PRIN ADAPT MICROBIOLOGY
Fastq files of fungal community present in harvested grapes and analysed by a culture-independent approach using next-generation sequencing (NGS). Grape berries of Aglianico and Cabernet Sauvignon were collected during the 2020 growing season at the full ripening stage in two sites Molise and Sicilia. In total, four experimental samples were considered: Aglianico Molise (AM), Aglianico Sicilia (AS), Cabernet Sauvignon Molise (CM), and Cabernet Sauvignon Sicilia (CS).
Steps to reproduce
Berries were collected during the 2020 growing season at the full ripening stage. Thirty clusters were harvested from different positions of the vineyard and from random positions on the plant to ensure the representation of the entire vineyard. At least ten berries were randomly selected from different parts of the cluster, avoiding those with visible damage and/or signs of pathogen infection, and pooled with berries from the other plants. For subsequent analyses, three independent pools (biological replicates) of 50 whole berries were selected, immediately frozen in liquid nitrogen, and stored at -80°C for subsequent analyses. For each analysis, four experimental samples were considered: Aglianico Molise (AM), Aglianico Sicilia (AS), Cabernet Sauvignon Molise (CM), and Cabernet Sauvignon Sicilia (CS). Fungal community composition was analysed by a culture-independent approach using next-generation sequencing (NGS). The grape samples from every vineyard were collected in duplicate, immediately transported to the laboratory and processed. Total genomic DNA was extracted using the Stool DNA Isolation Kit (Norgen, Biotek Corp., Thorold, ON, Canada) according to the manufacturer's instructions. The concentration and purity of the extracted nucleic acids were visualised and quantified, after agarose gel electrophoresis, by Nanodrop (NanoDropTM 2000/2000c; Thermo Fisher Scientific, Italy). DNA quantity was standardized to a concentration of 10 ng/μl. The ITS2 (internal transcribed spacer) region of the rRNA was amplified using primers 2024F and 2409R. Amplicons were sequenced using the Illumina MiSeq PE300 platform (Illumina, San Diego, CA, USA) at Biodiversa s.r.l. (Rovereto, Italy). Adapter sequences were removed using Cutadapt (Martin, 2011). Read quality was assessed using DADA2 (Callahan et al., 2016). The taxonomic references were assigned using trained OTUs at 99% from UNITE database version 8.2 (https://unite.ut.ee) within Qiime2 tools version 2020.2 (https://qiime2.org).
Ministero dell’Istruzione, dell’Università e della Ricerca
Research Projects of National Interest (PRIN) ADAPT - influence of agro-climatic conditions on the microbiome and genetic expression of grapevines for the production of red wines: a multidisciplinary approach (2017M83XFJ - CUP H34I19000590001)