Probe design method and positioning method for wheat exon sequencing gene positioning

A technology for exon sequencing and gene mapping, which is applied in the fields of biochemical equipment and methods, genomics, and microbial determination/inspection, and can solve the problem of high cost of genetic information.

Active Publication Date: 2021-05-25
成都天成未来科技有限公司
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  • Abstract
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  • Claims
  • Application Information

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Problems solved by technology

[0005] In view of the shortcomings of the prior art described above, the purpose of the present invention is to provide a probe design method for wheat exon sequencing gene localization, which is used to solve the problem that the large wheat genome in the prior art leads to the use of whole gene sequencing BSA- seq means to obtain the problem of high cost of gene information, meanwhile, the present invention will also provide a wheat exon sequencing gene positioning method

Method used

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  • Probe design method and positioning method for wheat exon sequencing gene positioning
  • Probe design method and positioning method for wheat exon sequencing gene positioning
  • Probe design method and positioning method for wheat exon sequencing gene positioning

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Embodiment 1

[0034] A probe design method for wheat exome sequencing gene localization, comprising the steps of:

[0035] Step 1. Select different tissues, environments, and developmental data through large-scale transcriptome sequencing data, and then perform sequencing on the second-generation Illumina high-throughput sequencing platform to obtain sequencing data for use;

[0036] Step 2: Use the STAR software to compare and analyze the sequencing data and the comparison reference genome, and then use the stringtie function to splice the transcripts, and filter the transcripts whose gene expression level TPM is less than 2, and keep the transcripts with TPM ≥ 2 for later use; The comparison reference genome is specifically IWGSCRefSeq (https: / / www.wheatgenome.org / );

[0037] Step 3. Merge the transcript in step 2 with the IWGSC CS Annotation transcript to obtain the merged transcript for use;

[0038] Step 4. Use TransDecoder (v5.5.0) to perform ORF prediction on the merged transcripts ...

Embodiment 2

[0053] A probe design method for wheat exome sequencing gene localization, comprising the steps of:

[0054] Step 1. Select different tissues, environments, and developmental data through large-scale transcriptome sequencing data, and then perform sequencing through the BGI BIGseq high-throughput sequencing platform to obtain sequencing data for use;

[0055] Step 2: Use the STAR software to compare and analyze the sequencing data and the comparison reference genome, and then use the stringtie function to splice the transcripts, and filter the transcripts whose gene expression level TPM is less than 2, and keep the transcripts with TPM ≥ 2 for later use; The comparison reference genome is specifically IWGSC RefSeq (https: / / www.wheatgenome.org / );

[0056] Step 3. Merge the transcript in step 2 with the IWGSC CS Annotation transcript to obtain the merged transcript for use;

[0057] Step 4. Use TransDecoder (v5.5.0) to perform ORF prediction on the merged transcripts in step 3,...

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Abstract

The invention relates to the technical field of wheat functional gene localization, in particular to a probe design method for wheat exon sequencing gene localization, which comprises the following steps of: sequencing through a high-throughput sequencing platform to obtain transcriptome data, comparing and analyzing the transcriptome data with a comparison reference genome, splicing and combining transcripts, and performing ORF prediction; and deleting the sequence of the repeated region, and performing high-density probe synthesis on the screened sequence to obtain the probe. The gene localization method comprises the following steps: breaking wheat DNA into fragments, hybridizing the broken wheat DNA with the high-density probe, enriching magnetic beads, eluting the liquid, and carrying out high-throughput sequencing, variation detection and statistical localization. The invention solves the problem of high gene positioning cost caused by huge wheat genome in the prior art, and by designing the superhigh-density multiple primer probe, sequencing is only carried out on the gene exon sequence, and the sequencing cost is reduced by 80% under the condition of the same gene sequencing depth.

Description

technical field [0001] The invention relates to the technical field of wheat functional gene positioning, in particular to a probe design method and a positioning method for wheat exon sequencing gene positioning. Background technique [0002] The existing wheat genome sequencing BSA-seq is to sequence and detect the whole wheat genome. Because the wheat genome is very large, the cost is too high. [0003] The existing wheat transcriptome sequencing BSR-seq uses gene expression data for detection, which is affected by factors such as sample organization, sample period, and environment, and has a very large data preference. Gene expression data itself is not genetic information and has certain false positive. [0004] Existing SNP chips cannot obtain gene sequence information and the SNP density is relatively low. SNP chips can only analyze mutation signals, but cannot obtain sequence information of materials and samples. Contents of the invention [0005] In view of the ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/20G16B25/10G16B30/10C12Q1/6874
CPCG16B20/20G16B30/10G16B25/10C12Q1/6874C12Q2535/122
Inventor 陈中旭
Owner 成都天成未来科技有限公司
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