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DNA-metabarcoding analyses of the grapevine wood fungal community in the Krasnodar Region and Crimea
- Authors: Blinova S.A.1,2, Shvartsev A.A.2, Alekseev Y.I.2,3, Stranishevskaya E.P.3, Ilnitskaya E.T.4, Makarkina M.V.4, Soloviev A.A.1
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Affiliations:
- All-Russia Research Institute of Agricultural Biotechnology
- LLC “Syntol”
- National Research Institute for Grape and Wine Magarach Russian Academy of Sciences
- North Caucasus Federal Scientific Center for Horticulture, Viticulture, Winemaking
- Issue: Vol 20, No 2 (2022)
- Pages: 89-100
- Section: Genetic basis of ecosystems evolution
- URL: https://journals.eco-vector.com/ecolgenet/article/view/106312
- DOI: https://doi.org/10.17816/ecogen106312
- ID: 106312
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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.
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About the authors
Sofiia A. Blinova
All-Russia Research Institute of Agricultural Biotechnology; LLC “Syntol”
Author for correspondence.
Email: sofya.blinova@yandex.ru
ORCID iD: 0000-0001-6782-8353
SPIN-code: 9148-3765
Scopus Author ID: 57217069755
Postgraduate Student, Junior Researcher
Russian Federation, Moscow; MoscowAleksey A. Shvartsev
LLC “Syntol”
Email: alexey.sva@yandex.ru
ORCID iD: 0000-0002-2786-9860
SPIN-code: 9792-6398
Researcher
Russian Federation, MoscowYakov I. Alekseev
LLC “Syntol”; National Research Institute for Grape and Wine Magarach Russian Academy of Sciences
Email: jalex01@mail.ru
ORCID iD: 0000-0002-1696-7684
SPIN-code: 8145-5586
Cand. Sci. (Biol.), Director of Science
Russian Federation, Moscow; YaltaElena P. Stranishevskaya
National Research Institute for Grape and Wine Magarach Russian Academy of Sciences
Email: stranishevskayaelena@gmail.com
ORCID iD: 0000-0002-2840-5638
Scopus Author ID: 57190218360
Dr. Sci. (Agricult.), Professor
Russian Federation, YaltaElena T. Ilnitskaya
North Caucasus Federal Scientific Center for Horticulture, Viticulture, Winemaking
Email: ilnitskaya79@mail.ru
ORCID iD: 0000-0002-2446-0971
SPIN-code: 7075-1328
Scopus Author ID: 57192072976
Cand. Sci. (Biol.), Head of Laboratory
Russian Federation, KrasnodarMarina V. Makarkina
North Caucasus Federal Scientific Center for Horticulture, Viticulture, Winemaking
Email: konec_citatu@mail.ru
ORCID iD: 0000-0002-3397-0666
SPIN-code: 3833-1636
Scopus Author ID: 57204108200
Junior Researcher
Russian Federation, KrasnodarAlexander A. Soloviev
All-Russia Research Institute of Agricultural Biotechnology
Email: a.soloviev70@gmail.com
ORCID iD: 0000-0003-4480-8776
SPIN-code: 3431-5168
Scopus Author ID: 35732425900
Dr. Sci. (Biol.), Professor RAS, Head of Laboratory
Russian Federation, MoscowReferences
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