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Chip for screening pospiviroid viroid and application of chip

A virus-like and potato-like technology, applied in the fields of bioinformatics and bio-quarantine identification, can solve problems such as adverse social impact, missed detection of dangerous virus-like viruses, spread and spread, and achieve good results and intuitive analysis results

Inactive Publication Date: 2012-10-10
CHINESE ACAD OF INSPECTION & QUARANTINE +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0003] Because this genus has the possibility of potentially emerging quarantine viroids, the methods currently used for the detection of viroids in this genus, such as indicator plant method, polyacrylamide gel electrophoresis, nucleic acid dot hybridization technology and molecular biology technology, can only Specific detection of known viroids of this genus is powerless for the monitoring of unknown and new viroids, so it is easy to cause dangerous viroids to be missed and spread, which will lead to huge economic losses and adverse social impacts

Method used

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  • Chip for screening pospiviroid viroid and application of chip
  • Chip for screening pospiviroid viroid and application of chip
  • Chip for screening pospiviroid viroid and application of chip

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0045] Example 1, Preparation of Chip for Screening Potato Spindle Tuber Viroids

[0046] 1. Design of genus-level highly compatible oligonucleotide probes

[0047]Download the whole genome and nucleic acid sequence of Viroids from the database of National Center for Biotechnology Information (NCBI) and the International Committee on Virology (ICTV); remove more than 90% of the nucleic acid sequences with 95% similarity to other sequences; use 5 Bases are used as intervals to continuously extract all 40mer nucleic acid sequences; 40%≤GC content≤60%, single base content≤50%, number of consecutive repeated bases≤4, and no hairpin structure of more than 6 bases is Nucleic acid sequences were screened for standards, and homology comparisons were performed in the NCBI database to ensure the specificity of the probes obtained.

[0048] According to the above principles, 19 probes (probe 1-probe 19) of viroids of the genus Potatotuber viroid were designed, and their nucleotide seque...

Embodiment 2

[0053] Example 2, Application of Chip for Screening Potato Spindle Tuber Viroids

[0054] 1. Screened chip test samples

[0055] 1. Extraction of total RNA from samples used for detection

[0056] 1) Take chrysanthemum leaves infected with chrysanthemum stunt viroid (Chrysanthemum stunt viroid, recorded in: Establishment and comparison of two detection methods for chrysanthemum stunt viroid, Plant Protection, 2002, 28 (2): 48 -50., the public can obtain from the Chinese Academy of Inspection and Quarantine.) and tomato leaves infected with tomato male strain viroid (tomato male strain viroid: Tomato planta macho viroid. Recorded in: Mexican papita viroid and tomato planta macho viroid belong to a single species in the genus Pospiviroid, Archives of Virology, 2011, 156(8): 1433-1437, the public can obtain from the Chinese Academy of Inspection and Quarantine.) Each 0.1g sample was ground into powder with liquid nitrogen, and transferred into Into a sterilized 1.5mL centrifuge...

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Abstract

The invention discloses a chip for screening pospiviroid viroid and application of the chip. A probe group identifying or assisting in identifying the pospiviroid viroid consists of 19 probes, and the nucleotide sequences of the 19 probes are the sequences from 1 to 19 in a sequence table respectively. The invention also provides a gene chip for screening the pospiviroid viroid, which is obtainedby fixing the probe group on the surface of a chip base. The experiment proves that the nucleotide sequence of the pospiviroid viroid is analyzed by a bioinformatics method, the compatible probes of the group are designed, and the standard viroid sample verification result indicates that a probe effect is good. The chip for screening the pospiviroid viroid disclosed by the invention can be applied to the quarantine identification of the pospiviroid viroid.

Description

technical field [0001] The invention relates to the technical fields of bioinformatics and bioquarantine identification, in particular to a chip for screening viroids of the potato spindle tuber genus and an application thereof. Background technique [0002] Potato spindle-shaped tuber viroids (Pospiviroid) belong to the potato spindle-shaped tuber viroid family (Pospivroidae), according to the eighth classification report of the International Committee on Taxonomy of Viruses (ICTV), this genus includes potato spindle Potato spindle tuber viroid (PSTVd), Chrysanthemum stunt viroid (CSVd), Citrus exocortis viroid (CEVd), Goldfish latent viroid (Columnea latent viroid, CLVd), Iresine viroid 1 (IrVd-1), Mexican papita viroid (MPVd-1), tomato apical stunt viroid (TASVd) and tomato male 8 types of viruses including Tomato planta macho viroid (TPMVd). Viroids of this genus can infect many important crops such as potato, tomato, pepper, avocado, chrysanthemum, citrus, goldfish fl...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/70C12Q1/68C12N15/11C40B40/06C12R1/94
Inventor 张永江朱水芳丁芳王国平李世访辛言言刘洪义粟智平
Owner CHINESE ACAD OF INSPECTION & QUARANTINE
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