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. 2022 Mar 7;4:100096. doi: 10.1016/j.fochms.2022.100096

Fig. 3.

Fig. 3

Benchmarking of the method using samples containing Bt rice at different concentrations. The data analysis workflow described in Fig. 1A was applied on PacBio sequencing data of DNA walking amplicons obtained from rice grain material containing Bt rice at different concentrations (1%, 0.1% and 0.01%), and noodles prepared from rice grains with 100% and 1% of Bt rice (Table 1) and MinION sequencing data of DNA walking amplicons obtained from rice grain material of Bt rice. The left panel shows analysis results obtained with database version B, containing both Bt rice insert sequences, whereby Bt rice represents as a known GMO. The right panel shows results obtained with database version A, lacking the Bt rice insert sequences, whereby Bt rice plays the role of an unknown GMO. Transgenic expression cassettes are shown schematically, elements are not drawn to scale. The same cassette is used to represent both transgenic inserts (Chr2 and Chr3, corresponding to inserts in chromosome 2 and 3 from the rice genome, respectively). Grey bars above the cassettes indicate schematically which elements and element combinations are present in the database. Elements that are represented in the database are indicated in grey colored boxes. Colored bars below the expression cassette show the longest amplicons that were observed for the first time during phase I, II and III (PI, PII, PIII) of the analysis as described in Fig. 1A. The green/blue/purple color gradient according to the color legend shows the number of reads (n) representing a given amplicon. Fragments that were manually reconstructed from reads (instead of clusters) during phase III are marked by a blue star. Fragments that are known to be present in the sample but that could not be detected in the current analysis are colored yellow. * Transgenic elements containing homologous regions with P-e35S. $ Transgenic elements containing homologous regions with CS-Cry1B. # Transgenic elements likely originating from the host plant genome. Transgenic elements are described in Supplementary File 3.