Efficiency to Discovery Transgenic Loci in GM Rice Using Next Generation Sequencing Whole Genome Re-sequencing
Molecular characterization technology in genetically modified organisms, in addition to how transgenic biotechnologies are developed now require full transparency to assess the risk to living modified and non-modified organisms. Next generation sequencing (NGS) methodology is suggested as an effecti...
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| Language: | English |
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BioMed Central
2015-09-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gni-13-81.pdf |
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| author | Doori Park Dongin Kim Green Jang Jongsung Lim Yun-Ji Shin Jina Kim Mi-Seong Seo Su-Hyun Park Ju-Kon Kim Tae-Ho Kwon Ik-Young Choi |
| author_facet | Doori Park Dongin Kim Green Jang Jongsung Lim Yun-Ji Shin Jina Kim Mi-Seong Seo Su-Hyun Park Ju-Kon Kim Tae-Ho Kwon Ik-Young Choi |
| author_sort | Doori Park |
| collection | DOAJ |
| description | Molecular characterization technology in genetically modified organisms, in addition to how transgenic biotechnologies are developed now require full transparency to assess the risk to living modified and non-modified organisms. Next generation sequencing (NGS) methodology is suggested as an effective means in genome characterization and detection of transgenic insertion locations. In the present study, we applied NGS to insert transgenic loci, specifically the epidermal growth factor (EGF) in genetically modified rice cells. A total of 29.3 Gb (~72× coverage) was sequenced with a 2 × 150 bp paired end method by Illumina HiSeq2500, which was consecutively mapped to the rice genome and T-vector sequence. The compatible pairs of reads were successfully mapped to 10 loci on the rice chromosome and vector sequences were validated to the insertion location by polymerase chain reaction (PCR) amplification. The EGF transgenic site was confirmed only on chromosome 4 by PCR. Results of this study demonstrated the success of NGS data to characterize the rice genome. Bioinformatics analyses must be developed in association with NGS data to identify highly accurate transgenic sites. |
| format | Article |
| id | doaj-art-d297f117fc714771adb306a3e44bf0cd |
| institution | Kabale University |
| issn | 1598-866X 2234-0742 |
| language | English |
| publishDate | 2015-09-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-d297f117fc714771adb306a3e44bf0cd2025-02-02T17:03:11ZengBioMed CentralGenomics & Informatics1598-866X2234-07422015-09-01133818510.5808/GI.2015.13.3.81157Efficiency to Discovery Transgenic Loci in GM Rice Using Next Generation Sequencing Whole Genome Re-sequencingDoori Park0Dongin Kim1Green Jang2Jongsung Lim3Yun-Ji Shin4Jina Kim5Mi-Seong Seo6Su-Hyun Park7Ju-Kon Kim8Tae-Ho Kwon9Ik-Young Choi10Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Korea.National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.Natural Bio-Materials Inc., Wanju 55322, Korea.Natural Bio-Materials Inc., Wanju 55322, Korea.Natural Bio-Materials Inc., Wanju 55322, Korea.Crop Biotech Institute, Green-Bio Science and Technology, Seoul National University, Pyeongchang 25354, Korea.Crop Biotech Institute, Green-Bio Science and Technology, Seoul National University, Pyeongchang 25354, Korea.Natural Bio-Materials Inc., Wanju 55322, Korea.Natural Bio-Materials Inc., Wanju 55322, Korea.Molecular characterization technology in genetically modified organisms, in addition to how transgenic biotechnologies are developed now require full transparency to assess the risk to living modified and non-modified organisms. Next generation sequencing (NGS) methodology is suggested as an effective means in genome characterization and detection of transgenic insertion locations. In the present study, we applied NGS to insert transgenic loci, specifically the epidermal growth factor (EGF) in genetically modified rice cells. A total of 29.3 Gb (~72× coverage) was sequenced with a 2 × 150 bp paired end method by Illumina HiSeq2500, which was consecutively mapped to the rice genome and T-vector sequence. The compatible pairs of reads were successfully mapped to 10 loci on the rice chromosome and vector sequences were validated to the insertion location by polymerase chain reaction (PCR) amplification. The EGF transgenic site was confirmed only on chromosome 4 by PCR. Results of this study demonstrated the success of NGS data to characterize the rice genome. Bioinformatics analyses must be developed in association with NGS data to identify highly accurate transgenic sites.http://genominfo.org/upload/pdf/gni-13-81.pdfgenetically modified organismsnext generation sequencing (NGS) T-DNAricerisk assessment |
| spellingShingle | Doori Park Dongin Kim Green Jang Jongsung Lim Yun-Ji Shin Jina Kim Mi-Seong Seo Su-Hyun Park Ju-Kon Kim Tae-Ho Kwon Ik-Young Choi Efficiency to Discovery Transgenic Loci in GM Rice Using Next Generation Sequencing Whole Genome Re-sequencing Genomics & Informatics genetically modified organisms next generation sequencing (NGS) T-DNA rice risk assessment |
| title | Efficiency to Discovery Transgenic Loci in GM Rice Using Next Generation Sequencing Whole Genome Re-sequencing |
| title_full | Efficiency to Discovery Transgenic Loci in GM Rice Using Next Generation Sequencing Whole Genome Re-sequencing |
| title_fullStr | Efficiency to Discovery Transgenic Loci in GM Rice Using Next Generation Sequencing Whole Genome Re-sequencing |
| title_full_unstemmed | Efficiency to Discovery Transgenic Loci in GM Rice Using Next Generation Sequencing Whole Genome Re-sequencing |
| title_short | Efficiency to Discovery Transgenic Loci in GM Rice Using Next Generation Sequencing Whole Genome Re-sequencing |
| title_sort | efficiency to discovery transgenic loci in gm rice using next generation sequencing whole genome re sequencing |
| topic | genetically modified organisms next generation sequencing (NGS) T-DNA rice risk assessment |
| url | http://genominfo.org/upload/pdf/gni-13-81.pdf |
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