Department of Animal Breeding and Genetics, Sari Agricultural Sciences and Natural Resources University, Sari, Iran.
Department of Animal Science, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran.
PLoS One. 2018 Sep 20;13(9):e0204028. doi: 10.1371/journal.pone.0204028. eCollection 2018.
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.
对骆驼全基因组范围内的遗传变异进行全面鉴定和注释尚处于起步阶段。本研究旨在利用 3 只单峰驼的全基因组测序数据，鉴定全基因组范围内的变异、对其进行功能注释，并对受影响基因进行富集分析。对 2 只主要用于生产肉和奶的伊朗雌性单峰驼进行测序，测序深度分别达到 41.9 倍和 38.6 倍。通过将原始读数映射到单峰驼参考组装（GenBank 访问号：GCA_000767585.1），共发现 4727238 个单核苷酸多态性（SNP）和 692908 个插入/缺失（插入和缺失）。在所研究样本中对发现的变异进行的计算机功能注释表明，大多数 SNP（2305738；48.78%）和插入/缺失（339756；49.03%）位于基因间区。将鉴定的 SNP 与非洲骆驼（BioProject 访问号：PRJNA269274）的 SNP 进行比较，发现它们有 993474 个 SNP 是共有的。在 3 只骆驼共享变异中发现了 15168 个非同义 SNP，这些 SNP 可能会影响基因功能和蛋白质结构。结果表明，在 Yazd 单峰驼、Trod 单峰驼和非洲单峰驼的 3436、3058 和 2882 个特定基因集中，分别有 7085、6271 和 4688 个非同义 SNP。对不同个体中预测受非同义变异影响的基因列表进行了基因本体论（GO）富集分析。
