ITIS, a bioinformatics tool for accurate identification of transposon insertion sites using next-generation sequencing data.

Chuan Jiang,Jerome Verdier,Chao Chen,Ziyue Huang,Renyi Liu

doi:10.1186/s12859-015-0507-2

Abstract

BackgroundTransposable elements constitute an important part of the genome and are essential in adaptive mechanisms. Transposition events associated with phenotypic changes occur naturally or are induced in insertional mutant populations. Transposon mutagenesis results in multiple random insertions and recovery of most/all the insertions is critical for forward genetics study. Using genome next-generation sequencing data and appropriate bioinformatics tool, it is plausible to accurately identify transposon insertion sites, which could provide candidate causal mutations for desired phenotypes for further functional validation.ResultsWe developed a novel bioinformatics tool, ITIS (Identification of Transposon Insertion Sites), for localizing transposon insertion sites within a genome. It takes next-generation genome re-sequencing data (NGS data), transposon sequence, and reference genome sequence as input, and generates a list of highly reliable candidate insertion sites as well as zygosity information of each insertion. Using a simulated dataset and a case study based on an insertional mutant line from Medicago truncatula, we showed that ITIS performed better in terms of sensitivity and specificity than other similar algorithms such as RelocaTE, RetroSeq, TEMP and TIF. With the case study data, we demonstrated the efficiency of ITIS by validating the presence and zygosity of predicted insertion sites of the Tnt1 transposon within a complex plant system, M. truncatula.ConclusionThis study showed that ITIS is a robust and powerful tool for forward genetic studies in identifying transposable element insertions causing phenotypes. ITIS is suitable in various systems such as cell culture, bacteria, yeast, insect, mammal and plant.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0507-2) contains supplementary material, which is available to authorized users.

Highlights

Transposable elements constitute an important part of the genome and are essential in adaptive mechanisms
The first step of the ITIS pipeline is to map PE reads to the reference genome sequences and the transposable element sequence using short read alignment program BWA [29]
In order to evaluate how genome coverage affected the effectiveness of different programs, we randomly sampled PE reads from the sequence dataset generated from NF54 into subsamples representing 3X, 5X, 10X, 15X, 20X, 30X, 40X, ... and 100X genome coverages and we examined the number of insertions that were identified using the four previously mentioned algorithms and ITIS

Summary

Introduction

Transposable elements constitute an important part of the genome and are essential in adaptive mechanisms. Gene function is determined using two opposite but complementary approaches: reverse genetics, which consists of deciphering the function of a gene by analyzing phenotypic effects of up- and Transposable elements (TEs) are mobile DNA sequences found in both prokaryote and eukaryote genomes. They usually represent a large proportion of the genome and under particular circumstances such as various stresses, some TEs become active and transpose themselves to other locations of the genome [1].

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