Novel qPCR-based test system for Acidovorax citrulli based on PAS domain S-box protein gene

Slovareva O.Yu.

Russian State Agrarian University — Moscow Agricultural Academy named after K.A. Timiryazev;
Federal State Organization «All-Russian Plant Quarantine Center»

Starikova E.V.

Federal State Organization «All-Russian Plant Quarantine Center»;
Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency

Novel qPCR-based test system for Acidovorax citrulli based on PAS domain S-box protein gene

Authors:

Slovareva O.Yu., Starikova E.V.

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Journal: Molecular Genetics, Microbiology and Virology. 2021;39(2): 46‑50

DOI: 10.17116/molgen20213902146

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To cite this article:

Slovareva OYu, Starikova EV. Novel qPCR-based test system for Acidovorax citrulli based on PAS domain S-box protein gene. Molecular Genetics, Microbiology and Virology. 2021;39(2):46‑50. (In Russ.)
https://doi.org/10.17116/molgen20213902146

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GOAL

The diagnosis of Acidovorax citrulli requires new highly specific methods based on qPCR. The goal of the study was to develop a new qPCR-based test for the identification of A. citrulli.

MATERIALS AND METHODS

By clustering the protein sequences of 9 A. citrulli genomes and 9 A. avenae genomes, the cd-hit program was used to identify 153 protein clusters present in all 9 A. citrulli strains and absent in all A. avenae strains. The resulting clusters were compared with known protein sequences (nr) using the blastp program to determine their specificity for A. citrulli. Coding sequences of A. citrulli-specific proteins were used for the selection of primers and the probe. The specificity of qPCR was tested by using the DNA of 6 A. citrulli strains and 188 non-target bacteria strains.

RESULTS

As a result of the search for A. citrulli-specific protein sequences, identified the S-box PAS domain protein. The qPCR tests performed showed 100% specificity both when testing target strains (all reactions were positive) and with non-target strains (all reactions were negative).

CONCLUSION

Thus, a new qPCR test was developed for the identification of A. citrulli, based on the sequence encoding the S-box protein of the PAS domain.

Keywords:

Acidovorax citrulli

qPCR

PAS domain

S-box protein

phytopathogen diagnostic

plant quarantine

Authors:

Slovareva O.Yu.

Russian State Agrarian University — Moscow Agricultural Academy named after K.A. Timiryazev;
Federal State Organization «All-Russian Plant Quarantine Center»

Starikova E.V.

Federal State Organization «All-Russian Plant Quarantine Center»;
Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency

Received:

07.02.2020

Accepted:

27.02.2020

List of references:

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European and Mediterranean Plant Protection Organization (EPPO), Acidovorax citrulli. Categorization. 2020. https://gd.eppo.int/taxon/PSDMAC/categorization
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