Additional file 1: Table S14)..
- Table 2 Size distribution of the CNVRs detected by CNVnator.
- Analysis of high-quality next-generation sequencing data clearly showed the difference of the distribution and im- pact of the genomic variations between dog and wolf.
- Our finding revealed the high precision of the identification of single-nucleotide mutations in this research.
- In addition, the results of this research, similar to previous study [62], showed that most of the SNPs are located within introns or between genes, and the number of synonymous SNPs was higher than non-synonymous SNPs.
- 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.
- We detected 10,571 CNVRs with a mean of 4143.83 CNVs per sample in the canine genome.
- This may mirror the greater relative hardness of identifying gains because of the smaller relative alteration in copy number (3,2 versus 2,1).
- and showed a high percentage of the CNVRs..
- In one another study, no difference in the olfactory capacity of the dog breeds, which have been chosen for their smelling ability and the hand-breaded grey wolves, was reported [54].
- Six of the GO terms belonged to CNV gain regions in this study are also similar to those that were presented using aCGH method in dog [12]..
- were only enriched in the CNV gain regions in Saluki dog breed.
- These results can be expected because Saluki is a hunting dog breed which is considered as the long marathon runner of the canine world and its incredible endurance enables the dog to run for many miles [4, 48]..
- Also in dog, a more recent study has re- ported specific CNVs related to hunting in the BRA breed [26].
- This compatibility with the previ- ous studies, in conjunction with the identification of the CNVs specific to the Saluki breed, lends more support to the CNVs identified in this work.
- The difference be- tween the CNVs detected in the study herein and those described previously can be related to the particular breeds studied and also the difference between the methods used.
- The total numbers of SNPs (10.45 million vs 7.82 mil- lion), Indels (3.11 million vs 2.24 million), deletions (18, 628 vs 13,059), inversions (401 vs 334), inter (706 vs 520) and intra (421 vs 359) chromosomal translocations re- gions were higher in the wolf genome than those in the dog genome, while the total number of CNVs located at gain (2277 vs 521) and insertions (352 vs 311) regions in the dog genome were higher than those in the wolf gen- ome.
- Our results from genome analysis for dog and wolf re- vealed reduction of the genomic diversity during dog do- mestication.
- A population bottleneck occurred in the wolves thousand years ago after a population expansion occurred by human through artificial selection on specific traits leading to different breeds of dogs [3, 30].
- primal ancestors of recent dogs to live on a diet with high starch compared to the carnivorous diet of wolves, which is an essential step in the primal domestication of dogs .
- was enriched among SVs in wolf and is indicative of redu- cing aggression in the first steps of animal domestication [70].
- It seems that domestication and its related processes such as relaxed selection have an important role in in- creasing the percentage of genomic variation in the cod- ing and the regulatory sequences of dog genome.
- The relaxation of selection likely increases the functional genetic diversity throughout the genome of the dog and this diversity includes both the genes and the elements involved in gene expression [14, 25].
- Also, it has been suggested that after domestication some subtle sources of genomic diversification such as changes in the inter- actions among genes products and in the timing of gene expression may have influenced the diversity of the forms observed in the domestic dog [17, 70].
- To better acknowledge this result, there is still the need for using mate pair sequences or merging long-insert mate pair and short-insert paired-end sequences to analyze the dog and wolf genomes and elucidate the difference of the distribution and impact of the genomic variations between dog and wolf during dog domestication.
- We resequenced the whole genomes of 6 canids from the Middle East for the first time and we compared the effect and distribution of the genomic variations between dog and wolf genomes.
- Downstream analysis of the identified SVs and CNVs revealed the changes between dog and wolf genome during dog domestication..
- The sources of the animals used in this study were as follow: one wolf was sampled from Kerman zoo, South of Iran, two wolves were used from Eram Park Zoo, Tehran, Iran.
- S19) with the consent of the owners.
- The quality of the reads was evaluated with FastQC program and outputs of quality control showed that all reads had high-quality and were without adaptor contamination.
- All of the .bam files were cleaned from PCR duplicates with Picard program.
- To compare the putative CNVRs from this study with the CNVRs reported in the previous studies, all coordinates related to CNVRs of the previous studies were converted.
- Statistics of the detected CNVs for Canine autosomes and X chromosome..
- ZAG prepared the genomic DNAs of the six samples.
- ZAG drafted the first version of the manuscript.
- All authors have read and approved the final version of the manuscript..
- 91531303), the international cooperation program of bureau of international cooperation of Chinese Academy of Sciences (No.GJHZ1559), and the Animal Branch of the Germplasm Bank of Wild Species, Chinese Academy of Sciences (the Large Research Infrastructure Funding).
- The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript..
- We obtained written informed consent to use the ani- mals in this study from the owners of the animals..
- Written informed consent for publication was obtained from all of the participants..
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