Chip for screening coleus scutellarioides viroid and application of chip

A colorful Su-like virus and virus-like technology, which is applied in the fields of bioinformatics and bio-quarantine identification, can solve the problems of low throughput and inability to detect virus-like viruses, 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

However, existing technologies such as biological assays, forward and reverse polyacrylamide gel electrophoresis, and RT-PCR have low throughput, and can only detect one type of virus in a sample at a time; Detection of viroids with many mutation sites

Method used

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  • Chip for screening coleus scutellarioides viroid and application of chip
  • Chip for screening coleus scutellarioides viroid and application of chip
  • Chip for screening coleus scutellarioides viroid and application of chip

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0040] Embodiment 1, the preparation of the chip of screening Wucai Viroid genus viroid

[0041] 1. Design of genus-level highly compatible oligonucleotide probes

[0042] 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 The standard screens the extracted nucleic acid sequences and performs homology comparisons in the NCBI database to ensure the specificity of the probes obtained.

[0043] According to the above principles, six probes for Viroids of the genus Wucai Viroid were designed, the nucleotide sequences of which were re...

Embodiment 2

[0048] Embodiment 2, the application of the chip of screening Wucai Siovirus genus viroid

[0049] 1. Screening chip detection samples

[0050] 1. Extraction of total RNA from samples used for detection

[0051] 1) Coleus tissues infected with Coleus blumeiviroid 1 (Coleus blumeiviroid1 (abbreviated as CbVd-1) in Latin name for Coleus blumeiviroid 1) were taken, which was recorded in: Detection of Coleus blumeiviroids in China and their molecular biological characteristics. 2006, Acta Phytopathology 36(3): 266-231. The public can obtain it from the Chinese Academy of Inspection and Quarantine; Coleus is recorded in: Epidemic Investigation and Detection of Colleus Viruses in Beijing and Tianjin, Su Qianfu Song Farui Wang Hongqing, Li Shifang, "Plant Protection", No. 6, 2006, the public can obtain from the Chinese Academy of Inspection and Quarantine) 0.1g sample, ground into powder with liquid nitrogen, transferred to a sterilized 1.5mL centrifuge tube, and then added 1mL of Tr...

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Abstract

The invention discloses a chip for screening coleus scutellarioides viroid and application of the chip. A probe group identifying or assisting in identifying the scutellarioides viroid consists of 6 probes, and the nucleotide sequences of the 6 probes are the sequences from 1 to 6 in a sequence table respectively. The invention also provides a gene chip for screening the scutellarioides viroid, which is obtained by fixing the probes on the surface of a chip base. The experiment proves that the nucleotide sequence of the scutellarioides 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 scutellarioides viroid disclosed by the invention can be applied to the quarantine identification of the scutellarioides 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 Wucai Viroid and its application. Background technique [0002] Coleus blumei viroids (Coleviroid) belong to the potato spindle tuber viroid family (Pospiviroidae). There are 6 species of Coleus blumei viroids discovered and reported so far (Coleus blumei viroid1-6, CbVd-1~CbVd-6) . Wucai Su-like virus was first discovered in Brazil, and later reported in Germany, Canada, Japan, India, Indonesia and China. Symptoms such as yellowing or mottling will appear after Wucai Su is infected with viroids, and a few have dwarf infection. [0003] Viruses of this genus are transmitted mechanically and can also be transmitted by seeds. With the increase of trade in plants and their products at home and abroad, the frequency of "new" viroids appearing in this genus is increasing. Two new Coleus viroid speci...

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 张永江辛言言朱水芳李世访李桂芬
Owner CHINESE ACAD OF INSPECTION & QUARANTINE
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