Method of DNA Extraction from Plant for Metagenomic Analysis as Example from Grape  Vitis amurensis  Rupr.

K. V. Kiselev; Киселев К. В.; N. N. Nityagovsky; Нитяговский Н. Н.; О. А. Aleynova; Алейнова О. А.

doi:10.31857/S055510992303011X

Method of DNA Extraction from Plant for Metagenomic Analysis as Example from Grape Vitis amurensis Rupr.

Authors: Kiselev K.V.¹, Nityagovsky N.N.¹, Aleynova О.А.¹
Affiliations:
1. Federal Scientific Center of the Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Laboratory of Biotechnology
Issue: Vol 59, No 3 (2023)
Pages: 281-288
Section: Articles
URL: https://journals.rcsi.science/0555-1099/article/view/138774
DOI: https://doi.org/10.31857/S055510992303011X
EDN: https://elibrary.ru/BBUGBY
ID: 138774

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Abstract
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Abstract

A new method for extracting DNA from plants is proposed, using the example of wild grapes Vitis amurensis Rupr., for further preparation of libraries for metagenomic analysis. The method is based on the isolation of DNA by an inexpensive CTAB method with an additional stage of DNA purification using silica spin columns (CTAB spin method). A comparative analysis of the results of metagenomic analysis of endophytes on DNA isolated using the proposed CTAB-spin method and using the commercial set ZymoBIOMICS DNA Miniprep (Zymo Research). It was found that when using the CTAB-spin method, the number of sequences of the 16S rRNA site and the diversity of bacterial genera were 2.8 and 1.2 times greater, respectively, than when using the ZymoBIOMICS kit. At the same time, the number of sequences of the internal transcribed spacer 1 (ITS1) and the biodiversity of endophytic fungi did not differ significantly during DNA extraction by two methods. Thus, the proposed method of DNA isolation for metagenomic analysis is an available and effective alternative to commercial kits for the isolation of plant DNA for new generation sequencing methods.

Keywords

grapes, DNA, metagenome, new-generation sequencing (NGS), bacteria, fungi, endophytes, Vitis amurensis

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