Additional file 1 of Grapevine wood microbiome analysis identifies key fungal pathogens and potential interactions with the bacterial community implicated in grapevine trunk disease appearance
Creators: name: Bekris, Fotios
name: Vasileiadis, Sotirios
name: Papadopoulou, Elena
name: Samaras, Anastasios
name: Testempasis, Stefanos
name: Gkizi, Danae
name: Tavlaki, Georgia
name: Tzima, Aliki
name: Paplomatas, Epaminondas
name: Markakis, Emmanuel
name: Karaoglanidis, George
name: Papadopoulou, Kalliope K.
name: Karpouzas, Dimitrios G.
Publisher: name: figshare
Year: 2022
Subjects: subject: Microbiology
subject: FOS: Biological sciences

description: Additional file 1. Figure S1. A map of Greece showing the sampling sites (Amyntaio, Nemea and Crete). Vineyards of Xinomavro, Agiorgitiko and Vidiano cultivars were sampled in Amyntaio, Nemea and Crete regions, respectively. Figure S2. Rarefaction curves for the wood samples analyzed for their fungal (a) and bacterial microbiome (b). Figure S3. Stacked bar plots showing the composition of the fungal community (at the class taxonomic level) in wood samples collected from GTD asymptomatic and symptomatic vines of the cultivars Agiorgitiko (a), Xinomavro (b), Vidiano (c) each located in a distinct viticultural zone in Greece. Figure S4. Fungal ASVs phylogenetically assigned to taxa previously identified as causal agents of GTDs that showed differential abundance in samples collected from symptomatic and asymptomatic vines. Data are presented collectively for all geographic locations/cultivars (a) and for each variety separately (b) Agiorgitiko (c) Xinomavro (d) Vidiano. ASV014: Phaeomoniella chlamydospora, ASV068: Kalmusia variispora, ASV13: Seimatosporium vitis, ASV52: Fomitiporia spp., ASV338: Seimatosporium vitis, ASV005: Phaeomoniella chlamydospora, ASV008: Phaeoacremonium iranianum, ASV75: Neosetophoma spp., ASV159: Neosetophoma spp., ASV074: Diaporthe spp., (Signif. Differences: ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05). Figure S5. Stacked bar plots showing the composition of the bacterial community (at the phylum taxonomic level and for the class Proteobacteria) in wood samples collected from GTP asymptomatic and symptomatic vines of the cultivars Agiorgitiko (a), Xinomavro (b), Vidiano (c) each located in a distinct viticultural zone in Greece. Figure S6. Out of bag (OOB) error rates of the Random Forest model parameter states next to the overall model error rates (7.94% shown with the black line) for each one of the 1000 model trees. The confusion matrix is also provided on the plot. Table S1: A list of the wood samples analyzed with all relevant information regarding vine cultivar and viticultural zone, GTD symptoms presence or absence, plant part sampled, vineyard code, plant code and geographic location. Table S2. Primers used for amplicon sequencing analysis. B000X-515f and FI000X-ITS4r are indexed primers used in the second amplification step, which are composed of the sequence of the universal primers 515f (bacteria) and ITS4r (fungi) (bold), the indexes used for samples barcoding (underlined) and a TT (linker) sequence at the 5' end of each primer. Table S3. PCR reagents and thermocycling conditions used for amplicon sequencing analysis. Table S4. PERMANOVA analysis of the fungal and bacterial wood microbiome (Signif. codes: 0.001 ‘***’ 0.01 ‘**’ 0.05 ‘*’). Table S5. ASVs detected in the wood microbiome of the vines studied that are considered as putative pathogens involved in GTDs. Each ASV was phylogenetically assigned to the closest verified taxonomic level (genus or species).