Genes & Genomics

, Volume 39, Issue 10, pp 1129–1138 | Cite as

Structural variations generated by simian foamy virus-like (SFV) in Crocodylus siamensis

  • Panupon Twilprawat
  • Songmi Kim
  • Kornsorn Srikulnath
  • Kyudong Han
Research Article

Abstract

Endogenous retrovirus (ERV) integrates into the germline of its host and could remain in the genome as a molecular fossil. ERV is one of sources that cause INDEL and recombination events in the vertebrate genomes, leading to various genomic and genetic changes in their hosts. There have been many studies conducted on ERVs in the vertebrate genomes to elucidate their evolutionary history. However, ERVs have not been studied well in Crocodylus siamensis. Here, we report structural variations among SFV1 elements (simian foamy virus-like), ERVs in C. siamensis. We initially identified 26 SFV1 candidates in the genome and experimentally verified 9 SFV1_1 and 5 SFV1_10 elements using PCR display. Their structural analyses showed that most of them are solitary-LTRs but two SFV1_1 elements are full-length. Through further analyses, we found that the two full-length elements retain intact ORFs. We examined transcription factor binding sites within their LTR sequences to predict promoter/enhancer activities. In sum, we identified 14 crocodile-specific SFV1 elements and the results of their structural analyses suggest that they could contribute to genomic or phenotypic variations in C. siamensis population.

Keywords

Crocodylus siamensis Endogenous retrovirus (ERV) Non-homologous end joining (NHEJ) SFV1 Structural variation 

Supplementary material

13258_2017_581_MOESM1_ESM.pptx (117 kb)
Supplementary Fig. 1 Cladogram between the SFV1_1 and SFV1_10 subfamilies.The maximum-likelihood cladogram of SFV1_1 and SFV1_10 subfamilies was constructed using 14 LTR sequences from SFV1 elements. The pink and green highlights represent SFV1_1 and SFV1_10 subfamilies, respectively. The red- and green-colored characters indicate SFV1_1 and SFV1_10 consensus LTR sequences, respectively. (PPTX 117 KB)
13258_2017_581_MOESM2_ESM.xlsx (10 kb)
Supplementary material 2 (XLSX 10 KB)
13258_2017_581_MOESM3_ESM.xlsx (17 kb)
Supplementary material 3 (XLSX 16 KB)

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Copyright information

© The Genetics Society of Korea and Springer Science+Business Media B.V. 2017

Authors and Affiliations

  1. 1.Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative MedicineDankook UniversityCheonanRepublic of Korea
  2. 2.Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of ScienceKasetsart UniversityBangkokThailand

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