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

Chuan Jiang (1, 2) , Chao Chen (1, 2) , Ziyue Huang (1) , Renyi Liu (1, 2) , Jérôme Verdier (1, 2)

1 PSC - Shanghai Center for Plant Stress Biology [CAS]
2 UCAS - University of Chinese Academy of Sciences [Beijing]

Background: Transposable elements constitute an important part of the genome and are essential in adaptivemechanisms. Transposition events associated with phenotypic changes occur naturally or are induced in insertionalmutant populations. Transposon mutagenesis results in multiple random insertions and recovery of most/all theinsertions is critical for forward genetics study. Using genome next-generation sequencing data and appropriatebioinformatics tool, it is plausible to accurately identify transposon insertion sites, which could provide candidatecausal mutations for desired phenotypes for further functional validation.Results: We developed a novel bioinformatics tool, ITIS (Identification of Transposon Insertion Sites), for localizingtransposon insertion sites within a genome. It takes next-generation genome re-sequencing data (NGS data), transposonsequence, and reference genome sequence as input, and generates a list of highly reliable candidate insertion sites aswell as zygosity information of each insertion. Using a simulated dataset and a case study based on an insertional mutantline from Medicago truncatula, we showed that ITIS performed better in terms of sensitivity and specificity than othersimilar algorithms such as RelocaTE, RetroSeq, TEMP and TIF. With the case study data, we demonstrated the efficiencyof ITIS by validating the presence and zygosity of predicted insertion sites of the Tnt1 transposon within a complex plantsystem, M. truncatula.Conclusion: This study showed that ITIS is a robust and powerful tool for forward genetic studies in identifyingtransposable element insertions causing phenotypes. ITIS is suitable in various systems such as cell culture, bacteria,yeast, insect, mammal and plant

Mots clés: Forward; forward genetics; insertion sites; itis; medicago truncatula; tnt1; transposable elements

Domaines: Sciences du Vivant [q-bio]

Chuan Jiang, Chao Chen, Ziyue Huang, Renyi Liu, Jérôme Verdier. ITIS, a bioinformatics tool for accurate identification of transposon insertion sites using next-generation sequencing data. BMC Bioinformatics, 2015, 16 (1), pp.72. ⟨10.1186/s12859-015-0507-2⟩. ⟨hal-01605647⟩