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. 2019 Oct 30;9(1):15595.
doi: 10.1038/s41598-019-51668-x.

Detection and identification of transgenic events by next generation sequencing combined with enrichment technologies

Frédéric Debode  1 , Julie Hulin  2 , Benoît Charloteaux  3 , Wouter Coppieters  3 , Marc Hanikenne  4 , Latifa Karim  3 , Gilbert Berben  2
Affiliations

Detection and identification of transgenic events by next generation sequencing combined with enrichment technologies

Frédéric Debode et al. Sci Rep. .

Abstract

Next generation sequencing (NGS) is a promising tool for analysing the quality and safety of food and feed products. The detection and identification of genetically modified organisms (GMOs) is complex, as the diversity of transgenic events and types of structural elements introduced in plants continue to increase. In this paper, we show how a strategy that combines enrichment technologies with NGS can be used to detect a large panel of structural elements and partially or completely reconstruct the new sequence inserted into the plant genome in a single analysis, even at low GMO percentages. The strategy of enriching sequences of interest makes the approach applicable even to mixed products, which was not possible before due to insufficient coverage of the different genomes present. This approach is also the first step towards a more complete characterisation of agrifood products in a single analysis.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Workflow of the enrichment technology prior to sequencing.
Figure 2
Figure 2
Bioinformatic workflow developed for detecting and identifying GMOs. The bioinformatic packages used are indicated in grey.
Figure 3
Figure 3
Detection and characterisation of GMOs by NGS. The structures of the inserts of seven GMOs are presented. The 281 × 3006 cotton has two GM inserts. The mixed sample contains 50% A2704 soybean and 50% LL62 rice. The structural elements in grey were present in the database used for enrichment and were detected by NGS. The reads associated with these structural elements were used to create contigs. Only larger contigs covering several structural elements are shown here. Larger structural elements not covered by the capture probes created gaps, making it impossible to reconstruct the entire sequence of the transgenic cassette. Junction regions covering the plant and transgenic insert were also obtained.
Figure 4
Figure 4
Sequence of GTS 40-3-2 soybean and alignments of the contigs obtained in this research. The structural elements in grey shown in the database were used for enrichment and were detected by NGS. (A) Expected sequences of the GTS-40-3-2 soybean, as announced by Monsanto and as described by Windels et al.. Additional sequence corresponds to a duplication of part of the EPSPS gene and an unknown rearranged sequence. (B) Positions of the contigs created for the samples containing GTS-40-3-2 soybean at 10%, 1% and 0.1%.
See this image and copyright information in PMC

References

    1. Michael, T. P. & Jackson, S. The first 50 plant genomes. Plant Genome6 (2013).
    1. Kovalic D, et al. The use of next generation sequencing and junction sequence analysis bioinformatics to achieve molecular characterization of crops improved through modern biotechnology. Plant Genome. 2012;5:149–163.
    1. Wahler D, et al. Next-generation sequencing as a tool for detailed molecular characterisation of genomic insertions and flanking regions in genetically modified plants: a pilot study using a rice event unauthorised in the EU. Food Anal. Meth. 2013;6:1718–1727. doi: 10.1007/s12161-013-9673-x. - DOI
    1. Yang, L. et al. Characterization of GM events by insert knowledge adapted re-sequencing approaches. Sci. Rep. 3 (2013). - PMC - PubMed
    1. Liang C, et al. Detecting authorized and unauthorized genetically modified organisms containing vip3A by real-time PCR and next-generation sequencing. Anal. Bioanal. Chem. 2014;406:2603–2611. doi: 10.1007/s00216-014-7667-1. - DOI - PubMed

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