Transposable element-mediated structural variation analysis in dog breeds using whole-genome sequencing

  • Songmi Kim
  • Seyoung Mun
  • Taemook Kim
  • Kang-Hoon Lee
  • Keunsoo Kang
  • Je-Yoel ChoEmail author
  • Kyudong HanEmail author


Naturally occurring diseases in dogs provide an important animal model for studying human disease including cancer, heart disease, and autoimmune disorders. Transposable elements (TEs) make up ~ 31% of the dog (Canis lupus familiaris) genome and are one of main drivers to cause genomic variations and alter gene expression patterns of the host genes, which could result in genetic diseases. To detect structural variations (SVs), we conducted whole-genome sequencing of three different breeds, including Maltese, Poodle, and Yorkshire Terrier. Genomic SVs were detected and visualized using BreakDancer program. We identified a total of 2328 deletion SV events in the three breeds compared with the dog reference genome of Boxer. The majority of the genetic variants were found to be TE insertion polymorphism (1229) and the others were TE-mediated deletion (489), non-TE-mediated deletion (542), simple repeat-mediated deletion (32), and other indel (36). Among the TE insertion polymorphism, 286 elements were full-length LINE-1s (L1s). In addition, the 49 SV candidates located in the genic regions were experimentally verified and their polymorphic rates within each breed were examined using PCR assay. Polymorphism analysis of the genomic variants revealed that some of the variants exist polymorphic in the three dog breeds, suggesting that their SV events recently occurred in the dog genome. The findings suggest that TEs have contributed to the genomic variations among the three dog breeds of Maltese, Poodle, and Yorkshire Terrier. In addition, the polymorphic events between the dog breeds indicate that TEs were recently retrotransposed in the dog genome.



This research was supported by the Bio & Medical Technology Development Program of the National Research Foundation (NRF) funded by the Ministry of Science & ICT (NRF-2016M3A9B6026771) and (NRF-2016M3A9B6026776).

Compliance with ethical standards

Conflict of interest

The authors declare that there is no conflict of interest regarding the publication of this paper.

Ethical approval

This study was reviewed and approved by the Seoul National University Institutional Animal Care and Use Committee (IACUC# SNU-170602-1).

Supplementary material

335_2019_9812_MOESM1_ESM.xlsx (11 kb)
Supplementary material 1 (XLSX 10 kb)
335_2019_9812_MOESM2_ESM.xlsx (2.5 mb)
Supplementary material 2 (XLSX 2607 kb). Raw data of five structural variations in three dog predicted from three dog breeds genome using BreakDancer
335_2019_9812_MOESM3_ESM.xlsx (205 kb)
Supplementary material 3 (XLSX 205 kb). A list of deletion SV candidates in each dog breed
335_2019_9812_MOESM4_ESM.xlsx (218 kb)
Supplementary material 4 (XLSX 217 kb). Five different types of deletion SV events
335_2019_9812_MOESM5_ESM.xlsx (9.2 mb)
Supplementary material 5 (XLSX 9458 kb). A list of full-length L1s identified in the three dog genome
335_2019_9812_MOESM6_ESM.pdf (59 kb)
Supplementary material 6 (PDF 58 kb). Molecular phylogenetic analysis of 10 mammals based on amino acids of 36 orthologs


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative MedicineDankook UniversityCheonanRepublic of Korea
  2. 2.Department of Biological SciencesKorea Advanced Institute of Science and TechnologyDaejeonRepublic of Korea
  3. 3.Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary MedicineSeoul National UniversitySeoulRepublic of Korea
  4. 4.Department of MicrobiologyDankook UniversityCheonanRepublic of Korea

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