Method for rapidly identifying transgenic or gene editing material and insertion site thereof by using whole genome resequencing data

Abstract

The invention discloses a method for rapidly identifying a transgenic or gene editing material and an insertion site thereof by using whole genome resequencing data. The method comprises the followingsteps: extracting a genome DNA; obtaining the double-end sequencing data of the whole genome; judging whether an expression vector sequence inserted into the plant to be detected and containing the T-DNA sequence is known or not; judging whether the to-be-detected plant has a transgenic event or a gene editing event or not, and whether a skeleton sequence transfer event occurs or not; and determining an insertion site of the T-DNA sequence. According to the invention, the method combines with a bioinformatics analysis means; under the condition that an expression vector is known or unknown, whether a transgenosis or gene editing event occurs or not is identified; under the condition that an expression vector is known, the accurate positioning, direction, copy number and flanking sequenceinformation of a target sequence inserted into a genome can be rapidly and accurately given; whether a skeleton sequence, namely a sequence except the target sequence, is inserted into the genome or not can also be identified, and the same positioning is given.

Description

technical field [0001] The invention relates to the technical field of bioinformatics, in particular to a method for rapidly identifying transgenic or gene editing materials and their insertion sites by using whole genome resequencing data. Background technique [0002] The method of quickly identifying transgenic materials or gene editing materials and their insertion sites refers to the "editing" or transformation of target genes in animals and plants by using transgenic technology or gene editing technology according to the principles of genetic engineering and according to people's wishes. A technology that realizes the targeted modification of the genetic traits of organisms such as the knockout and addition of specific DNA fragments. [0003] Traditional detection methods for transgenic or gene-edited exogenous gene fragments mainly include: 1. In situ hybridization: verify the integration, integrity and approximate gene copy number of the transgene; 2. Real-time fluor...

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Problems solved by technology

[0007] However, none of the above-mentioned patent documents takes into account that the insertion of foreign sequences leads to recombination or disorder of sequences around the insertion site of the genome, thereby reducing the sensitivity of the method and increasing the probability of false negatives and missed detections; When the vector sequence has partial homology to the genomic sequence, false positives increase

In addition, the above methods all use the mapping between the read sequence and the wild-type genome sequence of the plant to be tested, the process is cumbersome, time-consuming and laborious

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