ArticleBMC bioinformatics2015
ITIS, a bioinformatics tool for accurate identification of transposon insertion sites using next-generation sequencing data.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- The mitochondrial DnaJA protein LMA1 regulates reactive oxygen species homeostasis and anthocyanin biosynthesis inPlant diversity · 2026Article
- Application of next-generation sequencing in the detection of transgenic crop.Frontiers in genetics · 2024Review
- Homeostasis of flavonoids and triterpenoids most likely modulates starch metabolism for pollen tube penetration in rice.Plant biotechnology journal · 2023Article
- The F-box protein MIO1/SLB1 regulates organ size and leaf movement in Medicago truncatula.Journal of experimental botany · 2021Article
- Easymap: A User-Friendly Software Package for Rapid Mapping-by-Sequencing of Point Mutations and Large Insertions.Frontiers in plant science · 2021Article
- Epigenetic conflict on a degenerating Y chromosome increases mutational burden in Drosophila males.Nature communications · 2020Article
- TIP_finder: An HPC Software to Detect Transposable Element Insertion Polymorphisms in Large Genomic Datasets.Biology · 2020Article
- Identification and Genotyping of Transposable Element Insertions From Genome Sequencing Data.Current protocols in human genetics · 2020Review
- Insertional mutagenesis of Brachypodium distachyon using the Tnt1 retrotransposable element.The Plant journal : for cell and molecular biology · 2020Article
- Cloning and Functional Analysis of Dwarf GeneInternational journal of molecular sciences · 2020Article
- Next-generation forward genetic screens: using simulated data to improve the design of mapping-by-sequencing experiments in Arabidopsis.Nucleic acids research · 2019Article
- On the Population Dynamics of Junk: A Review on the Population Genomics of Transposable Elements.Genes · 2019Review
- A benchmark of transposon insertion detection tools using real data.Mobile DNA · 2019Article
- TDNAscan: A Software to Identify Complete and Truncated T-DNA Insertions.Frontiers in genetics · 2019Article
- Article
- TranSurVeyor: an improved database-free algorithm for finding non-reference transpositions in high-throughput sequencing data.Nucleic acids research · 2018Article
- Computational tools to unmask transposable elements.Nature reviews. Genetics · 2018Review
- Benchmarking computational tools for polymorphic transposable element detection.Briefings in bioinformatics · 2017Article
- McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data.G3 (Bethesda, Md.) · 2017Article
- Population and clinical genetics of human transposable elements in the (post) genomic era.Mobile genetic elements · 2017Review
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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