Chip for screening Pelamoviroid and application thereof

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

Inactive Publication Date: 2012-10-17
CHINESE ACAD OF INSPECTION & QUARANTINE +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

The establishment of effective screening technology is the key to improving the effect of viroid quarantine inspection, but the current international methods for the detection of viroids in this genus mainly include biological identification of woody indicator plants, RT-PCR, LAMP and nucleic acid molecular hybridization techniques. These technologies can only perform specific detection of known viroids of the genus, and are 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 bad society. influences

Method used

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  • Chip for screening Pelamoviroid and application thereof
  • Chip for screening Pelamoviroid and application thereof
  • Chip for screening Pelamoviroid and application thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0043] Example 1, Preparation of a Chip for Screening Peach Latent Mosaic Viroids

[0044] 1. Design of genus-level highly compatible oligonucleotide probes

[0045] 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.

[0046] Nine probes (probe 1-probe 9) of peach latent mosaic viroid genus viroids were designed according to the above principles, and their nucleotide se...

Embodiment 2

[0051] Example 2, application of the chip for screening peach latent mosaic viroids

[0052] 1. Screening chip detection samples

[0053] 1. Extraction of total RNA from samples used for detection

[0054] 1) Take peach tree leaves infected with peach latent mosaic viroid (Peach latent mosaic viroid, the Latin name of peach latent mosaic viroid, is recorded in: Cloning and sequence analysis of Chinese isolate P3 of peach latent mosaic viroid. 2005, Acta Phytopathology 35 (4): 300-304., the public can obtain from the Chinese Academy of Inspection and Quarantine.) and chrysanthemum leaves of chrysanthemum chlorotic mottle viroid (Chrysanthemum chlorotic mottle viroid. Add 1mL grinding buffer [Na 2 HPO 4 12H 2 O 3.58g, KH 2 PO 4 0.27g, NaCl 8g, KCl 0.2g, NaCl 2 SO 3 1.3g, polyvinylpyrrolidone (PVP) MW 24-40 000 20g, NaN 3 0.2g, chicken egg protein (pow dered egg album in) 2.0g, Tween-20 20.0mL, dissolve in 1000mL deionized water, adjust the pH value to 7.5], grind even...

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Abstract

The invention discloses a chip for screening Pelamoviroid and an application thereof. The invention provides probes for identification or assistant identification of Pelamoviroid, comprising nine probes, nucleotide sequences of the nine probs are respectively the sequence 1-9 in the sequence table. The invention also provides a gene chip for screening Pelamoviroid, and the gene chip is obtained by fixing the probes on the surface of a film base. Experiments of the invention prove that by analyzing the nucleotide sequence of Pelamoviroid through using bioinformatics methods, the compatible probes are designed, and the results of verifying standard viroid samples prove that the probes have good effect. The chip for screening Pelamoviroid disclosed herein can be used for quarantine and identification of Pelamoviroid.

Description

technical field [0001] The invention relates to the technical fields of bioinformatics and bioquarantine identification, in particular to a chip for screening peach latent mosaic viroids and its application. Background technique [0002] Peach latent mosaic viroids (Pelamoviroid) belong to the avocado sunspot virus family (Avsunviridae), according to the eighth classification report of the International Committee on Taxonomy of Viruses (ICTV), this genus includes peach Peach latent mosaic viroid (PLMVd) and Chrysanthemum chlorotic mottle viroid (CChMVd). Peach latent mosaic virus is distributed in North and South America, Australia, Austria, China, Croatia, France, Greece, Japan, Morocco, Romania, Serbia, Spain and Tunisia, and has been identified as the most dangerous system on fruit trees in many countries One of the invasive pathogens, it mainly infects stone fruit trees such as peaches, plums, and apricots. Infestation of peach trees generally manifests as mosaic leave...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/70C12Q1/68C12N15/11C40B40/06
Inventor 张永江邓丛良粟智平李桂芬辛言言
Owner CHINESE ACAD OF INSPECTION & QUARANTINE
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