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.
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The present work was conducted with funding from the Research Fund of Dankook University in 2015.
Conflict of interest
Panupon Twilprawat declares that he/she does not have conflict of interest. Songmi Kim declares that he/she does not have conflict of interest. Kornsorn Srikulnath declares that he/she does not have conflict of interest. Kyudong Han declares that he/she does not have conflict of interest.
Animal care and all experimental procedures were approved by the Animal Experiment Committee, Kasetsart University, Thailand (approval no. ACKU04959), and conducted according to the Regulations on Animal Experiments at Kasetsart University.
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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)
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Twilprawat, P., Kim, S., Srikulnath, K. et al. Structural variations generated by simian foamy virus-like (SFV) in Crocodylus siamensis . Genes Genom 39, 1129–1138 (2017). https://doi.org/10.1007/s13258-017-0581-0
- Crocodylus siamensis
- Endogenous retrovirus (ERV)
- Non-homologous end joining (NHEJ)
- Structural variation