nGMOs cT-DNA Sequence Dataset

Dataset OverviewThis dataset comprises T-DNA homologous sequences identified from 2,649 naturally genetically modified organisms (nGMOs) through systematic mining of publicly available sequencing data. Candidate cT-DNA fragments were recovered using assembly-based approaches and validated through a standardized bioinformatic pipeline.Data Sources and ScopeAll raw sequencing data were retrieved from public repositories, including the NCBI Sequence Read Archive (SRA) and Whole Genome Shotgun (WGS) database. The analysis comprehensively screened publicly available Embryophyte sequencing datasets released up to May 2025.Data Processing WorkflowThe dataset was generated using a unified bioinformatic workflow, including:- Retrieval of WGS and SRA datasets- Assembly and recovery of candidate cT-DNA sequences- Validation and filtering to remove false positivesSequence Format and NamingAll sequences are provided in FASTA format. Two naming conventions were used during different stages of the project:- Early datasets: [SRR_ID][_1/_2] for paired-end reads or single-end data- Later datasets: [SpeciesName][SRR_ID] to improve species traceabilityDespite differences in naming, all identifiers maintain clear links to their original sequencing runs.ApplicationsThis dataset enables:- Identification of T-DNA insertion sites from plant genome- Homology and comparative sequence analysis- Primer design for molecular detection- Evolutionary and phylogenetic studies of horizontal gene transferNotesThis dataset represents a snapshot of currently available sequencing resources. As new genomic data continue to be released, additional nGMOs are expected to be identified in future analyses.