Whole genome re-sequencing can improve basis for transgene safety assessments
Total genomic DNA was extracted from rice seeds using the DNeasy Plant Mini Kit (Qiagen). The quality of the extracted rice genomic DNA was evaluated by UV-photospectrometry with a Nanodrop ND-8000 (Thermo Scientific) and 1% agarose gel electrophoresis. The sequencing DNA library was created using Illumina Paired-End library preparation kits and Illumina Oligos for adaptor ligation according to the manufacturer’s instructions (Illumina). The mean fragment size was about 500 bp. The constructed DNA library was quantified by Pico-Green (Quant-iT; Invitrogen) and Agilent Bioanalyzer DNA 1000 kit (Agilent Technologies). 90 cycles of paired-end sequencing were performed on a single lane of an Illumina HiSeq 2000 DNA sequencer (Illumina). Paired-end sequencing and simple modification of the raw data to ensure sequencing quality were performed by BGI-Shenzhen (Shenzhen, China).