Method for identifying transgenic events through whole genome sequencing data

A technology for whole-genome sequencing and transgenic events, applied in the fields of genomics, electrical digital data processing, and special data processing applications, etc., can solve the problems of low throughput, long experiment cycle, single identification content, etc., and achieve high repeatability, short time effect

Active Publication Date: 2016-06-01
CHINA AGRI UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

However, these methods have shortcomings such as long experimental period, single identification content, and low throughput.

Method used

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  • Method for identifying transgenic events through whole genome sequencing data
  • Method for identifying transgenic events through whole genome sequencing data
  • Method for identifying transgenic events through whole genome sequencing data

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0057] 1. Experimental materials: pBS-CD46-neo vector sequence (as shown in SEQ ID NO.1), full-length 12864bp, pig reference genome sequence, Ensemble version ssc3, whole genome sequencing data of transgenic pigs, with an average sequencing depth of about 30×.

[0058] 2. Alignment: Merge the vector and reference genome sequences by inputting the vector sequences and reference genome sequences into the comparison software bwa-0.7.10, and using the comparison software bwa-0.7.10 to compare the sequencing data and It compares.

[0059] Use a high-throughput sequencer (illuminaHiseq2000) to perform paired-end sequencing on the transgenic whole genome sample ssc3 containing the carrier pBS-CD46-neo to obtain paired-end sequencing reads, and the read length of each end of the paired-end sequencing reads is The 100bp sequence is called the end read; compare the sequencing data of the end read with the wild-type known reference genome sequence ssc3 of the transgenic sample ssc3 to be...

Embodiment 2

[0113] 1. Experimental materials: HLF-HLYBAC1 carrier sequence (as shown in SEQ ID NO.2), full-length 128496bp; Duroc reference genome sequence, Vega version ssc_v57; whole genome sequencing data of transgenic pigs, with an average sequencing depth of about 12×.

[0114] 2. Alignment: Merge the reference genome sequences of the vector and Duroc, and use the alignment software bwa-0.7.10 to compare the sequencing data with the same method as in Example 1.

[0115] 3. Extract card position readings: use the same method as in Example 1 to screen card position readings, and obtain 21 preliminary card position readings and 138 supplementary card position readings, a total of 159.

[0116] 4. Card position and rough positioning: The boundary of S / H and M in the comparison results of 21 preliminary card position reads is used as the insertion site, and the results are as follows:

[0117]

[0118] In the output results, each row of data represents the alignment output of a prelimi...

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Abstract

The invention provides a method for identifying transgenic events through whole genome sequencing data. The method comprises the steps that transgenic events are identified through a bioinformatics means, and the position, direction, copying number and flanking sequence information of foreign fragments inserted into genomes and the homozygous and heterozygous state of transgenic samples can be rapidly and effectively identified. Compared with traditional Genome walking, real-time quantitative PCR and other experiments methods, the method has the advantages that time is short, repeatability is high, the result is stable, and explaining is easier. The method is the most comprehensive in existing transgenic event detection methods, can accurately analyze influences of transgenic events on the living body within a short time, carries out safety evaluation on transgenic animals and plants, and pushes the transgenic technology to be applied in agriculture.

Description

technical field [0001] The invention belongs to the field of biotechnology, and in particular relates to a method for identifying transgenic events by using whole genome sequencing data. Background technique [0002] Transgenic refers to the process of using the principle of genetic engineering to introduce gene fragments that determine good traits into target animals and plants, so as to obtain high-quality varieties. Transgenic technology is also applied to the adult level research of some target genes. Therefore, transgenic animals and plants have made important contributions in basic biochemical research, research models of human diseases, and improving the yield and quality of agricultural products. With the deepening of genetically modified technology, genetically modified products have been widely promoted around the world, followed by public doubts about the safety of genetically modified products. The traditional detection methods of transgenic exogenous gene fragm...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/18
CPCG16B20/00
Inventor 赵毅强许文杰王宇哲欧阳红生
Owner CHINA AGRI UNIV
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