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Chip for screening phytoplasma in 16SrXII group and application thereof

A plant-based, chip technology, applied in the field of bioinformatics and bio-quarantine identification, can solve problems such as cross-contamination, low sensitivity, lack of versatility and standardization, achieve good stability, improve customs clearance rate, and visualize analysis results Effect

Inactive Publication Date: 2014-05-28
CHINESE ACAD OF INSPECTION & QUARANTINE
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0005] At present, the detection methods for 16SrXII 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 phytoplasma in 16SrXII group and application thereof
  • Chip for screening phytoplasma in 16SrXII group and application thereof
  • Chip for screening phytoplasma in 16SrXII group and application thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0060] Example 1. Preparation of a chip for screening 16SrXII phytoplasma

[0061] 1. Design of group-level highly compatible oligonucleotide probes

[0062] 1) Download the 16SrXII group phytoplasma whole 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 for probe design.

[0063] 2) Sorting out the phytoplasma nucleic acid sequence, removing the nucleic acid sequences less than 200bp in length and grouping; all phytoplasma sequences in the same group are referred to as intra-group sequences, and all phytoplasma sequences not in this group are referred to as out-group sequences.

[0064] 3) Use Cluster W to match the sequence within the group to find the sequence conserved region to design probes. When designing the probe, use 2 to 3 bases as an interval in the sequence conserved region, and extract all the 19bp nucleic acid sequences continuously, and screen the...

Embodiment 2

[0075] Example 2. Application of the chip for screening 16SrXII group phytoplasma

[0076] 1. Screen the 16SrXII group phytoplasma chip test samples

[0077] 1. Extraction of total DNA from samples for testing

[0078] 1) Take the grape leaves infected with the Australian phytoplasma candidate species (the leaves show safflower and curl, the Latin name of the phytoplasma: candidatus phytoplasma australiense, recorded in: Candidatus Phytoplasma australiense is the phytoplasma associated with Australian grapevine yellows, papaya dieback and Phormium yellow leaf diseases, 1998, 104: 619-623. The public can obtain it from the Chinese Academy of Inspection and Quarantine Sciences.) 0.1g, take an appropriate amount of liquid nitrogen to grind, and then add the grinding liquid 2 HPO 4 .3H 2 O 2.17g, KH 2 PO 4 0.41g, sucrose 10g, BSA (Fraction V) 0.15g, PVP-102g dilute to 100mL, adjust DH to 7.6 and sterilize at high temperature) 2mL is fully grinded, centrifuged at 4°C, 20000rpm for 20min, ...

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Abstract

The invention discloses a chip for screening phytoplasma in a 16SrXII group and an application thereof. A probe for screening the phytoplasma in the 16SrXII group is formed by three probes, wherein the nucleotide sequences of the three probes are respectively sequences 1-3 in a sequence table. The invention also provides a gene chip for screening the phytoplasma in the 16SrXII group, and the gene chip is obtained by fixing the probe on the surface of a chip base. Experiments prove that the probe in the chip for screening the phytoplasma in the 16SrXII group provided by the invention has high compatibility on the level of the phytoplasma in the 16SrXII group and specificity in the phytoplasma group, screening for new phytoplasma possibly existing in a sample to be inspected is completed within some hours, the needed sample amount is less, and generally only 0.1g of sample is needed. In addition, data analysis and computer image processing software are combined, and analysis results can achieve visualization.

Description

Technical field [0001] The invention relates to the technical fields of bioinformatics and bioquarantine identification, in particular to a chip for screening 16SrXII group phytoplasma and its application. Background technique [0002] The 16Sr XII group of phytoplasma mainly includes Australian phytoplasma candidate species, Bois Noir phytoplasma, and stubborn phytoplasma (stolbur). Grape yellowing disease is the most economically affected grape yellowing disease in Europe, causing huge yield losses in European vineyards. Grape yellowing disease (hereinafter referred to as AusGY) caused by Australian phytoplasma candidate species frequently occurs in vineyards in the warm regions of New South Wales and Victoria, Australia. In addition, the Australian phytoplasma candidate species can also cause serious diseases of a variety of cash crops: when infecting grapes, it causes grape yellowing disease, and its symptoms and harm are similar to grape golden yellowing disease; when infec...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/68C12N15/11C40B40/06
Inventor 赵文军张永江朱水芳牟海青
Owner CHINESE ACAD OF INSPECTION & QUARANTINE