ArticleG3 (Bethesda, Md.)2013
The use of RelocaTE and unassembled short reads to produce high-resolution snapshots of transposable element generated diversity in rice.
Article in G3 (Bethesda, Md.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
29 citing papers in PubMed.
- Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen.Nature communications · 2025Article
- Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast.Mobile DNA · 2023Article
- Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast.bioRxiv : the preprint server for biology · 2023Article
- Bergerac strains of Caenorhabditis elegans revisited: expansion of Tc1 elements imposes a significant genomic and fitness cost.G3 (Bethesda, Md.) · 2022Article
- Exploring transposable element-based markers to identify allelic variations underlying agronomic traits in rice.Plant communications · 2022Article
- Finding and Characterizing Repeats in Plant Genomes.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Transposable element profiles reveal cell line identity and loss of heterozygosity in Drosophila cell culture.Genetics · 2021Article
- Genomic diversity generated by a transposable element burst in a rice recombinant inbred population.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Insertional mutagenesis of Brachypodium distachyon using the Tnt1 retrotransposable element.The Plant journal : for cell and molecular biology · 2020Article
- Miniature inverted-repeat transposable elements (MITEs), derived insertional polymorphism as a tool of marker systems for molecular plant breeding.Molecular biology reports · 2020Review
- T-lex3: an accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data.Bioinformatics (Oxford, England) · 2020Article
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- Article
- The Role of Transposable Elements in Speciation.Genes · 2018Review
- Tracking the genome-wide outcomes of a transposable element burst over decades of amplification.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data.G3 (Bethesda, Md.) · 2017Article
- Article
- Targeted identification of TE insertions in aMobile DNA · 2017Article
- RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing.PeerJ · 2017Article
- A novel method for identifying polymorphic transposable elements via scanning of high-throughput short reads.DNA research : an international journal for rapid publication of reports on genes and genomes · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
Transposable elements (TEs) are dynamic components of genomes that often vary in copy number among members of the same species. With the advent of next-generation sequencing TE insertion-site polymorphism can be examined at an unprecedented level of detail when combined with easy-to-use bioinformatics software. Here we report a new tool, RelocaTE, that rapidly identifies specific TE insertions that are either polymorphic or shared between a reference and unassembled next-generation sequencing reads. Furthermore, a novel companion tool, CharacTErizer, exploits the depth of coverage to classify genotypes of nonreference insertions as homozygous, heterozygous or, when analyzing an active TE family, as rare somatic insertion or excision events. It does this by comparing the numbers of RelocaTE aligned reads to reads that map to the same genomic position without the TE. Although RelocaTE and CharacTErizer can be used for any TE, they were developed to analyze the very active mPing element which is undergoing massive amplification in specific strains of Oryza sativa (rice). Three individuals of one of these strains, A123, were resequenced and analyzed for mPing insertion site polymorphisms. The majority of mPing insertions found (~97%) are not present in the reference, and two siblings from a self-crossed of this strain were found to share only ~90% of their insertions. Private insertions are primarily heterozygous but include both homozygous and predicted somatic insertions. The reliability of the predicted genotypes was validated by polymerase chain reaction.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.