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Chip for screening 16SrI group phytoplasmas and application thereof

A phytoplasma and gene chip technology, applied in the fields of bioinformatics and bio-quarantine identification, can solve the problems of low specificity, inability to detect and monitor phytoplasma, cumbersome steps, etc., and achieve good results and intuitive analysis results Effect

Inactive Publication Date: 2012-06-13
CHINESE ACAD OF INSPECTION & QUARANTINE
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0004] The current detection methods for 16SrI group phytoplasma include ordinary PCR, fluorescent PCR, electron microscopy, fluorescence microscopy, etc. These methods have limitations such as low specificity and cumbersome steps, and for unknown and new phytoplasma Unable to detect and monitor

Method used

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  • Chip for screening 16SrI group phytoplasmas and application thereof
  • Chip for screening 16SrI group phytoplasmas and application thereof
  • Chip for screening 16SrI group phytoplasmas and application thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0071] Embodiment 1, the preparation of the chip of screening 16SrI group phytoplasma

[0072] 1. Design of group-level highly compatible oligonucleotide probes

[0073] 1) Download the 16SrI 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 for designing probes.

[0074] 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.

[0075] 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 t...

Embodiment 2

[0086] Embodiment 2, the application of the chip of screening 16SrI group phytoplasma

[0087] 1. Chip detection samples for screening 16SrI group phytoplasma

[0088] 1. Extraction of total DNA from samples used for testing

[0089] 1) get the strawberry leaf (Latin name: Strawberry Phylloid Fruit Phytoplasma, recorded in: Molecular Identification and Classification of Strawberry Phylloid Fruit Phytoplasma in Group 16SrI, New Subgroup.Plant disease, 2002, 86 (8) that infects strawberry branch fruit phytoplasma : 920., the public can obtain from the Chinese Academy of Inspection and Quarantine.) and Paulownia leaves infected with Paulownia witches'broom phytoplasma. Preparation and application, Acta Phytopathology, 2011, 41(2): 161-170.) each 0.1g, take an appropriate amount of liquid nitrogen to grind, then add 2ml of grinding liquid to fully grind, centrifuge at 20000rpm at 4°C for 20min, discard the supernatant.

[0090] 2) Add 1ml DNA extraction solution, 40ul proteinase...

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Abstract

The invention discloses a chip for screening 16SrI group phytoplasmas and application thereof. The nucleotide sequences of five probes for screening 16SrI group phytoplasmas are sequence 1 to sequence 5 in order in a sequence table. The invention also provides a gene chip for screening 16SrI group phytoplasmas, and the probes are fixed on the surface of the chip, so that the gene chip is formed. An experiment proves that the invention adopts a bioinformatic method to analyze the 16S rDNA, 16S-23S rDNA spacer, imp and tuf nucleotide sequences of 16SrI group phytoplasmas and designs the compatible probe for the group, and a standard phytoplasma sample test result proves that the effect of the probe is good. The chip for screening 16SrI group phytoplasmas can be used in the quarantine and identification of 16SrI group phytoplasmas.

Description

technical field [0001] The invention relates to the technical fields of bioinformatics and bioquarantine identification, in particular to a chip for screening 16SrI group phytoplasma and its application. Background technique [0002] The 16SrI group is the aster yellow group (Ca.Phytoplasma asteris), which is divided into 11 subgroups. At present, the 16SrI group is the group containing the most types of phytoplasma, containing more than 200 phytoplasma strains, mainly including asters Yellow phytoplasma, onion yellow phytoplasma, potato purple top phytoplasma, alfalfa dwarf phytoplasma, strawberry dwarf phytoplasma, paulownia arbuscular phytoplasma, etc. Symptoms of damage mainly include yellowing or reddening of leaves, shortening of internodes, stunt, little leaves, and excessive growth of branches. proliferation of shoots resulting in a witches' broom), phyllody, leaf-like petals and sepals, virescence, excess ive greening of floral tissue, sterile flowers, necrosis of ...

Claims

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Application Information

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IPC IPC(8): C12Q1/68C12N15/11C40B40/06
Inventor 张永江牟海清赵文军朱水芳
Owner CHINESE ACAD OF INSPECTION & QUARANTINE
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