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

Document Type : Research Paper


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


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.


  1. Axelsson, E., Ratnakumar, A., Arendt, M. L., Maqbool, K., Webster, M. T., Perloski, M., Liberg, O., Arnemo, J. M., Hedhammar, Å. & Lindblad-Toh, K. (2013). The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature, 495(7441), 360-366.
  2. Boeva, V., Zinovyev, A., Bleakley, K., Vert, J. P., Janoueix-Lerosey, I., Delattre, O. & Barillot, E. (2010). Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. Bioinformatics, 27(2), 268-269.
  3. Bolger, A. M., Lohse, M. & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114-2120.
  4. Choi, J. W., Liao, X., Park, S., Jeon, H. J., Chung, W. H., Stothard, P., Park, Y. S., Lee, J. K., Lee, K. T., Kim, S. H. & OH, J. D. (2013). Massively parallel sequencing of Chikso (Korean brindle cattle) to discover genome-wide SNPs and InDels. Molecules and Cells, 36(3), 203-211.
  5. Clop, A., Vidal, O. & Amills, M. (2012). Copy number variation in the genomes of domestic animals. Animal Genetics, 43(5), 503-517.
  6. Doan, R., Cohen, N. D., Sawyer, J., Ghaffari, N., Johnson, C. D. & Dindot, S. V. (2012). Whole-genome sequencing and genetic variant analysis of a Quarter Horse mare. BMC Genomics, 13(1), 78-88.
  7. Drögemüller, C., Distl, O. & Leeb, T. (2001). Partial deletion of the bovine ED1 gene causes anhidrotic ectodermal dysplasia in cattle. Genome Research, 11(10), 1699-1705.
  8. Fagerberg, L., Hallström, B. M., Oksvold, P., Kampf, C., Djureinovic, D., Odeberg, J., Habuka, M., Tahmasebpoor, S., Danielsson, A., Edlund, K. & Asplund, A. (2014). Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Molecular & Cellular Proteomics, 13(2), 397-406.
  9. Fitak, R. R., Mohandesan, E., Corander, J. & Burger, P. A. (2016). The de novo genome assembly and annotation of a female domestic dromedary of North African origin. Molecular Ecology Resources, 16(1), 314-324.
  10. Gorla, E., Cozzi, M. C., Román-Ponce, S. I., López, F. R., Vega-Murillo, V. E., Cerolini, S., Bagnato, A. & Strillacci, M. G. (2017). Genomic variability in Mexican chicken population using copy number variants. BMC Genetics, 18(1), 61-71.
  11. Henrichsen, C. N., Chaignat, E. & Reymond, A. (2009). Copy number variants, diseases and gene expression. Human Molecular Genetics, 18, 1-8.
  12. Huang D. W., Sherman B. T. & Lempicki R. A. (2009). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature protocols, 4, 44-57.
  13. Iafrate, A. J., Feuk, L., Rivera, M. N., Listewnik, M. L., Donahoe, P. K., Qi, Y., Scherer, S. W. & Lee, C. (2004). Detection of large-scale variation in the human genome. Nature Genetics, 36(9), 949.
  14. Jenkins, G. M., Goddard, M. E., Black, M. A., Brauning, R., Auvray, B., Dodds, K. G., Kijas, J. W., Cockett, N. & McEwan, J. C. (2016). Copy number variants in the sheep genome detected using multiple approaches. BMC Genomics, 17(1), 441-455.
  15. Jun, J., Cho, Y. S., Hu, H., Kim, H. M., Jho, S., Gadhvi, P., Park, K. M., Lim, J., Paek, W. K., Han, K. & Manica, A. (2014). Whole genome sequence and analysis of the Marwari horse breed and its genetic origin. BMC Genomics, 15(9), 4.
  16. Khalkhali-Evrigh, R., Hafezian, S. H., Hedayat-Evrigh, N., Farhadi, A. & Bakhtiarizadeh, M. R. (2018). Genetic variants analysis of three dromedary camels using whole genome sequencing data. PloS one, 13(9), 204-218.
  17. Letaief, R., Rebours, E., Grohs, C., Meersseman, C., Fritz, S., Trouilh, L., Esquerré, D., Barbieri, J., Klopp, C., Philippe, R. & Blanquet, V. (2017). Identification of copy number variation in French dairy and beef breeds using next-generation sequencing. Genetics Selection Evolution, 49(1), 77.
  18. Li, H. & Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25(14), 1754-1760.
  19. Liu, M., Zhou, Y., Rosen, B. D., Van Tassell, C. P., Stella, A., Tosser-Klopp, G., Rupp, R., Palhière, I., Colli, L., Sayre, B. & Crepaldi, P. (2019). Diversity of copy number variation in the worldwide goat population. Heredity, 122(5), 636-646.
  20. Mandoiu, I. & Zelikovsky, A. (2016). Computational Methods for Next Generation Sequencing Data Analysis. John Wiley & Sons.
  21. McCarroll, S. A., Huett, A., Kuballa, P., Chilewski, S. D., Landry, A., Goyette, P., Zody, M. C., Hall, J. L., Brant, S. R., Cho, J. H. and Duerr, R. H. (2008). Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease. Nature Genetics, 40(9), 1107- 1112.
  22. Mei, C., Junjvlieke, Z., Raza, S. H. A., Wang, H., Cheng, G., Zhao, C., Zhu, W. & Zan, L. (2019). Copy number variation detection in Chinese indigenous cattle by whole genome sequencing. Genomics. In press.
  23. Norris, B. J. & Whan, V. A. (2008). A gene duplication affecting expression of the ovine ASIP gene is responsible for white and black sheep. Genome Research, 18(8), 1282-1293.
  24. Revilla, M., Puig-Oliveras, A., Castelló, A., Crespo-Piazuelo, D., Paludo, E., Fernández, A. I., Ballester, M. & Folch, J. M. (2017). A global analysis of CNVs in swine using whole genome sequence data and association analysis with fatty acid composition and growth traits. PloS one, 12(5), 1-17.
  25. Sebat, J., Lakshmi, B., Troge, J., Alexander, J., Young, J., Lundin, P., Månér, S., Massa, H., Walker, M., Chi, M. & Navin, N. (2004). Large-scale copy number polymorphism in the human genome. Science, 305(5683), 525-528.
  26. Serres-Armero, A., Povolotskaya, I.S., Quilez, J., Ramirez, O., Santpere, G., Kuderna, L. F., Hernandez-Rodriguez, J., Fernandez-Callejo, M., Gomez-Sanchez, D., Freedman, A. H. & Fan, Z. (2017). Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing. BMC Genomics, 18(1), 977-992.
  27. Singleton, A. B., Farrer, M., Johnson, J., Singleton, A., Hague, S., Kachergus, J., Hulihan, M., Peuralinna, T., Dutra, A., Nussbaum, R. & Lincoln, S. (2003). α-Synuclein locus triplication causes Parkinson's disease. Science, 302(5646), 841-841.
  28. Stothard, P., Choi, J. W., Basu, U., Sumner-Thomson, J. M., Meng, Y., Liao, X. & Moore, S. S. (2011). Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery. BMC Genomics, 12(1), 559-573.
  29. Tashiro, F., Kanai‐Azuma, M., Miyazaki, S., Kato, M., Tanaka, T., Toyoda, S., Yamato, E., Kawakami, H., Miyazaki, T. & Miyazaki, J. I. (2010). Maternal‐effect gene Ces5/Ooep/Moep19/Floped is essential for oocyte cytoplasmic lattice formation and embryonic development at the maternal‐zygotic stage transition. Genes to Cells, 15(8), 813-828.
  30. Wennmann, D. O., Schmitz, J., Wehr, M. C., Krahn, M. P., Koschmal, N., Gromnitza, S., Schulze, U., Weide, T., Chekuri, A., Skryabin, B. V. and Gerke, V. (2014). Evolutionary and molecular facts link the WWC protein family to Hippo signaling. Molecular Biology and Evolution, 31(7), 1710-1723.
  31. Wu, H., Guang, X., Al-Fageeh, M.B., Cao, J., Pan, S., Zhou, H., Zhang, L., Abutarboush, M. H., Xing, Y., Xie, Z. & Alshanqeeti, A. S. (2014). Camelid genomes reveal evolution and adaptation to desert environments. Nature Communications, 5, 5188-5197.
  32. Yang, L., Xu, L., Zhou, Y., Liu, M., Wang, L., Kijas, J. W., Zhang, H., Li, L. & Liu, G. E. (2018). Diversity of copy number variation in a worldwide population of sheep. Genomics, 110(3), 143-148.
  33. Yi, G., Qu, L., Liu, J., Yan, Y., Xu, G. & Yang, N. (2014). Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing. BMC Genomics, 15(1), 962-978.
  34. Zhang, R. Q., Wang, J. J., Zhang, T., Zhai, H. L. & Shen, W. (2019). Copy-number variation in goat genome sequence: A comparative analysis of the different litter size trait groups. Gene, 696, 40-46.