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Method for detecting differential methylation region of plant genomes

A plant genome and detection method technology, applied in the field of detection of differentially methylated regions of the plant genome, can solve the problems of unclear relationship and mechanism of plant response to drought, time-consuming detection and analysis process, unfavorable rapid analysis and detection, etc.

Active Publication Date: 2019-04-16
KUNMING INST OF BOTANY - CHINESE ACAD OF SCI
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  • Abstract
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Problems solved by technology

However, the research on DNA methylation is limited to a few species, and the relationship and mechanism with plant response to drought are not clear, and more research and discoveries are urgently needed
[0004] At present, the application publication number is CN102061337A, a patent for tDMR detection method of tissue-specific differential methylation region discloses a detection method of differential methylation region, although this method has good applicability to a variety of genome sources , but the detection and analysis process takes a long time, which is not conducive to the realization of rapid analysis and detection

Method used

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  • Method for detecting differential methylation region of plant genomes
  • Method for detecting differential methylation region of plant genomes
  • Method for detecting differential methylation region of plant genomes

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0058] 1. Cultivation and drought treatment of Physcomitrella patens

[0059] Use BCDAT medium to cultivate Physcomitrella patens, get the protocelium material to polish and subculture, and light it for 14 hours (light intensity 500 μmol·m -2 ·s -1 ) / 10 hours of darkness, cultured in a culture room at 25°C for 40 days. The plant material is removed and dried and rehydrated. After about 2 hours of drying treatment, when the water loss reaches about 80%, take a sample. BCDAT medium: 0.1% TES, 1% stock solution B, 1% stock solution D, 1% stock solution C, 5mmol / L ammonium tartrate, 1mmol / L CaCl2 2H 2 O, 0.8% agar powder (solid). After autoclaving, store at room temperature.

[0060] 2. Genomic DNA extraction

[0061] The control group (M01) and the drought treatment (M02) were selected as samples, and genomic DNA was extracted by CTAB method. The quality of the extracted genomic DNA was tested by Nanodrop-2000 and agarose gel electrophoresis. CTAB extract: 2% cetyltriethy...

Embodiment 2

[0070] The methylation information of a single cytosine site on all chromosomes in the whole genome of the control group (M01) and the treatment group (M02) obtained in Example 1 is stored in a python dictionary. In order to quickly find the methylation information of a certain region on the chromosome later, the storage time is segmented (50 bp for each region) to store the information of the cytosine site. The specific form of the dictionary is {chr:{binOrder:{type:[support,unsupport,total]}}}, such as {chr1:{2:{CG:1580,265,25}}}, which means: in the first In the chromosome, in the second region (50bp is a region, starting from 1), there are a total of 25 CG-type cytosine sites, and the total number of reads that support methylation at these 25 sites is 1580, and the number of reads that do not support methylation The total number of base-based reads was 265.

[0071] Compare the methylation information of a single cytosine site on all chromosomes in the whole genome of the...

Embodiment 4

[0077] The present invention uses online databases to analyze biological processes, see the websites http: / / wego.genomics.org.cn / and http: / / kobas.cbi.pku.edu.cn / for details. The main biological processes involved in genes regulated by methylation under drought treatment were obtained through analysis (see Figure 4 ).

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Abstract

The invention provides a method for detecting a differential methylation region of plant genomes, and belongs to the technical field of genomics and bioinformatics. Single-locus methylation data on whole genomes of a treatment group and a control group is obtained separately through methylation sequencing of the whole plant genomes; single-locus methylation information on the whole genomes of thetreatment group and the control group is read separately and stored by section; stored methylation information of each section of the whole genomes is stored with 200 bp as a window and 50 bp as a step length sliding window, and the scanned methylation information is stored into a python dictionary by section; the methylation information, stored in the python dictionary, of each section of the whole genomes is screened, and the methylation information of each section in each window is counted according to the obtained single-locus methylation information on the effective whole genomes. By means of the method, the python dictionary is utilized for storing a whole chromosome with 50 bp as a section, subsequent operations are facilitated, and a lot of time is saved.

Description

technical field [0001] The invention belongs to the technical fields of genomics and bioinformatics, and in particular relates to a method for detecting differentially methylated regions of plant genomes. Background technique [0002] Since the beginning of the 21st century, affected by extreme weather, the economic losses caused by drought in my country have been increasing. According to statistics, in 2015, the direct economic loss caused by drought in my country was as high as 57.9 billion RMB. Under such severe drought conditions, it is particularly important and urgent to study the drought resistance mechanism of plants. In 1942, Waddington proposed the term "epigenetics", which was later defined by Wolff et al. as a discipline in which the DNA sequence does not change but the gene expression undergoes heritable changes. In subsequent studies, DNA methylation, histone methylation, acetylation and other epigenetic modifications were discovered. DNA methylation refers ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/20G16B25/00
Inventor 刘莉刘高京杨红李萍徐伟温从发任昭杰
Owner KUNMING INST OF BOTANY - CHINESE ACAD OF SCI
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