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Parsing of biological core genome information through low-cost assembling based on apparent group information

A genome and genome sequence technology, applied in the field of biological assembly analysis, can solve the problems of underestimated polymorphism, high requirements for genome sequence information, and difficulty in meeting the genetic analysis of large genome species populations.

Active Publication Date: 2019-10-11
CAS CENT FOR EXCELLENCE IN MOLECULAR PLANT SCI
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

It is widely used in human research, and its advantage is that it directly enriches the sequence of the coding region, and the subsequent functional analysis is relatively simple, but it requires high information on the existing genome sequence, and the initial investment cost of making a capture chip is high, and the chip produced can only It is used for groups with small genetic variation. For groups with large genetic variation, techniques relying on reference genomes, including exome sequencing and even whole-genome resequencing, will significantly underestimate polymorphisms (Comprehensive comparison of three commercial human whole -exomecapture platforms. Genome Biology, 12, R95)
However, the genetic diversity among different lines of economic crops is much higher than the inter-race differences, and these alternative methods are difficult to meet the needs of population genetic analysis for large-genome species with relatively high polymorphism

Method used

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  • Parsing of biological core genome information through low-cost assembling based on apparent group information
  • Parsing of biological core genome information through low-cost assembling based on apparent group information
  • Parsing of biological core genome information through low-cost assembling based on apparent group information

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0073] Embodiment 1, genetic polymorphism experimental method and calculation process of the present invention

[0074] 1. Chromatin immunoprecipitation (ChIP)

[0075] 1. Select the materials of the corresponding organizations in the required period.

[0076] 2. Put the materials in pre-cooled Fix Buffer on ice (use 100ml Fix Buffer for each material). If the material is too large, the material can be cut into pieces.

[0077] 3. Vacuum pumping (10min), cover the mouth of the bottle with gauze to prevent the material from spraying out during pumping.

[0078]4. Add 5ml of 2.5M glycine and continue pumping for 5 minutes.

[0079] 5. Wash 5 times with deionized water, the last time remove as much excess water as possible.

[0080] 6. Fully grind the material with liquid nitrogen, and grind at least 4 times.

[0081] 7. Pour the powder into a 50ml Falcon tube and quantify. The process was performed in liquid nitrogen. Can be stored at -80°C.

[0082] 8. Add 15ml of CLB1 ...

Embodiment 2

[0127] Embodiment 2, the assay analysis of wheat

[0128] In this example, taking Chinese spring wheat as an example, the important evaluation parameters after the simplified genome sequencing scheme are analyzed in sequence.

[0129]Chinese spring wheat was obtained, and H3K4me3 and H3K27me3 antibodies were used to perform co-immunoprecipitation using the method described in Example 1 above. Afterwards, ChIP-seq library construction and sequencing were performed. Then perform CGT-Seq de novo assembly. After that, the steps of assembling, filling and extending are carried out.

[0130] The effect evaluation is as follows:

[0131] 1. Accuracy

[0132] Using Circos (http: / / circos.ca / ) mapping software, compare the sequence obtained by using the method in Example 1 above with the sequenced Chinese spring wheat data (the latest RefSeq version v1.0 published by the International Wheat Sequencing Consortium) , the result is as figure 2 As shown, the fragments captured by H3K...

Embodiment 3

[0144] Embodiment 3, the assay analysis of rice

[0145] Chinese spring wheat was obtained, and H3K4me3, H3K4me1, H3K27me3, H3K27ac, H3K36me3 were used as co-immunoprecipitation antibodies, and the co-immunoprecipitation was carried out by the method described in the foregoing Example 1. Afterwards, ChIP-seq library construction and sequencing were performed, followed by CGT-Seq de novo assembly.

[0146] The effect evaluation is as follows:

[0147] First, by comparing with gene position and gene expression ( Image 6 ), it can be seen that H3K4me3, H3K4me1, H3K27ac, and H3K36me3 modifications are positively correlated with gene expression, and are mainly distributed near highly expressed genes, among which H3K4me3 is most widely modified; H3K27me3 is negatively correlated with gene expression, mainly distributed in non-expressed and low-expressed genes. near expressed genes. Therefore in all subsequent experiments the combination of H3K4me3 and H3K27me3 was used for analy...

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Abstract

The invention relates to a method for parsing biological genome information through low-cost assembling of a core genome based on apparent group information and application of the method. The novel method for obtaining the core genome sequence information includes the steps of capturing one or more nucleotide sequences used for regulating and controlling gene activity and combined with apparent modification, and conducting database creating, sequencing, splicing, assembling and the like on the obtained sequences to obtain sequence information. By means of the method, gene region sequences or regulation and control region sequences of long segments can be obtained from the species without reference genomes and the species with large genetic difference without depending on any existing sequence information.

Description

technical field [0001] The invention belongs to the field of biological assembly and analysis, and more specifically, the invention relates to a method for assembling and analyzing biological genome information at low cost based on epigroup information and its application. Background technique [0002] In the past decade, whole genome sequencing and resequencing have been widely used to discover the genetic differences among different strains of crops, which has promoted major changes in the field of genetic breeding from research methods to economic applications. Resequencing refers to the genome resequencing of different individuals or different tissues of an individual within a species when the genome of the species is known, and the differences between different individuals or tissue cells can be found at the genome-wide level. [0003] However, many economic species have undergone long-term domestication and have complex and large genomes. For example, the currently co...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6806C12Q1/6869C12Q1/6827
CPCC12Q1/6806C12Q1/6869C12Q1/6827
Inventor 张一婧齐美芳
Owner CAS CENT FOR EXCELLENCE IN MOLECULAR PLANT SCI
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