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Chip for screening apscaviroid viroid and application of chip

A rust-like virus and virus-like technology, which is applied in the fields of bioinformatics and bio-quarantine identification, can solve problems such as adverse social impact, spread and economic loss, and achieve good 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 apscaviroid viroid and application of chip
  • Chip for screening apscaviroid viroid and application of chip
  • Chip for screening apscaviroid viroid and application of chip

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0045] Embodiment 1, the preparation of the chip of screening apple rust fruit viroid genus viroid

[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, 35 probes (probe 1-probe 35) of viroids of the genus Apple Rust Viroid were designed, and their...

Embodiment 2

[0053] Embodiment 2, the application of the chip of screening apple rust fruit viroid genus viroid

[0054] 1. Screening chip detection samples

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

[0056] 1) Take apple leaves infected with apple rust-like virus (Apple scar skin viroid, recorded in: Several extraction methods of apple rust-like virus and comparison of RT-PCR detection sensitivity. Plant Protection, 2006, 32(2):95-97., publicly available from the Chinese Academy of Inspection and Quarantine.) and citrus leaves infected with citrus virus III (citrus virus III Latin name Citrus viroid III. Documented in: Molecules of Citrus Viruses Identification and typing. Chinese Agricultural Sciences, 2008, 41(9): 2670-2677, 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 sterilized 1.5 mL centrifuge tube, then add 1 mL of Trizol reagent, shake vig...

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Abstract

The invention discloses a chip for screening apscaviroid viroid and application of the chip. A probe group identifying or assisting in identifying the apscaviroid viroid consists of 35 probes, and the nucleotide sequences of the 35 probes are the sequences from 1 to 35 in a sequence table respectively. The invention also provides a gene chip for screening the apscaviroid viroid, which is obtained by fixing the probes on the surface of a chip base.. The experiment proves that the nucleotide sequence of the apscaviroid 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 apscaviroid viroid disclosed by the invention can be applied to the quarantine identification of the apscaviroid 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 genus Viroid of apple rust and its application. Background technique [0002] The genus Apscaviroid belongs to Pospiviridae, according to the eighth classification report of the International Committee on Taxonomy of Viruses (ICTV), this genus includes apple rust Apple scar skin viroid (ASSVd), Apple dimple fruit viroid (ADFVd), Citrus bent leaf viroid (CiBLV), Australian grapevine viroid (AGVd) , Citrus viroid III (CiVd III), Grapevine yellow speckle viroid 1 (GYSVd-1), Grapevine yellow speckle viroid 2 (GYSVd-2) And 8 kinds of viruses such as pear blister canker viroid (PBCVd). Viroids of this genus can infect many important fruit trees such as apples, pears, peaches, citrus and grapes. Its representative species, apple rust viroid, infects apples and can cause apple rust disease, resulting in flatt...

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 张永江李世访邓子牛朱水芳辛言言赵文军沈建国廖富荣魏梅生李桂芬
Owner CHINESE ACAD OF INSPECTION & QUARANTINE
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