Structural variations generated by simian foamy virus-like (SFV) in Crocodylus siamensis
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.
KeywordsCrocodylus siamensis Endogenous retrovirus (ERV) Non-homologous end joining (NHEJ) SFV1 Structural variation
The present work was conducted with funding from the Research Fund of Dankook University in 2015.
Compliance with ethical standards
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.
- Cui P, Lober U, Alquezar-Planas DE, Ishida Y, Courtiol A, Timms P, Johnson RN, Lenz D, Helgen KM, Roca AL et al (2016) Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome. PeerJ 4:e1847CrossRefPubMedPubMedCentralGoogle Scholar
- Hall TA (1999) BioEdit: a user-friendly biolodgical sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Sympos 41:95–98Google Scholar
- Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 275–282Google Scholar
- Pray LA (2008) Transposons: the jumping genes. Nat Educ 1:204Google Scholar
- Ross JP (1988) Crocodiles, 2nd edn. IUCN, GlandGoogle Scholar
- Ross FD, Mayer GC (1983) On the dorsal armor of the Crocodilia. Adv Herpetol Evol Biol 305–331Google Scholar
- Supikamolseni A, Ngaoburanawit N, Sumontha M, Chanhome L, Suntrarachun S, Peyachoknagul S, Srikulnath K (2015) Molecular barcoding of venomous snakes and species-specific multiplex PCR assay to identify snake groups for which antivenom is available in Thailand. Genet Mol Res 14:13981–13997CrossRefPubMedGoogle Scholar