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

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...

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Autores principales: Nakagome, Mariko, Solovieva, Elena, Takahashi, Akira, Yasue, Hiroshi, Hirochika, Hirohiko, Miyao, Akio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4004357/
https://www.ncbi.nlm.nih.gov/pubmed/24629057
http://dx.doi.org/10.1186/1471-2105-15-71
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author Nakagome, Mariko
Solovieva, Elena
Takahashi, Akira
Yasue, Hiroshi
Hirochika, Hirohiko
Miyao, Akio
author_facet Nakagome, Mariko
Solovieva, Elena
Takahashi, Akira
Yasue, Hiroshi
Hirochika, Hirohiko
Miyao, Akio
author_sort Nakagome, Mariko
collection PubMed
description 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.
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spelling pubmed-40043572014-04-30 Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements Nakagome, Mariko Solovieva, Elena Takahashi, Akira Yasue, Hiroshi Hirochika, Hirohiko Miyao, Akio BMC Bioinformatics Research Article 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. BioMed Central 2014-03-14 /pmc/articles/PMC4004357/ /pubmed/24629057 http://dx.doi.org/10.1186/1471-2105-15-71 Text en Copyright © 2014 Nakagome et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Nakagome, Mariko
Solovieva, Elena
Takahashi, Akira
Yasue, Hiroshi
Hirochika, Hirohiko
Miyao, Akio
Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements
title Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements
title_full Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements
title_fullStr Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements
title_full_unstemmed Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements
title_short Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements
title_sort transposon insertion finder (tif): a novel program for detection of de novo transpositions of transposable elements
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4004357/
https://www.ncbi.nlm.nih.gov/pubmed/24629057
http://dx.doi.org/10.1186/1471-2105-15-71
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