Abstract
Detection of transposition events of a transposon from short reads of next-generation sequencing (NGS) is challenging because transposons are repetitive and difficult to be distinguished from already existing transposons in the genome. Many transposons generate target site duplication (TSD) as the result of chromosomal integration. Since TSDs flanking the 5′-end (head) and 3′-end (tail) of a transposon has the identical sequences which are absent from the reference copy, the short reads containing the head or tail sequences of the transposon following the same TSD sequence may reveal the evidence of transposition. Transposon Insertion Finder (TIF) focuses on the TSD with flanking sequence of transposon and detects transposition events from NGS data. TIF software is available at https://github.com/akiomiyao/tif.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Feschotte C, Jiang N, Wessler SR (2002) Plant transposable elements: where genetics meets genomics. Nat Rev Genet 3:329–341. https://doi.org/10.1038/nrg793
Hirochika H et al (1996) Retrotransposons of rice involved in mutations induced by tissue culture. Proc Natl Acad Sci U S A 93:7783–7788. https://doi.org/10.1073/pnas.93.15.7783
Miyao A et al (2003) Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome. Plant Cell 15:1771–1780. https://doi.org/10.1105/tpc.012559
Miyao A et al (2012) Molecular spectrum of somaclonal variation in regenerated rice revealed by whole-genome sequencing. Plant Cell Physiol. 53:256–264. https://doi.org/10.1093/pcp/pcr172
Jiang N et al (2003) An active DNA transposon family in rice. Nature 421:163–167. https://doi.org/10.1038/nature01214
O'Hare K, Rubin GM (1983) Structures of P transposable elements and their sites of insertion and excision in the Drosophila melanogaster genome. Cell 34:25–35. https://doi.org/10.1016/0092-8674(83)90133-2
Nakagome M et al (2014) Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements. BMC Bioinformatics 15:71. https://doi.org/10.1186/1471-2105-15-71
IRGSP (2005) The map-based sequence of the rice genome. Nature 436:793–800. https://doi.org/10.1038/nature03895
Altschul SF et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402. https://doi.org/10.1093/nar/25.17.3389
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Miyao, A. (2021). Detection of Transposition Events from Next-Generation Sequencing Data. In: Cho, J. (eds) Plant Transposable Elements. Methods in Molecular Biology, vol 2250. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1134-0_12
Download citation
DOI: https://doi.org/10.1007/978-1-0716-1134-0_12
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-1133-3
Online ISBN: 978-1-0716-1134-0
eBook Packages: Springer Protocols