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شناسایی تنوع تعداد کپی و تأثیرات آنها بر ژن‌های شترهای تک‌کوهانه ایرانی با استفاده از داده‌های ‏توالی‌یابی کامل ژنوم

نوع مقاله : مقاله پژوهشی

نویسندگان

1 دانش‌آموختۀ دکتری، گروه علوم دامی، دانشکده علوم دامی و شیلات، دانشگاه علوم کشاورزی و منابع طبیعی ساری، ‏ساری، ایران

2 دانشیار، گروه علوم دامی، دانشکده کشاورزی و منابع طبیعی، دانشگاه محقق اردبیلی، اردبیل، ایران

3 دانشیار، گروه علوم دامی، دانشکده علوم دامی و شیلات، دانشگاه علوم کشاورزی و منابع طبیعی ساری، ساری، ایران

4 دانشیار، گروه علوم دام و طیور، پردیس ابوریحان، دانشگاه تهران، پاکدشت، ایران

چکیده

مطالعه حاضر به‌منظور شناسایی تنوع تعداد کپی و بررسی اثرات آنها بر ژن‌های شترهای تک‌کوهانه با استفاده از داده‌های توالی‌یابی کامل ژنومی دو نفر شتر ایرانی (شتر یزدی و شتر طرودی) انجام شد. توالی‌یابی کامل ژنوم نمونه‌های یزدی و طرودی، به ترتیب حدود 456 و 8/418 میلیون خوانش با اندازه 100 جفت‌بازی تولید کرد. پس از هم‌ردیفی خوانش‌های پالایش شده در ژنوم مرجع (شماره دسترسی در NCBI: GCA_000767585.1)، از الگوریتم مبتنی بر عمق خوانش، برای شناسایی تنوع تعداد کپی‌ها استفاده شد. تنوع تعداد کپی شناسایی‌شده برای نمونه‌های موردمطالعه برابر با 831 برای شتر یزدی و 312 برای شتر طرودی بود. نزدیک به 60 درصد (606 ژن برای شتر یزدی و 288 ژن برای شتر طرودی) از تنوعات شناسایی‌شده، با ژن‌ها دارای تداخل بودند و ما بقی در نواحی خارج ژنی قرار داشتند. نتایج به‌دست‌آمده نشان داد که ژن‌های مهمی از جمله ژن‌های دخیل در عملکرد سیستم ایمنی و مرگ سلولی برنامه‌ریزی‌شده دارای تنوع تعداد کپی هستند. همچنین دو ژن مهم OOEP و WWC3 که در عملکرد تولیدمثلی پستانداران نقش دارند، در نمونه‌های مورد مطالعه دارای تنوع تعداد کپی بودند.

کلیدواژه‌ها


عنوان مقاله [English]

Identification the copy number variation and its impacts on the genes of Iranian dromedary ‎camels using whole genome sequencing data

نویسندگان [English]

  • Reza Khalkhali-Evrigh 1
  • Nemat Hedayat-Evrigh 2
  • Hassan Hafezian 3
  • Ayoub Farhadi 3
  • Mohammad reza Bakhtiarizadeh 4
1 Former Ph.D. Student, Department of Animal Science, Faculty of Animal Science and Fisheries, Sari ‎Agricultural Sciences and Natural Resources University, Sari, Iran
2 Associate Professor, Department of Animal Science, Faculty of Agriculture and Natural Resources, University of Mohaghegh ‎Ardabili, Ardebil, Iran
3 Associate Professor, Department of Animal Science, Faculty of Animal Science and Fisheries, Sari Agricultural Sciences and ‎Natural Resources University, Sari, Iran
4 Associate Professor, Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Pakdasht, Iran
چکیده [English]

The present study was performed to identify the copy number variations and their impacts on the genes of dromedary camels using whole genome sequencing data of two Iranian dromedary camels (Yazdi camel and Trodi camel). Whole genome sequencing of the Yazdi and Trodi samples produced about 456 and 418.8 paired-end reads with a read length of 100 bp, respectively. After mapping of trimmed reads to reference genome (NCBI accession number: GCA_000767585.1), a read-depth based algorithm was used to identify copy number variations. Identified copy number variations of studied samples, were 831 for Yazdi and 312 for Trodi camels. Nearly 60% (606 genes for Yazdi and 288 for Trodi camel) of the identified variants overlapped with the genes, and the rest were in the none genic regions. The obtained results showed that important genes including genes involved in immune system function and programmed cell death have copy number variation. As well as, two important genes of studied samples, OOEP and WWC3, which are involved in mammalian reproductive function, had copy number variation.

کلیدواژه‌ها [English]

  • gene ontology
  • Genomics
  • Next generation sequencing
  • reproduction
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