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A bioinformatics approach for identifying transgene insertion sites using whole genome sequencing data

机译：使用全基因组测序数据鉴定转基因插入位点的生物信息学方法

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BackgroundGenetically modified crops (GM crops) have been developed to improve the agricultural traits of modern crop cultivars. Safety assessments of GM crops are of paramount importance in research at developmental stages and before releasing transgenic plants into the marketplace. Sequencing technology is developing rapidly, with higher output and labor efficiencies, and will eventually replace existing methods for the molecular characterization of genetically modified organisms. MethodsTo detect the transgenic insertion locations in the three GM rice gnomes, Illumina sequencing reads are mapped and classified to the rice genome and plasmid sequence. The both mapped reads are classified to characterize the junction site between plant and transgene sequence by sequence alignment. ResultsHerein, we present a next generation sequencing (NGS)-based molecular characterization method, using transgenic rice plants SNU-Bt9–5, SNU-Bt9–30, and SNU-Bt9–109. Specifically, using bioinformatics tools, we detected the precise insertion locations and copy numbers of transfer DNA, genetic rearrangements, and the absence of backbone sequences, which were equivalent to results obtained from Southern blot analyses. ConclusionNGS methods have been suggested as an effective means of characterizing and detecting transgenic insertion locations in genomes. Our results demonstrate the use of a combination of NGS technology and bioinformatics approaches that offers cost- and time-effective methods for assessing the safety of transgenic plants.
机译：背景技术已经开发了转基因作物（GM作物）以改善现代作物品种的农业特性。在研发阶段以及将转基因植物投放市场之前，对转基因作物的安全性评估至关重要。测序技术发展迅速，具有更高的产量和劳动效率，并将最终取代现有的转基因生物分子鉴定方法。方法为检测三个转基因水稻侏儒中的转基因插入位置，对Illumina测序读物进行定位并分类到水稻基因组和质粒序列。两种定位的读段都被分类以通过序列比对来表征植物和转基因序列之间的连接位点。结果在此，我们提出了一种基于下一代测序（NGS）的分子表征方法，该方法使用转基因水稻植物SNU-Bt9-5，SNU-Bt9-30和SNU-Bt9-109。具体而言，使用生物信息学工具，我们检测到了转移DNA的精确插入位置和拷贝数，遗传重排以及没有骨架序列，这与从Southern印迹分析获得的结果相当。结论已提出NGS方法作为表征和检测基因组中转基因插入位置的有效手段。我们的研究结果表明，结合使用NGS技术和生物信息学方法，可提供经济高效的方法来评估转基因植物的安全性。

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