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Method for mining endophytic microbiome information from animal and plant transcriptome data

A transcriptome, animal and plant technology, applied in the fields of bioinformatics, digital data information retrieval, informatics, etc., can solve the problem of high cost and achieve the effect of saving the cost of experimental research

Pending Publication Date: 2021-08-20
ANHUI AGRICULTURAL UNIVERSITY
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Problems solved by technology

The use of amplicon analysis, or whole genome sequencing of animal and plant tissues requires separate experimental operations, and the cost is high

Method used

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  • Method for mining endophytic microbiome information from animal and plant transcriptome data
  • Method for mining endophytic microbiome information from animal and plant transcriptome data

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Embodiment 1

[0021] This embodiment provides a method for mining endogenous microbiome information from animal and plant transcriptome data, such as figure 1 As shown, the steps include:

[0022] (1) Cleaning of raw data of host animal and plant transcriptome sequencing: use the open source software trimmomatic, use the default parameters: java-jar trimmomatic-0.33.jar PE input_forward.fq.gz input_reverse.fq.gzoutput_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10LEADING:3TRAILING:3SLIDINGWINDOW:4:15MINLEN:36

[0023] (2) Obtain transcriptome data files containing microbial sequences

[0024] Use the open source software hisat2-build to build the host animal and plant reference genome index file, refer to the command: hisat2-build genome.fa geome_index. Use hisat2 to compare the transcriptome sequencing file with the host animal and plant reference genome index file, and output the unmatched f...

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Abstract

The invention discloses a method for mining endophytic microbiome information from animal and plant transcriptome data, which comprises the following steps of: (1) cleaning host animal and plant transcriptome sequencing original data to obtain transcriptome data only containing high-quality sequences; (2) comparing the transcriptome data with a host reference genome to obtain a data file containing a microbial sequence; and (3) analyzing the data file to obtain the composition information of the endophytic microorganisms. Compared with the method for analyzing microorganism composition information through amplicon analysis or animal and plant tissue whole genome sequencing, the method has the advantages that the composition and content information of various microorganisms can be analyzed, original host animal and plant gene expression information can be obtained, and the experimental research cost is saved.

Description

technical field [0001] The invention relates to the technical field of biological high-throughput data analysis, in particular to a method for mining endogenous microbiome information from animal and plant transcriptome data. Background technique [0002] Microorganisms are found almost everywhere in nature, such as rivers, lakes, oceans, soil, air, human surfaces and interiors of humans, animals and plants. Many microorganisms including bacteria, archaea and fungi can live in the tissues of plants. Endophytes are microorganisms that exist in various tissues of the host plant in a symbiotic or beneficial manner or do not cause any harmful effects. A small number of endophytes can enhance host plant tolerance to abiotic stresses (e.g., heat tolerance), while others can promote phytohormone production, dissolution of phosphorus and potassium, biological nitrogen fixation, inhibition of ethylene biosynthesis plant growth. In addition, many endophytes can protect plants from ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B30/00G16B25/00G16B40/00G16B50/30G06F16/2458G06F16/215
CPCG16B30/00G16B25/00G16B40/00G16B50/30G06F16/2465G06F16/215
Inventor 韩国民王先进邱贵萍陈枫程备久
Owner ANHUI AGRICULTURAL UNIVERSITY
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