Method for identifying specific sequence fragments of key enzyme genes in specific plant species

A technology of key enzyme genes and sequence fragments, applied in the field of bioinformatics analysis, can solve problems such as long time and difficult cloning

Active Publication Date: 2020-02-18
GUANGZHOU BAIYUSN HUTCHISON WHAMPOA CHINESE MEDICINE
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, because the basic research of most medicinal materials is not deep enough, it is not only time-consuming to use these methods but also it is difficult to clone genes accurately

Method used

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  • Method for identifying specific sequence fragments of key enzyme genes in specific plant species
  • Method for identifying specific sequence fragments of key enzyme genes in specific plant species
  • Method for identifying specific sequence fragments of key enzyme genes in specific plant species

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0103] Example 1 Identification of the Specific Sequence Fragment of Pinoresinol-lariciresinol Reductase (PLR) in Woad

[0104] 1. Obtaining homologous sequences

[0105] In order to systematically ascertain the distribution of larch-resinol reductase genes in plant groups, systematically classify them, and explore the phylogenetic relationship of PLR genes in different plant groups, it is necessary to search as many groups as possible to obtain a comprehensive molecular data.

[0106] The flax PLR protein sequence with clear function and PLR gene family structure characteristics was selected as the query sequence (Transcript Name: Lus10012143; Transcript Name: Lus10010403; Transcript Name: Lus10012145; and Transcript Name: Lus10012147) to search for homologous sequences in the database, in 64 The homologous sequence of the PLR ​​gene was obtained by BLAST (Basic Local Alignment Search Tool) in a plant with complete genome sequence information. The main parameters of BLAST...

Embodiment 2

[0149] Example 2 Characterization of the position of specific sequence fragments in the three-dimensional structure of proteins

[0150] In order to infer the distribution position of the specific conserved sequence in the protein structure and the distribution of possible functional sites, the PLR ​​homologous sequence in Isatis indigo was selected and carried out by Swiss-Model (http: / / swissmodel.expasy.org / ) Three-dimensional structural simulation of proteins.

[0151] In order to ensure the accuracy of the simulation, based on the optimal comparison results, according to the global model quality estimation (Global Model Quality Estimation, GMQE) score and the qualitative model energy analysis (QualitativeModel Energy Analysis, QMEAN) score (score The larger the value, the higher the reliability), select the most reliable homologous template, that is, the chain B, Pinoresinol-lariciresinol reductase, 1qyd.1.B) for homology modeling, see the table below 4.

[0152] Table...

Embodiment 3

[0156] Example 3 Application of the 3 sequences obtained in the present invention and their key sites as identification basis

[0157] The present invention has discovered 3 fragments and key sites thereof in Isatis indigo, namely:

[0158] SEQ ID NO: 1: MR E NNSGEK T RV, corresponding to motif 15;

[0159] SEQ ID NO: 2: LQ Q PETRVDIEKVQLLYSYKRLGARLIEAS, corresponding to motif 10;

[0160] SEQ ID NO: 3: DH EVGDDE, corresponding to motif 9.

[0161] The protein sequences of larch resin alcohol reductase from 4 different species were searched in NCBI (https: / / www.ncbi.nlm.nih.gov / ) database, and compared with the sequence of Isatis indica. The different larch resin alcohol reductase protein sequences are poplar: Populus alba, TKS01263.1; japonicus: Lotus japonicus, BAF34846.1; strong spiny ball: Ferocactus pilosus, AYU58880.1; cactus: Echinocactus platyacanthus, AYU58879. 1). After comparison, it can be found that motif 15, motif 10 and motif 9 and their specific site...

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Abstract

The invention provides a method for identifying specific sequence fragments of key enzyme genes in specific plant species. According to the method, a phylogenetic relationship of key enzyme genes in different plant groups is reconstructed by using analysis methods of molecular systematics and bioinformatics, sequences, structures and differentiation among the different groups are compared and analyzed, and specific sequence fragments and key variation sites of the enzyme in specific plant species are identified. The invention also provides application of the obtained specific sequence fragmentin plant or specific medicinal material source identification, variety improvement or breeding.

Description

technical field [0001] The invention belongs to the technical field of bioinformatics analysis. Specifically, the present invention relates to a method for studying specific sequence fragments and functional differentiation sites of key enzyme gene families derived from different species by using analysis methods of bioinformatics and molecular systematics, and particularly relates to the analysis of key enzyme genes in A capture and mining method and application of specific sequence fragments and functional differentiation sites in specific plant species. Background technique [0002] Bioinformatics is a research method that takes nucleic acid, protein and other biomacromolecular databases as the main object. It uses mathematics, informatics, and computer science as the main means, and uses computer hardware, software, and networks as the main tools to analyze a large amount of raw data. Store, manage, annotate, and process to make it biological information with clear biol...

Claims

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Application Information

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IPC IPC(8): G16B30/10G16B40/00C12N9/02G01N33/573
CPCG16B30/10G16B40/00C12N9/0004G01N33/573G01N2333/902
Inventor 黄远李楚源李淑如
Owner GUANGZHOU BAIYUSN HUTCHISON WHAMPOA CHINESE MEDICINE
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