Jolien E’aes from Sciensano in Belgium presented at the Nanopore Community Meeting 2021. The title of the presentation is “Characterization of genetically modified microorganisms is facilitated by long-read whole-genome sequencing.” I don’t think I have watched this session before! D’aes explained how Sciensano, the Belgian Institute for Public and Animal Health. They focus on food safety and animal health. They monitor the presence and abundance of GMOs. Genetically modified microorganisms (GMM) can be used to make fermentation products though European legislation limits presence in the final product. Sciensano has identified sequences and even isolated viable GMM from some products, according to E’aes. The team performed hybrid and long-read assembly of data from two MinION flow cells and five samples on each run. Hybrid assembly with Unicycler indicated transgenic construct in an episomal plasmid. HybridSpades placed the construct inside the chromosomal scaffold integrated into the host. With long-read assembly using Canu, the contigs made up of the transgenic construct seemed linear. Thus, different assemblers showed different results. Read lengths showed a distinct six kb fragment that appears like the plasmid. After filtering reads shorter than the plasmid length, the assembly of long reads revealed variant plasmid constructs and a limited number of integrated constructs. E’aes concluded that the transgenic construct was identified as both plasmids and integrated constructs in the GMM. I found the multiple assemblies and different results intriguing. It seems that filtering shorter reads improved results.
