Genome editing technology is evolving fast, and many labs worldwide are generating crop plants with improved traits. If transgenes were used to generate the edits, foreign DNA must be effectively removed by outcrossing. After an evaluation of various technologies, we show that long-read whole-genome sequencing (WGS) is at present the only reliable approach to confirm the absence of foreign DNA. We suggest using long-read WGS before requesting exemption from classification as genetically modified organisms and provide a guide for interpreting WGS data.
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Change history
15 October 2025
Since the version of the article initially published, ref. 4 has been updated to include the DOI. This correction has been made to the HTML and PDF versions of the article.
22 December 2025
In the version of the article initially published, in Table 1, the top entry of the "Adapted for plant genome editing" column was "3–50× (or higher for large genomes)" and has now been corrected to "30–50× (or higher for large genomes)" in the HTML and PDF versions of the article.
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Acknowledgements
This work was supported in parts by the Gates Foundation to H.H.U. (Investment ID INV-008733 and Investment ID INV-063189), Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany´s Excellence Strategy – EXC-2048/1 – project ID 390686111 (CEPLAS), and an Alexander von Humboldt Professorship (W.F.).
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W.F., F.F.W. and B.Y. conceived of the study, J.H.T., E.L., T.H., B.Y. and F.F.W. were instrumental for the WGS analyses and evaluation of different technologies, E.P. & W.F. were responsible for all aspects of standard technologies (such as PCR and DNA gel blotting), and M.B., B.Y. and W.F. were responsible for compliance with country-specific regulations. J.H.T., E.L. and W.F. wrote the manuscript, and all authors were involved in revisions.
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Huguet-Tapia, J.C., Loo, E.P.I., Buchholzer, M. et al. Ensuring effective removal of transgenes before release of genome-edited crops. Nat Biotechnol 43, 1603–1605 (2025). https://doi.org/10.1038/s41587-025-02805-7
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DOI: https://doi.org/10.1038/s41587-025-02805-7
