USE OF HIGH THROUGHPUT SEQUENCING FOR DETECTION OF GMOS AND PLANT SPECIES IN FOOD AND FEED
- Debode, F. , Hulin, J. , Janssen, E. & Berben, G. (2019). USE OF HIGH THROUGHPUT SEQUENCING FOR DETECTION OF GMOS AND PLANT SPECIES IN FOOD AND FEED. edited by Pulkrabová J., Tomaniová M., Nielen M. and Hajšlová J. Proceedings in: 9th International Symposium on RECENT ADVANCES IN FOOD ANALYSIS, Prague, Czech Republic, November 5–8, UCT Prague, Book of Abstracts, p. 207, lecture L128. ISBN 978-80-7592-055-03.
|Year of conference
|USE OF HIGH THROUGHPUT SEQUENCING FOR DETECTION OF GMOS AND PLANT SPECIES IN FOOD AND FEED
|edited by Pulkrabová J., Tomaniová M., Nielen M. and Hajšlová J.
|9th International Symposium on RECENT ADVANCES IN FOOD ANALYSIS
|Prague, Czech Republic
|Book of Abstracts, p. 207, lecture L128. ISBN 978-80-7592-055-03
|NGS, GMO, plant, detection
|High Throughput Sequencing (HTS) is a new way to detect and characterize genetically modified organisms (GMOs). Whole genome sequencing approaches are not always able to detect a genetic modification due to the largely varying genome sizes from one plant species to another one and because some regions of the plant genome can be deeply sequenced while others are not covered. This issue is increased if the sample to be analysed contains a mix of several plant species. In the framework of GMO analysis it is also interesting to determine which plant species are present in a sample. A first strategy that was adopted triggered the sequencing to a set of defined DNA segments. Results focused essentially on data going beyond them. To that purpose, DNA was sheared in fragments of ~400 bp that were caught with capture probes of 100-120 bp using the SureSelect technology (Agilent Technologies, Santa Clara, CA). These probes were designed on the basis of a collection of sequences gathering structural elements (promoters, genes, terminators,…) that can be met in transgenic constructs or consisting of DNA segments that are specific to plant species. To analyse the large amount of collected data, a bioinformatic workflow was created. The workflow was divided into two parts. A first part aimed at the detection of the sequences, filtering and assigning the reads according to their alignment scores, and a second part focussed on the creation of contigs in an attempt to reconstruct the whole transgene or the sequence of the gene specific to the plant species. Compared to the 328 GM events listed in the GMOSeek matrix (Block et al., 2013), the adopted strategy would detect all of them except 2 GM events because they don’t contain any of the 40 targeted structural elements used for enrichment. Furthermore, the methodology theoretically enables the detection of 20 plant species. Practically, the approach showed its capacity to reconstruct partially or completely all of the 13 GM events tested that related to 7 plant species. This was possible even at GMO levels as low as 0.1%. Moreover, this is the first step towards a more informative analysis as the collection of probes is constantly updated in order to always propose a more powerful tool. Enrichment can be extended to sequences corresponding to additional structural elements, plant species, allergens and contaminants. In order to design a more general methodology unlimited by the availability of specific plant species sequences, a second strategy based on metagenomics was proposed. It is built on three universal plant targets with one of them being of nuclear origin while the 2 others are of mitochondrial origin. This approach was able to detect a large panel of plant species in mastered samples
|Debode, F., Hulin, J., Janssen, E., Berben, G.