Iranian Journal of animal Science

Iranian Journal of animal Science

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

Document Type : Research Paper

Authors
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
10.22059/ijas.2020.294708.653761
Abstract
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.
Keywords
Gene ontology
genomics
next generation sequencing
reproduction
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Iranian Journal of animal Science
Volume 51, Issue 2
Summer 2020
Pages 113-119

  • Receive Date 29 December 2019
  • Revise Date 27 May 2020
  • Accept Date 15 June 2020