CTREP-finder: A web service for quick identification and visualization of clean transgenic and genome-edited plants

To feed 10 billion people in 30 years from now will heavily depend on new higher yield, yet safe, biotech crop varieties, which are developed using biotechnologies, particularly genetic transformation and genome editing. A clean transgenic plant (CTP) contains only the defined transgene, whilst a clean edited plant (CEP) is transgene-free. Currently, it is difficult and time-consuming to identify and locate transgenes within plant genomes due to the complex nature of transfer DNA (T-DNA) or plasmid backbone integration, which has led to a major obstacle in mass scale production of clean transgenic/edited plants (CTREPs). Here we have built a web-based portal, CTREP-finder, for fast detection, characterization and visualization of foreign DNA fragments in plants, based on next-generation whole genome sequencing data. We invented a novel bioinformatics strategy to handle three scenarios of transgene integration and successfully identified CTREPs by testing 132 samples. Furthermore, we compared the CTREP-finder with three public programs, FED, transgeneR and TDNAscan, and it showed that the CTREP-finder outperforms those programs particularly on the localization of transgene integration. The use of CTREP-finder needs little requirement for bioinformatics expertise. Therefore, it is a user-friendly web-based portal that could be used by plant breeders and regulatory agencies for the rapid selection/detection of CTREPs for crop breeding and production.