Genetic variants analysis of three dromedary camels using whole genome sequencing data

Reza Khalkhali-Evrigh; Seyed Hasan Hafezian; Nemat Hedayat-Evrigh; Ayoub Farhadi; Mohammad Reza Bakhtiarizadeh

doi:10.1371/journal.pone.0204028

Genetic variants analysis of three dromedary camels using whole genome sequencing data

PLoS One. 2018 Sep 20;13(9):e0204028. doi: 10.1371/journal.pone.0204028. eCollection 2018.

Authors

Reza Khalkhali-Evrigh¹, Seyed Hasan Hafezian¹, Nemat Hedayat-Evrigh², Ayoub Farhadi¹, Mohammad Reza Bakhtiarizadeh³

Affiliations

¹ Department of Animal Breeding and Genetics, Sari Agricultural Sciences and Natural Resources University, Sari, Iran.
² Department of Animal Science, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran.
³ Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Pakdasht, Iran.

Abstract

Whole genome wide identification and annotation of genetic variations in camels is in its first steps. The aim of this study was the identification of genome wide variants, functional annotations of them and enrichment analysis of affected genes using whole genome sequencing data of three dromedary camels. The genomes of two Iranian female dromedary camels that mostly used to produce meat and milk were sequenced to 41.9-fold and 38.6-fold coverage. A total of 4,727,238 single-nucleotide polymorphisms (SNPs) and 692,908 indels (insertions and deletions) were found by mapping raw reads to the dromedary reference assembly (GenBank Accession: GCA_000767585.1). In-silico functional annotation of the discovered variants in under study samples revealed that most SNPs (2,305,738; 48.78%) and indels (339,756; 49.03%) were located in intergenic regions. A comparison of the identified SNPs with those of the African camel (BioProject Accession: PRJNA269274) indicated that they had 993,474 SNPs in common. We found 15,168 non-synonymous SNPs in the shared variants of the three camels that could affect gene function and protein structure. Obtained results revealed that there were 7085, 6271 and 4688 non-synonymous SNPs among the 3436, 3058 and 2882 genes in the specific gene sets of Yazd dromedary, Trod dromedary and African dromedary, respectively. The list of genes predicted to be affected by non-synonymous variants in different individuals was subjected to gene ontology (GO) enrichment analysis.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Camelus / genetics*
Female
Genome*
High-Throughput Nucleotide Sequencing
Polymorphism, Single Nucleotide*
Whole Genome Sequencing

Grants and funding

This work was supported by the University of Mohaghegh Ardabili and the Sari Agricultural Sciences and Natural Resources University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.