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Chip for screening 16SrXIX group phytoplasma and application of chip

A technology of implants and chips, applied in the fields of bioinformatics and bio-quarantine identification, can solve the problems of cross-contamination, low sensitivity, lack of versatility and standardization, achieve cross-contamination prevention, improve customs clearance rate, and visualize analysis results Effect

Inactive Publication Date: 2013-08-07
CHINESE ACAD OF INSPECTION & QUARANTINE
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0004] At present, the detection methods for 16SrXIX group phytoplasma are mainly ①serological detection method, which is not sensitive and prone to false positives; ②nucleic acid-based molecular biology detection technology, mainly including PCR, real-time fluorescent PCR and other technologies, with high sensitivity and specificity. Relatively high, but there is cross-contamination, and there are deficiencies in versatility and standardization

Method used

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  • Chip for screening 16SrXIX group phytoplasma and application of chip
  • Chip for screening 16SrXIX group phytoplasma and application of chip
  • Chip for screening 16SrXIX group phytoplasma and application of chip

Examples

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Effect test

Embodiment 1

[0046] Example 1. Preparation of a chip for screening 16SrXIX group phytoplasma

[0047] 1. Design of group-level highly compatible oligonucleotide probes

[0048] 1) Download the 16SrXIX group phytoplasma genome and nucleic acid sequence data from the National Center for Biotechnology Information (NCBI) and the official website of the Ribosome Database Project (RDP) database to design probes.

[0049] 2) Organize phytoplasma nucleic acid sequences, remove nucleic acid sequences less than 200 bp in length and group them; all phytoplasma sequences in the same group are referred to as in-group sequences, and all phytoplasma sequences not in this group are referred to as out-group sequences.

[0050] 3) Use ClusterW to align the sequences in the group, find the sequence conserved regions and design probes. When designing the probe, use 2 to 3 bases as the interval in the conserved region of the sequence, continuously extract all 19 bp nucleic acid sequences, and screen the selec...

Embodiment 2

[0061] Example 2, the application of the chip for screening 16SrXIX group phytoplasma

[0062] 1. Chip detection samples for screening 16SrXIX group phytoplasma

[0063] 1. Extraction of total DNA from samples used for detection

[0064] 1) Take chestnut leaves infected with Chestnut yellow crinkle phytoplasma (leaves show yellowing and shrinking symptoms, phytoplasma Latin name: Chinese chestnut yellow crinkle phytoplasma, recorded in: Molecular identification and characterization of a new phytoplasma strain associated with Chinese chestnut yellow crinkle disease in China.Forest Pathology, 2011, 41 (3): 233-236., the public can obtain from the Chinese Academy of Inspection and Quarantine.) 0.1g, take an appropriate amount of liquid nitrogen to grind, then add 2ml of grinding liquid to grind fully, Centrifuge at 20,000 rpm at 4°C for 20 min, and discard the supernatant.

[0065] 2) Add 1ml DNA extraction solution, 40ul proteinase K (5mg / ml), mix gently, add 160ul 10% sodium ...

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Abstract

The invention discloses a chip for screening a 16SrXIX group phytoplasma and application of the chip and provides a DNA (Deoxyribonucleic Acid) segment and the chip for screening the 16SrXIX group phytoplasma, wherein the nucleotide sequence of the DNA segment is shown by a sequence 1 in a sequence table. The chip is a gene chip obtained by fixing the DNA segment on the surface of the chip. Proved by tests, according to the chip disclosed by the invention, the 16SrDNA nucleotide sequence of the 16SrXIX group phytoplasma is analyzed by adopting a bioinformatics method, a compatible probe of the group is designed and the effect of the probe is proved to be favorable by a verification result of a standard phytoplasma sample. The chip for screening the 16SrXIX group phytoplasma, which is disclosed by the invention, can be used for quarantine and identification for the 16SrXIX group phytoplasma.

Description

technical field [0001] The invention relates to the technical fields of bioinformatics and bioquarantine identification, in particular to a chip for screening 16SrXIX group phytoplasma and its application. Background technique [0002] The 16Sr XIX group of phytoplasma mainly includes Chinese chestnut phytoplasma yellow shrunken and Japanese chestnut arbuscular phytoplasma. Chestnut phytoplasma disease was first reported on Japanese chestnut species in Japan, and was named as chestnut yellows disease. It was later confirmed as a phytoplasma-related disease by electron microscope observation. Chestnut little leaf (CLL) caused by phytoplasma reported in South Korea also occurred on Japanese chestnuts. The results of heteroduplex analysis suggested that it was relatively close to the aster yellow phytoplasma group. Later, Jung et al. The pathogen of chestnut witches'-broom (CnWB), which causes typical arbuscular symptoms, was identified as a new candidate species, Candidatus p...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12N15/11C12Q1/68C12Q1/04
Inventor 牟海青张永江赵文军朱水芳
Owner CHINESE ACAD OF INSPECTION & QUARANTINE