Iranian Journal of animal Science

Iranian Journal of animal Science

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

Document Type : Research Paper

Authors
Zeinab Amirighanatsaman 1
Ali Esmailizadeh Koshkoiyeh 2
Masood Asadi Fozi 3
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
10.22059/ijas.2016.59032
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
Single-nucleotide polymorphism
small insertions and deletions
structural variant
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Iranian Journal of animal Science
Volume 47, Issue 2 - Serial Number 2
Autumn 2016
Pages 271-277

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