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Construction method of plant paired NLR resistance gene database and multi-species paired NLR gene database thereof

A resistance gene and construction method technology, applied in the field of gene sequence data processing, can solve the problems of plant disease resistance gene cloning, analysis and application obstacles, frequent NLR gene duplication and loss, uneven genome distribution, etc., to achieve accelerated resistance The effect of disease breeding

Pending Publication Date: 2021-11-09
NANJING UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, these NLR genes have the following evolutionary characteristics: their distribution in the whole genome is not uniform, mainly in concentrated distribution, mostly in clusters, and in the same cluster, they are mainly tandem repeats; the same NBS-LRR gene is even distributed among different species There are large nucleotide differences between different strains of the same species; between different strains of plants, the duplication and loss of NLR genes are very frequent
The above characteristics have created great obstacles for the cloning, analysis and application of plant disease resistance genes.

Method used

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  • Construction method of plant paired NLR resistance gene database and multi-species paired NLR gene database thereof
  • Construction method of plant paired NLR resistance gene database and multi-species paired NLR gene database thereof
  • Construction method of plant paired NLR resistance gene database and multi-species paired NLR gene database thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0044] Identification of paired NLR genes in Brachypodium distachyon

[0045] 1. Collection of basic data: Collect the genome sequence, protein sequence and gene annotation information of Brachypodium distachyon from the JGI public database (https: / / phytozome.jgi.doe.gov);

[0046] 2. Identification of NLR genes and gene clusters: (1) Firstly, based on the protein sequence information of the whole genome, obtain the structural domain information of all protein sequences through the Hmmscan tool, and screen the proteins containing the NB-ARC domain (PF00931), parameters Set to E-value≤1e-4; (2) Then use the NLR-parser tool to detect the LRR domain and screen for proteins with motif 9, 11 or 19, and have both the NB-ARC domain and the LRR domain The gene of the NLR gene is the main NLR gene, and the gene with only the NB-ARC domain is the candidate NLR gene; (3) Then based on the physical distance and gene number of the NLR gene on the chromosome in the gene annotation, we put t...

Embodiment 2

[0052] Identification of paired NLR genes in barley (Hordeum vulgare)

[0053]1. Collection of basic data: Collect genome sequence, protein sequence and gene annotation information of barley from Ensembl public database (http: / / plants.ensembl.org);

[0054] 2. Identification of NLR genes and gene clusters: (1) Firstly, based on the protein sequence information of the whole genome, obtain the structural domain information of all protein sequences through the Hmmscan tool, and screen the proteins containing the NB-ARC domain (PF00931), parameters Set to E-value≤1e-4; (2) Then use the NLR-parser tool to detect the LRR domain and screen for proteins with motif 9, 11 or 19, and have both the NB-ARC domain and the LRR domain The gene of the NLR gene is the main NLR gene, and the gene with only the NB-ARC domain is the candidate NLR gene; (3) Then based on the physical distance and gene number of the NLR gene on the chromosome in the gene annotation, we put the physical distance on t...

Embodiment 3

[0060] Identification of paired NLR genes in sorghum (Sorghum bicolor)

[0061] 1. Collection of basic data: Collect genome sequence, protein sequence and gene annotation information of sorghum from JGI public database (https: / / phytozome.jgi.doe.gov);

[0062] 2. Identification of NLR genes and gene clusters: (1) Firstly, based on the protein sequence information of the whole genome, obtain the structural domain information of all protein sequences through the Hmmscan tool, and screen the proteins containing the NB-ARC domain (PF00931), parameters Set to E-value≤1e-4; (2) Then use the NLR-parser tool to detect the LRR domain and screen for proteins with motif 9, 11 or 19, and have both the NB-ARC domain and the LRR domain The gene of the NLR gene is the main NLR gene, and the gene with only the NB-ARC domain is the candidate NLR gene; (3) Then based on the physical distance and gene number of the NLR gene on the chromosome in the gene annotation, we put the physical distance o...

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Abstract

The invention discloses a construction method of a plant paired NLR resistance gene database and a multi-species paired NLR gene database thereof. The method comprises the following steps: collecting genome data of a target species from JGI or Ensembl; identifying an NLR gene through an Hmmscan tool and an NLR-parser tool; screening clustered NLR genes in combination with gene annotation information; analyzing the special structural domain of the NLR gene through an Hmmscan tool and a Blast tool; based on the evolution characteristics of the paired NLR genes, retrieving the paired NLR genes of a target species for multiple rounds through tools such as Blast, Clustalw2 and MEGA7.0; and establishing a paired NLR gene database by taking the characteristic values corresponding to the paired NLR genes as data item identifiers. By utilizing the method provided by the invention, the paired NLR resistance genes in different plant species can be retrieved and analyzed in a whole genome range, and molecular evidence is provided for researching and improving resistance breeding of crops.

Description

technical field [0001] The invention relates to a gene sequence data processing method, in particular to a method for constructing a plant paired NLR gene database and a multi-species paired NLR gene database. Background technique [0002] Plants are important members of the earth's ecology and an indispensable and important part of human life. Human clothing, food, housing, and transportation are often inseparable from the direct or indirect participation of plants, but the growth and development of plants is not smooth, often accompanied by the occurrence of various biological stresses, most of which come from the source of biological stress Due to the infection of microorganisms, they often damage the growth and reproduction of plants, and in severe cases, they are more likely to cause a large reduction in plant production. [0003] At present, the prevention and control measures against pathogens are still based on the application of pesticides, but the use of pesticide...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B50/00G16B30/00
CPCG16B50/00G16B30/00
Inventor 田大成秦超杨四海张小辉
Owner NANJING UNIV
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