Retrieving sequences of genetically modified plants from public databases to widen screening approaches

Abstract The development of effective screening methods and implementation of official controls on genetically modified organisms (GMOs) relies heavily on the availability of comprehensive and reliable GMO sequence repositories. Existing GMO databases, including the one developed by the Joint Research Centre (JRC), do not cover all events authorised worldwide. To bridge this gap, we designed a bioinformatics pipeline to retrieve new GMO sequences from public databases. We used for our initial query a 25 bp Ti plasmid sequence, which is commonly retained in the host genome after Agrobacterium tumefaciens -mediated transformation. Analysis of the initial dataset enabled us to identify longer query sequences, subsequently used to retrieve additional GMO sequences. This approach yielded the complete sequences of 23 GMOs. The bioinformatics strategy can be extended to other genetic targets frequently used in GMO development, facilitating the design of more effective screening approaches. As a proof of concept, we developed a new real-time PCR screening method targeting the Agrobacterium -derived region, using common sequences identified in our bioinformatics analysis. The resulting method demonstrated good sensitivity and specificity, successfully detecting 13 unauthorised GMOs in the European Union that were developed using Agrobacterium -mediated transformation.