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

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.

Genome-Wide Identification and Analysis of Variants in Domestic and Wild Bactrian Camels Using Whole-Genome Sequencing Data

“…The heterozygote to homozygote SNP ratio in DC399 (1.75), DC408 (1.79), and Bac2 (1.82) was close, while this value was 3.77 for Bac1. This result was consistent with our previous work on the Iranian dromedary camel which showed higher heterozygosity in them [15]. Based on the microsatellite data, there is introgression between Bactrian and dromedary camels in Iran [6]; therefore, observing higher heterozygosity in a portion of the Iranian camel's population is not unexpected.…”

“…Annotation results revealed that most portion of the discovered variants throughout the genome of Bactrian camels (more than 88 percent) are located in the intergenic and intronic regions. Our results were consistent with these values for Iranian (87.7% for SNPs, 88.9% for INDELs) and African dromedary camels (88% for SNPs, 89.1% for INDELs; [15]).…”

“…Here, we considered common homozygote SNPs among domestic Bactrian camels as fixed SNPs for them, if these variants were absent in the genome of both wild Bactrian camels. It is likely that human selection after domestication is the cause of the fixation of these alleles in domestic Bactrian camels [15]. According to the mentioned criteria, we found 43,944 SNPs, and 16,201 of them were located in the genic region and affected 3,405 genes (Supplementary 1).…”

“…Marking duplication was performed using Picard (http://broadinstitute.github.io/picard), and GATK [13] was used for local realignment and base quality score recalibration. We used SAMtools [14] to call SNPs and INDELs for individuals and called variants filtered as described by Khalkhali-Evrigh et al [15].…”

“…Due to the flexibility of SnpEff [16] to annotate genomic variants of animals without a database, we selected it for annotation of identified variants in the present work. Similar to our previous project on dromedary camels [15], due to the lack of database for Bactrian camels among the prebuilt databases for SnpEff, we built a database for Bactrian camels using the Bactrian reference genome and its GFF file using the database building guidelines (http://snpeff.sourceforge.net/ SnpEff_manual.html#databases) in SnpEff.…”