DNA-metabarcoding analyses of the grapevine wood fungal community in the Krasnodar Region and Crimea

Abstract

Grapes are an economically important agricultural plant. Studies of the Grapevine microbiota and rhizosphere have become increasingly important in the last decade. The importance of such research is also supported by the fact that grapes are a perennial, long-used crop.

In this work, we present the results of a DNA-metabarcoding analysis of the fungal community of grape wood, collected from vineyards in the Krasnodar Territory and the Southern Coast of Crimea, and considered approaches to the analysis of DNA-metabarcoding data. Classifier is Naïve base (“sklearn”) based on machine learning is more informative metagenomic data classifier than BLAST+ (local alignment) and Vsearch (global alignment). Analysis of the ITS locus revealed the largest number of taxa, which was confirmed for all types of classifiers used in the study. Primers for the ITS locus showed a high specificity of fungal DNA in comparison with the LSU and SSU loci. The most common genera in the fungal community are Acidea, Alternaria, Cladosporium and Fusarium. Significant differences were revealed in the assessment of alpha and beta diversity in the analysis of samples from different regions. This article presents an analysis of the wood grapevine fungal community and ways to ASV classification. This study is the first to describe the endophytic fungal communities of the Krasnodar Territory and the Crimea vines using the analysis of DNA metabarcoding data.

Keywords

grapes / data-analysis / metagenomic data classifier / ITS locus / diversity / SSU locus / LSU locus