PL231512B1 - Method and a kit for identification of Longidorus intermedius nematode that is harmful to fruit trees and bushes, by Real Time PCR based method - Google Patents

Abstract

The subject of the application is a method and kit for identifying the nematode Longidorus intermedius, a pest of fruit trees and shrubs, using the Real Time PCR method. Thanks to specifically selected primers and probes, this solution enables precise identification of selected nematode species regardless of the type of samples tested, their origin and purpose, and the stage of development.

Description

Description of the invention

The subject of the invention is a method and a kit for the identification of Longidorus intermedius nematode harming fruit trees and shrubs by the Real Time PCR method.

79 species of Longidoridae have been found in Europe, 13 of which occur in Poland. Representatives of this family are classified as plant parasites, they are also vectors of viruses attacking plants. They reproduce in the soil. The period of their development is long and may last up to several months. They can parasitize on many useful plants. Infested plants are stunted or die, especially when infected early in their development. Some of these species, e.g. Longidorus attenuatus, L. elongatus and L. macrosoma, can transmit Tomato Black Spot Virus and Raspberry Ringspot Virus. Identification of nematode species is based on the analysis of morphological and morphometric features, including the diagnosis of female coloration at various stages of development, cyst shape, length and shape of dagger tumors, length of invasive larvae, pattern on the perineal plate. However, this is a very laborious and time-consuming analysis. It requires a lot of knowledge and experience in working with biological material. Moreover, there is the possibility of overlapping dimensions of different species. The method based on the analysis of morphological and morphometric features cannot be used to identify adolescents in which morphological features are not yet developed.

Currently, techniques based on the analysis of nucleic acids, including the polymerase chain reaction (PCR), are increasingly used in nematological diagnostics. The basis of the PCR technique is the amplification of a DNA fragment (s) specific for a specific organism to a level that allows for its quick and simple detection using electrophoresis. This is achieved by using short single-stranded oligonucleotides (12-40 nucleotides), the so-called primers, specific for the amplified DNA fragment, and the enzyme - thermostable polymerase, which enables the amplification of the desired fragment in a cyclic, three-step reaction consisting of denaturation, primer binding and DNA synthesis. Typically, after about 30 reaction cycles, more than a million copies of the amplified DNA fragment are obtained, which can be identified by gel electrophoresis.

An improvement on the polymerase chain reaction is Real Time PCR, that is, a PCR reaction with the measurement of the amount of amplified fragment in each reaction cycle. To measure the amount of the amplified fragment, fluorochromes (fluorescent dyes) are used, e.g. SYBR Green I, SYTO9, Eva Green, SYBR Gold, the fluorescence of which is proportional to the amount of the amplified fragment. Identification of the resulting products is carried out by measuring the amount of fluorescence and analyzing the melting curve of the reaction products without electrophoresis. The sensitivity of Real Time PCR is much higher than that of traditional PCR, and the lack of electrophoresis shortens the analysis time. The disadvantage of Real Time PCR with fluorescent dyes (similar to traditional PCR) is the limited specificity of the reaction. In most cases, the PCR reaction occurs not only when the primer sequence is 100% identical to the template sequence but also when 1-2 nucleotides are non-identical. This property of traditional PCR and Real Time PCR with fluorescent dyes requires precise setting of the thermal parameters of the reaction. Moreover, fluorescent dyes bind to each double-stranded DNA fragment, also resulting from primer amplification (primer-primer, primer-dimer products), which also requires careful selection of the appropriate concentration of primers.

An alternative to fluorescent dyes are fluorescently labeled DNA probes. These are short sections of DNA, complementary to the searched sequence, which, when attached to DNA during PCR reactions, emit fluorescence at a specific wavelength. Currently, several types of probes are known, e.g. TaqMan, FRET, molecular beacons, and scorpions. The specificity of the Real Time PCR reaction with labeled probes is much higher than with fluorescent dyes. Unlike primers, a single nucleotide mismatch in the probe sequence usually leads to no reaction or a very significant reduction in yield, which is easy to see when monitoring the course of the reaction or analyzing the results of the reaction.

So far, the most frequently used method of molecular identification of nematodes has been PCR. McCuiston J.L, Hudson L.C. Subbotin S.A., Davis E.L., Warfield C.Y Conventional and PCR Detection of Aphelenchoides fragariae in Diverse Ornamental Host Plant Species. J Nematol. Dec 2007; 39 (4): 343-355 developed primers for the identification of Aphelenchoides fragariae. Wang X, Bosselut N, Castagnone C, Voisin R, Abad P, Esmenjaud D. Multiplex polymerase chain reaction identification of single individuals of the Longidorid nematodes Xiphinema index, X. diversicaudatum, X vuittenezi, and X. italiae using

PL231 512 Β1 specific primers from ribosomal genes. Phytopathology. 2003; 93: 160-166 describe primer sequences for the identification of four Xiphinema species.

The method of restriction fragment length polymorphism analysis PCR-RFLP (Restriction Fragments Length Polymorphism) using restriction enzymes that cut the DNA strand in a specific place was also used.

The differences in the length of the cut DNA fragments indicate the variability, which allowed the authors to develop a method for the identification of 11 species: Longidorus aetnaeus, L. africanus, L. andalusicus, L. artemisiae.L. caespiticola, L. distinclus, L. elongatus, L euonymus, L intermedius, L. leptocephalus and L. lignosus (Subbotin SA, Rogozhin EA, Chizhov VN Molecular characterization and diagnostics of some Longidorus species (Nematoda: Longidoridae) from Russia and other countries using rRNA genes. 2014 Eur J Plant Pathol 138: 377-390).

In the current state of the art, there is still a need to provide a tool for the detection of nematode species that have not been identified by genetic methods so far, as well as for an improved method of identifying those nematode species that are detected by known genetic techniques, but do not ensure high precision and do not exclude errors in the analysis.

The aim of the invention is to provide a method enabling the identification of the Longidorus intermedius nematode with high sensitivity and specificity, as well as providing new nucleotide sequences of primers and probes, applicable in the method of nematode detection by PCR, especially Real Time PCR, regardless of the type of test, their origin and purpose and stage. development. The above objectives have been achieved in the present invention.

The subject of the invention is a method of identifying the Longidorus intermedius nematode in a sample, comprising the following steps:

(a) providing a soil sample containing nematodes for identification;

b) rinsing the nematodes from the soil;

c) DNA isolation;

d) performing a PCR reaction, especially Real-Time PCR, using a 3 'and 5' primer pair and probe;

e) comparison of the amplification curve of the test sample with the amplification curves of the blank sample and the negative control, with the identification of Longidorus intermedius in PCR, especially Real-Time PCR using species-specific 3 'and 5' primers and a probe:

Type 5 'starter 3 'Sulficr Probe Name Sequence Name Sequence Name Sequence Longidorus imermedius Loninfv GCGATTTGAGGT GGAAAC Loninry AGCACTATAGCCA GTGTC Lonins AGTTCGTCGGCTTCT AATCGC

The subject of the invention is also a kit for the identification of the Longidorus intermedius nematode by PCR, especially Real-Time PCR, containing species-specific 3 'and 5' primers and a probe:

Ga uii ek 5 'starter 3 'starter Probe Name Sequence Name Sequence Name Sequence Longidorus iwermedius l.onmtY GCGATTTGAGG TGGAAAC Loninrv AGCACTATAGCC AGTGTC Lonins AGTTCGTCGGCTTCT AATCGC

The reaction mixture contains a buffer, thermostable Taq polymerase, magnesium ions, primers and a probe. The concentration of primers in the reaction mixture is 1-2 μM, probes 50-100 nM, magnesium ions 2-5 mM. The reaction is carried out at an annealing temperature of the primers of 55-60 ° C, in a volume of the reaction mixture of 10-20 µΙ, using 35 to 40 reaction cycles. Product identification is accomplished by comparing the amplification curves of the test sample with the amplification curves of the blank.

An example of the identification of Longidorus intermedius is given below. In each case, the same isolation and amplification conditions were applied to the blank (deionized H2O free from nuclease) and the negative sample. The material for the negative sample was DNA of a nematode species belonging to the same genus as the test.

PL231 512 Β1

Example

Identification of the nematodes of the species Lonsidorus intermedius.

DNA was isolated using Macherey-Nagel's commercial NucleoSpin Tissue XS DNA isolation kits. The reaction used primers and probes with the following sequences:

Start er / probe Sequence Loninfv GCGATTTOAGGTGGAAAC Lontnrv AGCACTATAGCCAGTGTC Lonins AGTTCGTCGGCTTCTAATCGC

The Real Time PCR reaction was performed in a 20 μΙ mixture in a Qiagen RotorGene 6000 apparatus using reagents from the LuminoCt qPCR ReadyMix kit (Sigma-Aldrich) in the following amounts:

- Nuclease-free H2O up to a volume of 20 μΙ,

- 2 μ110.0 μΜ of each of the Loninfv and Loninrv primers,

- 1 μΙ 4.0 μΜ of the Lonins probe labeled at the 5 'end with JOE dye, and at the 3' end with HBQ1 quencher,

- 10 μΙ 2X LuminoCt qPCR ReadyMix (Sigma-Aldrich),

- -2 μΙ DNA.

The reaction mixture was placed in a 20 μΙ tube, placed in the rotor of a RotorGene 6000 thermal cycler, and the amplification reaction was performed for 40 cycles under the following conditions:

Stage Temperature (° C) Time [s] Fluorescence measurement Pre-incubation 95 180 - Amplification denaturation 95 thirty - connecting 55 thirty ... single synthesis 72 and 30 - Cooling 40 20 -

DNA of Longidorus attenuatus was a negative control.

The amplification curves obtained as a result of the performed analysis are presented in Fig. 1

The solution according to the invention allows the detection of Longidorus intermedius in soil within a few hours, including the stages of sample preparation, DNA isolation and Real-Time PCR reactions. The method according to the invention can be used to identify the above-mentioned species, regardless of the type of test samples, their origin and destination, and the stage of development.

The proposed set of probes allows to identify the above-mentioned species of nematode in the Real Time PCR reaction, which is much more sensitive and faster than other PCR methods. The use of probes in the Real Time PCR reaction significantly increases the specificity of the reaction in relation to the Real Time PCR reaction with fluorescent dyes.

Claims (2)

Patent claims 1. A method of identifying the nematode Longidorus intermedius in a soil sample, comprising the following steps: (a) providing a soil sample containing nematodes for identification; b) rinsing the nematodes from the soil; c) DNA isolation; d) performing a PCR reaction, especially Real-Time PCR, using a 3 'and 5' primer pair and probe; e) comparison of the amplification curve of the tested sample with the amplification curves of the blank and negative control, PL231 512 Β1 characterized in that for the identification of the species Longidorus intermedius in PCR, especially Real-Time PCR, primers specific for a given species are used 5 '(No. 1) and 3' (No. 2) and probe No. 3. 2. Kit for identification of Longidorus intermedius nematode by PCR, especially Real-Time PCR, containing species-specific primers 5 '(# 1) and 3' (# 2) and probe # 3.