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. 2009 Oct 8:9:87.
doi: 10.1186/1472-6750-9-87.

Characterization of unknown genetic modifications using high throughput sequencing and computational subtraction

Torstein Tengs  1 , Haibo Zhang, Arne Holst-Jensen, Jon Bohlin, Melinka A Butenko, Anja Bråthen Kristoffersen, Hilde-Gunn Opsahl Sorteberg, Knut G Berdal
Affiliations

Characterization of unknown genetic modifications using high throughput sequencing and computational subtraction

Torstein Tengs et al. BMC Biotechnol. .

Abstract

Background: When generating a genetically modified organism (GMO), the primary goal is to give a target organism one or several novel traits by using biotechnology techniques. A GMO will differ from its parental strain in that its pool of transcripts will be altered. Currently, there are no methods that are reliably able to determine if an organism has been genetically altered if the nature of the modification is unknown.

Results: We show that the concept of computational subtraction can be used to identify transgenic cDNA sequences from genetically modified plants. Our datasets include 454-type sequences from a transgenic line of Arabidopsis thaliana and published EST datasets from commercially relevant species (rice and papaya).

Conclusion: We believe that computational subtraction represents a powerful new strategy for determining if an organism has been genetically modified as well as to define the nature of the modification. Fewer assumptions have to be made compared to methods currently in use and this is an advantage particularly when working with unknown GMOs.

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Figures

Figure 1
Figure 1
Construct-derived sequences found in the transgenic EST libraries generated using the ABF3 rice line and SunUp papaya. 15 sequences were found in the rice library, whereas the SunUp papaya cDNA collection contained 23 construct-derived sequences. Two versions of the papaya ringspot virus coat protein (PRSVcp) transcripts were found, and labeled in green are sequences from the cucumber mosaic virus coat protein (CMVcp) gene. When present in the sequences, poly(A) tails have been indicated and the sequences have been labeled with their GenBank EST accession numbers. Construct maps were modified from [18,19,21] and . Ubi1 - maize ubiquitin promoter 1. ABF3 - abscisic acid responsive elements-binding factor 3. 3'pinII - 3' region of potato proteinase inhibitor II. 35S - Cauliflower Mosaic Virus (CaMV) P35S promoter. bar - phosphinothricin acetyltransferase. 3'nos - 3' region of nopaline synthase. 5'nos - 5' region of nopaline synthase. nptII - neomycin phosphotransferase II. PRSVcp - Papaya Ringspot Virus coat protein. t35S - CaMV P35S terminator. UidA - beta glucuronidase.
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References

    1. Thompson CJ, Movva NR, Tizard R, Crameri R, Davies JE, Lauwereys M, Botterman J. Characterization of the herbicide-resistance gene bar from Streptomyces hygroscopicus. EMBO J. 1987;6:2519–2523. - PMC - PubMed
    1. Sheehy RE, Kramer M, Hiatt WR. Reduction of polygalacturonase activity in tomato fruit by antisense RNA. Proc Natl Acad Sci USA. 1988;85:8805–8809. doi: 10.1073/pnas.85.23.8805. - DOI - PMC - PubMed
    1. Ye X, Al-Babili S, Kloti A, Zhang J, Lucca P, Beyer P, Potrykus I. Engineering the provitamin A (beta-carotene) biosynthetic pathway into (carotenoid-free) rice endosperm. Science. 2000;287:303–305. doi: 10.1126/science.287.5451.303. - DOI - PubMed
    1. Weber G, Shendure J, Tanenbaum DM, Church GM, Meyerson M. Identification of foreign gene sequences by transcript filtering against the human genome. Nat Genet. 2002;30:141–142. - PubMed
    1. Tengs T, LaFramboise T, Den RB, Hayes DN, Zhang J, DebRoy S, Gentleman RC, O'Neill K, Birren B, Meyerson M. Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments. Nucleic Acids Res. 2004;32:e121. doi: 10.1093/nar/gnh120. - DOI - PMC - PubMed

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