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A bioinformatics approach for identifying transgene insertion sites using whole genome sequencing data
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Park, Doori | - |
dc.contributor.author | Park, Su-Hyun | - |
dc.contributor.author | Ban, Yong Wook | - |
dc.contributor.author | Kim, Youn Shic | - |
dc.contributor.author | Park, Kyoung-Cheul | - |
dc.contributor.author | Kim, Nam-Soo | - |
dc.contributor.author | Kim, Ju-Kon | - |
dc.contributor.author | Choi, Ik-Young | - |
dc.date.accessioned | 2017-10-31T07:40:03Z | - |
dc.date.available | 2017-10-31T16:45:26Z | - |
dc.date.issued | 2017-08-15 | - |
dc.identifier.citation | BMC Biotechnology, 17(1):67 | ko_KR |
dc.identifier.issn | 1472-6750 | - |
dc.identifier.uri | https://hdl.handle.net/10371/137430 | - |
dc.description | This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. | ko_KR |
dc.description.abstract | Abstract
Background Genetically 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. Methods To 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. Results Herein, 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. Conclusion NGS 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. | ko_KR |
dc.language.iso | en | ko_KR |
dc.publisher | BioMed Central | ko_KR |
dc.subject | Genetically modified organism (GMO) | ko_KR |
dc.subject | GM rice | ko_KR |
dc.subject | Next-generation sequencing (NGS) | ko_KR |
dc.subject | Molecular characterization | ko_KR |
dc.subject | GM safety | ko_KR |
dc.subject | Bioinformatics | ko_KR |
dc.title | A bioinformatics approach for identifying transgene insertion sites using whole genome sequencing data | ko_KR |
dc.type | Article | ko_KR |
dc.contributor.AlternativeAuthor | 박두리 | - |
dc.contributor.AlternativeAuthor | 박수현 | - |
dc.contributor.AlternativeAuthor | 반용욱 | - |
dc.contributor.AlternativeAuthor | 김윤식 | - |
dc.contributor.AlternativeAuthor | 박경철 | - |
dc.contributor.AlternativeAuthor | 김남수 | - |
dc.contributor.AlternativeAuthor | 김주곤 | - |
dc.contributor.AlternativeAuthor | 최익영 | - |
dc.identifier.doi | 10.1186/s12896-017-0386-x | - |
dc.language.rfc3066 | en | - |
dc.rights.holder | The Author(s). | - |
dc.date.updated | 2017-10-03T16:47:08Z | - |
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