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بررسی تنوع ساختاری ژنگان سگ و گرگ بومی ایران با روش توالی‌یابی کل ژنوم

نوع مقاله: مقاله پژوهشی

نویسندگان

1 دانشجوی دکتری اصلاح نژاد دام، بخش مهندسی علوم دامی، دانشکدة کشاورزی، دانشگاه شهید باهنر کرمان، کرمان، ایران و عضو انجمن پژوهشگران جوان، دانشگاه شهید باهنر کرمان

2 استاد، بخش مهندسی علوم دامی، دانشکدة کشاورزی، دانشگاه شهید باهنر کرمان، کرمان، ایران

3 دانشیار، بخش مهندسی علوم دامی، دانشکدة کشاورزی، دانشگاه شهید باهنر کرمان، کرمان، ایران

چکیده

در این پژوهش، از سه قلاده سگ و سه قلادة گرگ بومی ایران نمونه­گیری شد. توالی­یابی کل ژنگان (ژنوم) برای هر نمونه سگ و گرگ با استفاده از روش توالی‌یابی نسل جدید انجام شد. داده­ها توسط برنامة BWA با ژنگان مرجع (رفرنس) همردیف شدند. چندریختی‌های تک نوکلئوتیدی و حذف و اضافه­های کوچک ژنگان با برنامة GATK  شناسایی شد­ند. تغییرپذیری (واریانت)­های ساختاری با برنامة  BreakDancer-1.1تعیین شدند. مستندسازی چندریختی­های تک نوکلئوتیدی و حذف و اضافه­های کوچک ژنگان با برنامةSnpEff  انجام شد. مقادیر تنوع نوکلئوتیدی در نمونه­های سگ و گرگ با VCFtools  محاسبه شد­ند. در این پژوهش 12459651 چندریختی تک نوکلئوتیدی به دست آمد که 7819789 و 10454994 به ترتیب مربوط به نمونه‌های سگ و گرگ بودند. از شمار کل چندریختی­های تک نوکلئوتیدی 57/53، 989/31 و 811/0 درصد به ترتیب در ناحیة بین ژنی، اینترون و اگزون قرار گرفتند. نتایج تجزیه‌وتحلیل داده‌ها نشان داد که تنوع ساختاری در ژنگان گرگ بیشتر از سگ است.

کلیدواژه‌ها


عنوان مقاله [English]

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

نویسندگان [English]

  • 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
چکیده [English]

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.

کلیدواژه‌ها [English]

  • Single-nucleotide polymorphism
  • small insertions and deletions
  • structural variant
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