ArticleBMC biotechnology2017
A bioinformatics approach for identifying transgene insertion sites using whole genome sequencing data.
Article in BMC biotechnology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed.
- Read-mapping signatures for molecular characterization of transgenic DNA insertions in paired-end Illumina data.BMC biotechnology · 2026Article
- Breeding and Molecular Characterization of Insect-Resistant Transgenic Cotton.Plants (Basel, Switzerland) · 2026Article
- Deciphering the complex molecular architecture of the genetically modified soybean FG72 through paired-end whole genome sequencing.Food chemistry. Molecular sciences · 2025Article
- Enhancing quality and climate resilient traits in vegetatively propagated polyploids: transgenic and genome editing advancements, challenges and future directions.Frontiers in genetics · 2025Review
- Review of the technology used for structural characterization of the GMO genome using NGS data.Genomics & informatics · 2024Article
- Co-inheritance of recombined chromatids maintains heterozygosity in a parthenogenetic ant.Nature ecology & evolution · 2024Article
- Unselfish meiotic drive maintains heterozygosity in a parthenogenetic ant.bioRxiv : the preprint server for biology · 2024Article
- Identifying transgene insertions inPeerJ · 2024Article
- Molecular Characterization and Efficacy Evaluation of Transgenic Maize HarboringPlants (Basel, Switzerland) · 2023Article
- A Brief Review of Plant Cell Transfection, Gene Transcript Expression, and Genotypic Integration for Enhancing Compound Production.Methods in molecular biology (Clifton, N.J.) · 2023Review
- T-LOC: A comprehensive tool to localize and characterize T-DNA integration sites.Plant physiology · 2022Article
- Development and performance evaluation of whole-genome sequencing with paired-end and mate-pair strategies in molecular characterization of GM crops: One GM rice 114-7-2 line as an example.Food chemistry. Molecular sciences · 2022Article
- A paired-end whole-genome sequencing approach enables comprehensive characterization of transgene integration in rice.Communications biology · 2022Article
- The Arabidopsis T-DNA mutant SALK_008491 carries a 14-kb deletion on chromosome 3 that provides rare insights into the plant response to dynamic light stress.Plant direct · 2022Article
- Whole-genome sequencing identifies I-SceI-mediated transgene integration sites in Xenopus tropicalis snai2:eGFP line.G3 (Bethesda, Md.) · 2022Article
- Forward and reverse genetic dissection of morphogenesis identifies filament-competent Candida auris strains.Nature communications · 2021Article
- Small compounds targeting tyrosine phosphorylation of Scaffold Protein Receptor for Activated C Kinase1A (RACK1A) regulate auxin mediated lateral root development inPlant signaling & behavior · 2021Article
- Influence of transgenesis on genome variability in cucumber lines with aPhysiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- Molecular characterization for food safety assessment of a genetically modified late blight resistant potato: an unusual case.Transgenic research · 2021Article
- Elucidation of genomic organizations of transgenic soybean plants through de novo genome assembly with short paired-end reads.Molecular breeding : new strategies in plant improvement · 2021Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenetically modified crops (GM crops) have been developed to improve the agricultural traits of modern crop cultivars. Safety assessments of GM crops are of paramount importance in research at developmental stages and before releasing transgenic plants into the marketplace. Sequencing technology is developing rapidly, with higher output and labor efficiencies, and will eventually replace existing methods for the molecular characterization of genetically modified organisms.
methodsTo detect the transgenic insertion locations in the three GM rice gnomes, Illumina sequencing reads are mapped and classified to the rice genome and plasmid sequence. The both mapped reads are classified to characterize the junction site between plant and transgene sequence by sequence alignment.
resultsHerein, we present a next generation sequencing (NGS)-based molecular characterization method, using transgenic rice plants SNU-Bt9-5, SNU-Bt9-30, and SNU-Bt9-109. Specifically, using bioinformatics tools, we detected the precise insertion locations and copy numbers of transfer DNA, genetic rearrangements, and the absence of backbone sequences, which were equivalent to results obtained from Southern blot analyses.
conclusionNGS methods have been suggested as an effective means of characterizing and detecting transgenic insertion locations in genomes. Our results demonstrate the use of a combination of NGS technology and bioinformatics approaches that offers cost- and time-effective methods for assessing the safety of transgenic plants.
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