Open Access Highly Accessed Research article

Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements

Mariko Nakagome1, Elena Solovieva12, Akira Takahashi1, Hiroshi Yasue1, Hirohiko Hirochika1 and Akio Miyao1*

Author Affiliations

1 Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2, Kannondai, Tsukuba, Ibaraki 305-8602, Japan

2 Current Address: Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Central 2, 1-1-1, Umezono, Tsukuba, Ibaraki 305-8568, Japan

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BMC Bioinformatics 2014, 15:71  doi:10.1186/1471-2105-15-71

Published: 14 March 2014

Abstract

Background

Transposition event detection of transposable element (TE) in the genome using short reads from the next-generation sequence (NGS) was difficult, because the nucleotide sequence of TE itself is repetitive, making it difficult to identify locations of its insertions by alignment programs for NGS. We have developed a program with a new algorithm to detect the transpositions from NGS data.

Results

In the process of tool development, we used next-generation sequence (NGS) data of derivative lines (ttm2 and ttm5) of japonica rice cv. Nipponbare, regenerated through cell culture. The new program, called a transposon insertion finder (TIF), was applied to detect the de novo transpositions of Tos17 in the regenerated lines. TIF searched 300 million reads of a line within 20 min, identifying 4 and 12 de novo transposition in ttm2 and ttm5 lines, respectively. All of the transpositions were confirmed by PCR/electrophoresis and sequencing. Using the program, we also detected new transposon insertions of P-element from NGS data of Drosophila melanogaster.

Conclusion

TIF operates to find the transposition of any elements provided that target site duplications (TSDs) are generated by their transpositions.

Keywords:
Transposable elements; Rice; NGS; TSD