T-LOC: A comprehensive tool to localize and characterize T-DNA integration sites

文献类型： 外文期刊

第一作者： Li, Shaofang

作者： Li, Shaofang;Wang, Chenyang;Zhou, Xueping;Zhou, Huanbin;Wang, Chenyang;You, Chenjiang;You, Chenjiang;Zhou, Xueping

作者机构：

期刊名称：PLANT PHYSIOLOGY （ 影响因子：8.005； 五年影响因子：9.115 ）

ISSN： 0032-0889

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收录情况： SCI

摘要： T-LOC is a robust approach to studying T-DNA integration sites (TISs) independently of the integration pattern and can recover all types of TISs in transgenic plants. Scientists have developed many approaches based on PCR or next-generation sequencing to localize and characterize integrated T-DNAs in transgenic plants generated by Agrobacterium tumefaciens-mediated T-DNA transfer. However, none of these methods has the robust ability to handle all transgenic plants with diversified T-DNA patterns. Utilizing the valuable information in the whole-genome sequencing data of transgenic plants, we have developed a comprehensive approach (T-LOC) to localize and characterize T-DNA integration sites (TISs). We evaluated the performance of T-LOC on genome sequencing data from 48 transgenic rice (Oryza sativa) plants that provide real and unbiased resources of T-DNA integration patterns. T-LOC discovered 75 full TISs and reported a diversified pattern of T-DNA integration: the ideal single-copy T-DNA between two borders, multiple-copy of T-DNAs in tandem or inverted repeats, truncated partial T-DNAs with or without the selection hygromycin gene, the inclusion of T-DNA backbone, the integration at the genome repeat region, and the concatenation of multiple ideal or partial T-DNAs. In addition, we reported that DNA fragments from the two A. tumefaciens plasmids can be fused with T-DNA and integrated into the plant genome. Besides, T-LOC characterizes the genomic changes at TISs, including deletion, duplication, accurate repair, and chromosomal rearrangement. Moreover, we validated the robustness of T-LOC using PCR, Sanger sequencing, and Nanopore sequencing. In summary, T-LOC is a robust approach to studying the TISs independent of the integration pattern and can recover all types of TISs in transgenic plants.

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