Study of structural diversity of genome Iranian native dog and wolf with the method whole genome sequencing

Document Type : Research Paper


1 Ph.D. Student of Animal Breeding, Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran and Yang Reseaechers Society, Shahid Bahonar University of Kerman, Kerman, Iran

2 Professor, Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran

3 Associat Professor, Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran


In this research, samples were collected from three Iranian native dogs and three wolves. Whole-genome sequencing for each individual was performed using next-generation sequencing technology. All short reads were aligned to the reference genome using BWA tool. Single-nucleotide polymorphisms (SNPs) and small insertions and deletions (Indels) were detected using the genome analysis toolkit (GATK). Structural variants were predicted using the BreakDancer software. Annotating single-nucleotide polymorphisms and small insertions and deletions was done using SnpEff Software. Nucleotide diversity values in dogs and wolves samples were calculated using VCFtools. In current researche, 12459651 SNPs were detected that 7819789 and 10454994 were for dog and wolf, respectively. Of the total number of Single-nucleotide polymorphisms, 53.57%, 31.989% and 0.811% were located within intergenic, introns and exon regions. The results showed that structural diversity of wolf genome is higher than that in dog.


  1. Atanur, S. S., Diaz, A. G., Maratou, K., Sarkis, A., Rotival, M., Game, L. & Keane, T. M. (2013). Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat. Cell, 154(3), 691-703.
  2. Chen, K., Wallis, J. W., McLellan, M. D., Larson, D. E., Kalicki, J. M., Pohl, C. S. & Mardis, E. R. (2009). BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nature methods, 6(9), 677-681.
  3. Cingolani, P., Patel, V. M., Coon, M., Nguyen, T., Land, S. J., Ruden, D. M. & Lu, X. (2012). Using drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, snpsift. In Toxicogenomics in non-mammalian species, (Vol. 3, P. 35). Frontiers E-books.
  4. Cingolani, P., Platts, A., Wang, L. L., Coon, M., Nguyen, T., Wang, L. & Ruden, D. M. (2012). A program for annotating and predicting the effects of single nucleotide polymorphisms, snpeff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly6(2), 80-92.
  5. Collins, D. W. & Jukes, T. H. (1994). Rates of transition and transversion in coding sequences since the human-rodent divergence. Genomics, 20(3), 386-396.
  6. Coppinger, R. & Coppinger, L. (2002). Dogs: a new understanding of canine origin, behavior and evolution. University of Chicago Press.
  7. da Silva, J. M., Giachetto, P. F., da Silva, L. O. C., Cintra, L. C., Paiva, S. R., Caetano, A. R. & Yamagishi, M. E. B. (2015). Genomic variants revealed by invariably missing genotypes in nelore cattle. Plos one, 10(8), e0136035.
  8. Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A. & Durbin, R. (2011). The variant call format and vcftools. Bioinformatics, 27(15), 2156-2158.
  9. Davis, S. J. & Valla, F. R. (1978). Evidence for domestication of the dog 12,000 years ago in the Natufian of Israel. Nature, 276, 608-610.
  10. Ebersberger, I., Metzler, D., Schwarz, C. & Pääbo, S. (2002). Genomewide comparison of DNA sequences between humans and chimpanzees. The American Journal of Human Genetics, 70(6), 1490-1497.
  11. Fang, M., Larson, G., Ribeiro, H. S., Li, N. & Andersson, L. (2009). Contrasting mode of evolution at a coat color locus in wild and domestic pigs. PLoS Genet, 5(1), e1000341.
  12. Freedman, A. H., Gronau, I., Schweizer, R. M., Ortega-Del Vecchyo, D., Han, E., Silva, P. M. & Beale, H. (2014). Genome sequencing highlights the dynamic early history of dogs. PLoS Genetics, 10(1), e1004016.
  13. Hare, B., Wobber, V. & Wrangham, R. (2012). The self-domestication hypothesis: evolution of bonobo psychology is due to selection against aggression.  Animal Behaviour, 83(3), 573-585.
  14. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N. & Durbin, R. (2009). The sequence alignment/map format and sam tools. Bioinformatics, 25(16), 2078-2079.
  15. Li, H. & Durbin, R. (2009). Fast and accurate short read alignment with burrows–wheeler transform. Bioinformatics, 25(14), 1754-1760.
  16. McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A. & DePristo, M. A. (2010). The genome analysis toolkit: a mapreduce frame work for analyzing next-generation dna sequencing data.  Genome research, 20(9), 1297-1303.
  17. McLaren, W., Pritchard, B., Rios, D., Chen, Y., Flicek, P. & Cunningham, F. (2010). Deriving the consequences of genomic variants with the ensembl api and snp effect predictor. Bioinformatics, 26(16), 2069-2070.
  18. Ovodov, N. D., Crockford, S. J., Kuzmin, Y. V., Higham, T. F., Hodgins, G. W. & van der Plicht, J. (2011). A 33,000-year-old incipient dog from the altai mountains of Siberia: evidence of the earliest domestication disrupted by the last glacial maximum. PLoS One, 6 (7), e22821.
  19. Pang, J. F., Kluetsch, C., Zou, X. J., Zhang, A. B., Luo, L. Y., Angleby, H. & Savolainen, P. (2009). MtDNA data indicate a single origin for dogs south of Yangtze river, less than 16,300 years ago, from numerous wolves. Molecular biology and evolution, 26(12), 2849-2864.
  20. Pollinger, J. P., Lohmueller, K. E., Han, E., Parker, H. G., Quignon, P., Degenhardt, J. D. & Wayne, R. K. (2010). Genome-wide snp and haplotype analyses reveal a rich history underlying dog domestication. Nature, 464(7290), 898-902.
  21. Skoglund, P., Götherström, A. & Jakobsson, M. (2011). Estimation of population divergence times from non-overlapping genomic sequences: examples from dogs and wolves. Molecular biology and evolution, 28(4), 1505-1517.
  22. Rubin, C. J., Zody, M. C., Eriksson, J., Meadows, J. R., Sherwood, E., Webster, M. T. & Andersson, L. (2010). Whole-genome resequencing reveals loci under selection during chicken domestication. Nature, 464(7288), 587-591.
  23. Saetre, P., Lindberg, J., Leonard, J. A., Olsson, K., Pettersson, U., Ellegren, H. & Jazin, E. (2004). From wild wolf to domestic dog: gene expression changes in the brain. Molecular Brain Research, 126(2), 198-206.
  24. Stenson, P. D., Ball, E. V., Mort, M., Phillips, A. D., Shiel, J. A., Thomas, N. S. & Cooper, D. N. (2003). Human gene mutation database (HGMD®): update. Human mutation, 21(6), 577-581.
  25. 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.
  26. Varki, A. & Altheide, T. K. (2005). Comparing the human and chimpanzee genomes: searching for needles in a haystack. Genome research, 15(12), 1746-1758.
  27. Wang, G. D., Zhai, W., Yang, H. C., Fan, R. X., Cao, X., Zhong, L. & Zhang, Y. P. (2013). The genomics of selection in dogs and the parallel evolution between dogs and humans. Nature communications, 4, 1860.