Whole genome sequence analysis of unidentified genetically modified papaya for development of a specific detection method

•Unknown genetically modified (GM) papaya (Carica papaya Linnaeus) was identified by whole genome sequence analysis.•Contigs having transgenic construct- and event-specific DNA sequences in GM papaya were found.•Searches of GM papaya whole genome sequence data were possible using common transgenic sequences (>17bp).•A method for real-time PCR detection of GM papaya from whole genome sequence data was developed. Identification of transgenic sequences in an unknown genetically modified (GM) papaya (Carica papaya L.) by whole genome sequence analysis was demonstrated. Whole genome sequence data were generated for a GM-positive fresh papaya fruit commodity detected in monitoring using real-time polymerase chain reaction (PCR). The sequences obtained were mapped against an open database for papaya genome sequence. Transgenic construct- and event-specific sequences were identified as a GM papaya developed to resist infection from a Papaya ringspot virus. Based on the transgenic sequences, a specific real-time PCR detection method for GM papaya applicable to various food commodities was developed. Whole genome sequence analysis enabled identifying unknown transgenic construct- and event-specific sequences in GM papaya and development of a reliable method for detecting them in papaya food commodities.