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Pipeline publication

[…] es, we first searched for variants that showed the same genotype in all the clones, discarding those specific to a single clone. Among the whole set of called SNVs, 636,323 (95.6%) were shared by all three ‘Nebbiolo’ clones (Table ), including 157,574 SNVs located in protein-coding regions, as defined by the V1 annotation of the PN40024 genome. As reported above for the putative varietal genes, several SNVs identified in ‘Nebbiolo’ were present also in the genomes of ‘Tannat’ and ‘Corvina’. Excluding these SNVs, we identified 5,458 genes containing SNVs that are not present in PN40024, ‘Tannat’, or ‘Corvina’ (Table ). These genes were analysed by Gene Ontology (GO) enrichment analysis using BiNGO, a Cytoscape plug-in. The processes of response to stress, cell death, and protein modification were significantly over-represented (Figure ). The impact of the detected SNVs on the genes was classified according to SNPeff ver. 3.0 and is shown in Table . SNVs having a “high” impact included missense mutations or nonsense ones, such as the loss of the start or stop codon, the generation of a premature stop codon, or the alteration of splicing sites. The analysis showed that 455 genes were affected by at least one SNV common to the three ‘Nebbiolo’ clones (in total 498 SNVs with high impact) that contain potentially disruptive mutations (Fig. ). In this group of genes, the biological processes of response to stress and cell death were significantly over-represented (Fig. ). In addition, SNVs affecting 185 of these genes were absent in the ‘Corvina’ and ‘Tannat’ genomes (Table ), and 34 showed SNVs also i […]

Pipeline specifications

Software tools BiNGO, Cytoscape, SnpEff
Organisms Vitis vinifera
Chemicals Nucleotides