Study of structural diversity of genome Iranian native dog and wolf with the method whole genome sequencing

Document Type : Research Paper

Authors

1 Ph.D. Student of Animal Breeding, Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran and Yang Reseaechers Society, Shahid Bahonar University of Kerman, Kerman, Iran

2 Professor, Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran

3 Associat Professor, Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran

Abstract

In this research, samples were collected from three Iranian native dogs and three wolves. Whole-genome sequencing for each individual was performed using next-generation sequencing technology. All short reads were aligned to the reference genome using BWA tool. Single-nucleotide polymorphisms (SNPs) and small insertions and deletions (Indels) were detected using the genome analysis toolkit (GATK). Structural variants were predicted using the BreakDancer software. Annotating single-nucleotide polymorphisms and small insertions and deletions was done using SnpEff Software. Nucleotide diversity values in dogs and wolves samples were calculated using VCFtools. In current researche, 12459651 SNPs were detected that 7819789 and 10454994 were for dog and wolf, respectively. Of the total number of Single-nucleotide polymorphisms, 53.57%, 31.989% and 0.811% were located within intergenic, introns and exon regions. The results showed that structural diversity of wolf genome is higher than that in dog.

Keywords

References

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Iranian Journal of animal Science
Volume 47, Issue 2 - Serial Number 2
October 2016
Pages 271-277

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History

  • Receive Date: 26 January 2016
  • Revise Date: 28 March 2016
  • Accept Date: 17 May 2016

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