In inoculated V. cinerea B9, the 197 DE genes (T2 vs T0 at FDR ≤ 0.001) were unevenly distributed across 19 chromosomes (1.5–12.7% per chromosome), with inoculation enriching DE of genes on chromosomes 2, 9, 10, 16 and 18 (Fig. 4). Notably, genes on chromosome 15 showed a 2.9-fold repression of DE over time in treated samples, from 4.4% in mock inoculated to 1.5% in inoculated (Fig. 4). A greater number of genes (754) were DE in mock-inoculated vines, but had a less uneven distribution across 19 chromosomes (3.7–7.5% per chromosome).Fig. 4Chromosomal distribution of differentially expressed (DE) genes of V. cinerea B9 after inoculation with sterile water (mock DE, n = 751) or D. ampelina (inoculated DE, n = 290). For both treatments, genes with differential expression values between T0 (before inoculation) and T2 (48 h post-inoculation) were determined at FDR ≤ 0.001