There were 122 shared DE genes between mock and D. ampelina inoculated samples. Inoculated-exclusive DE genes were strongly enriched in pathways associated with ethylene signaling and phenylpropanoid biosynthesis and significantly enriched in pathways associated with anthocyanin biosynthesis and nitrogen metabolism (Supplementary Table S2). Out of the 75 inoculated-exclusive DE genes, 56 genes (74.6%) were down-regulated 48 h after inoculation (Table 2), including several ethylene-responsive transcription factors and auxin-related proteins. Among others, pathogenesis proteins, peroxidases, stilbene synthase, tropinone reductase, dirigent protein and the cytochrome P450 hydroxylase CYP86A1 were up-regulated at 48 h after inoculation.Table 2Vitis cinerea B9 transcripts with Diaporthe ampelina inoculation-exclusive differential expression (DE) genes at 2 days post-inoculation, using false-discovery rate (FDR) ≤ 0.001GeneIDFunctional annotationFDRlogFCVIT_03s0063g00460Ethylene-responsive transcription factor ERF1095.0 × 10−10− 8.01VIT_07s0005g05910Auxin-binding protein ABP195.2 × 10−4− 6.30VIT_11s0016g00660DREB sub A-5 of ERF/AP2 transcription factor2.7 × 10−10− 5.34VIT_16s0013g01060Ethylene-responsive transcription factor ERF1051.2 × 10−4− 4.29VIT_16s0013g01030Ethylene-responsive transcription factor ERF1053.4 × 10−6− 3.63VIT_09s0002g02030Pyruvoyl-dependent arginine decarboxylase7.9 × 10−4− 3.60VIT_09s0002g080602-Hydroxyacid dehydrogenases, D-isomer specific8.2 × 10−7− 3.56VIT_16s0013g00950Ethylene-responsive transcription factor ERF1051.9 × 10−7− 3.53VIT_06s0009g03670F-box family protein1.0 × 10−5− 3.45VIT_08s0007g08520Unknown protein9.6 × 10−14− 3.31VIT_03s0180g00210Myb domain protein R12.5 × 10−5− 3.29VIT_14s0066g02350Galactinol synthase9.6 × 10−8− 3.26VIT_01s0127g00700Unknown protein1.1 × 10−15− 3.24VIT_07s0005g01140Unknown protein6.3 × 10−4− 3.21VIT_13s0064g01110No hit5.3 × 10−7− 3.17VIT_16s0013g01050Ethylene-responsive transcription factor ERF1051.2 × 10−7− 3.15VIT_06s0009g01620Harpin-induced protein3.4 × 10−6− 3.11VIT_16s0013g00990Ethylene-responsive transcription factor ERF1053.3 × 10−7− 3.10VIT_06s0080g01090CCR4-NOT transcription complex subunit 7/88.4 × 10−11− 3.10VIT_11s0016g01810Unknown protein1.8 × 10−13− 3.10VIT_18s0001g073202-Oxoglutarate/malate carrier protein, Mitochondrial2.4 × 10−9− 3.08VIT_12s0134g00240Avr9/Cf-9 rapidly elicited protein 201.3 × 10−8− 2.98VIT_14s0081g00520ERF128.8 × 10−5− 2.93VIT_06s0004g04180Zinc finger (C2H2 type) protein (ZAT11)6.2 × 10−4− 2.82VIT_18s0001g09230Salt-tolerance zinc finger2.3 × 10−5− 2.79VIT_16s0013g00970Ethylene-responsive element-binding factor 53.5 × 10−7− 2.72VIT_02s0025g02490Unknown protein2.0 × 10−4− 2.70VIT_16s0013g00980Ethylene-responsive transcription factor ERF1055.3 × 10−4− 2.67VIT_19s0093g005509-Cis-epoxycarotenoid dioxygenase 21.4 × 10−4− 2.59VIT_09s0054g01410Beta-amyrin synthase7.7 × 10−9− 2.59VIT_17s0000g01630Calmodulin CML374.7 × 10−4− 2.59VIT_12s0028g03270Ethylene-responsive transcription factor 91.5 × 10−5− 2.54VIT_18s0001g11170Myb domain protein 739.2 × 10−6− 2.54VIT_12s0134g00170No hit2.5 × 10−5− 2.53VIT_16s0013g01000Ethylene-responsive transcription factor ERF1058.2 × 10−4− 2.51VIT_02s0012g02820Geraniol 10-hydroxylase2.1 × 10−4− 2.46VIT_07s0255g00020OBF-binding protein 12.8 × 10−4− 2.44VIT_08s0105g00190U-box domain-containing protein1.5 × 10−5− 2.43VIT_19s0014g02240Ethylene-responsive element-binding factor 46.7 × 10−9− 2.43VIT_18s0122g00300Unknown protein1.2 × 10−5− 2.42VIT_05s0077g01970Zinc finger (C3HC4-type ring finger)3.6 × 10−9− 2.39VIT_09s0002g08030Arogenate dehydrogenase isoform 24.5 × 10−5− 2.34VIT_01s0011g04550Unknown protein1.1 × 10−6− 2.32VIT_18s0001g06560No hit8.1 × 10−9− 2.30VIT_05s0020g04570CBL-interacting protein kinase 7 (CIPK7)2.7 × 10−5− 2.20VIT_03s0038g02140Auxin transporter protein 25.4 × 10−4− 2.19VIT_18s0122g00980Glucan endo-1,3-beta-glucosidase 7 precursor2.5 × 10−4− 2.16VIT_17s0000g09270MATE efflux family protein1.5 × 10−5− 2.16VIT_00s0267g00030Unknown2.9 × 10−4− 2.15VIT_18s0166g00190U-box domain-containing protein4.1 × 10−4− 2.15VIT_00s0218g00140Anthocyanidine rhamnosyl-transferase4.8 × 10−4− 2.14VIT_18s0001g09910l-Asparaginase3.7 × 10−7− 2.14VIT_02s0012g02810CYP76C41.2 × 10−4− 2.13VIT_15s0048g02070BON2-associated protein (BAP2)3.4 × 10−4− 2.09VIT_16s0050g01580UDP-glucose: anthocyanidin 5,3-O-glucosyltransferase8.2 × 10−4− 2.06VIT_03s0063g00830Carboxyesterase 5 CXE51.7 × 10−4− 2.04VIT_15s0107g00550Tetratricopeptide repeat domain male sterility MS51.2 × 10−52.14VIT_16s0100g00930Stilbene synthase 21.5 × 10−42.61VIT_00s0229g00190Inositol 2-dehydrogenase like protein1.4 × 10−62.66VIT_16s0039g01300Phenylalanine ammonia-lyase (Vitis vinifera)4.3 × 10−42.73VIT_16s0100g00810Stilbene synthase (Vitis vinifera)3.3 × 10−72.82VIT_05s0077g01560Pathogenesis protein 10.3 (Vitis quinquangularis)3.8 × 10−93.12VIT_16s0100g00900Stilbene synthase (Vitis pseudoreticulata)3.5 × 10−73.22VIT_16s0100g00860Chalcone synthase1.4 × 10−73.48VIT_16s0100g01030Stilbene synthase (Vitis quinquangularis)1.2 × 10−53.54VIT_05s0077g01550Pathogenesis protein 10.3 (Vitis quinquangularis)8.9 × 10−53.56VIT_18s0001g06850Peroxidase GvPx2b class III1.1 × 10−73.67VIT_05s0077g01530Pathogenesis protein 10 (Vitis vinifera)1.7 × 10−83.71VIT_05s0077g01570Pathogenesis protein 10 (Vitis vinifera)3.2 × 10−123.80VIT_16s0100g01150Stilbene synthase (Vitis vinifera)1.4 × 10−64.13VIT_08s0007g00920Tropinone reductase8.8 × 10−54.13VIT_04s0069g00730Glutamate receptor protein7.3 × 10−44.18VIT_07s0031g01680CYP86A15.1 × 10−44.34VIT_06s0004g01020Dirigent protein4.3 × 10−54.62VIT_16s0100g00940Stilbene synthase 3 (Vitis sp. cv. ‘Norton’)2.9 × 10−44.94Fifty-six ###genes with negative log2 fold change (logFC) were down-regulated after inoculation (logFC < − 2), and nineteen genes with positive logFC were up-regulated after inoculation (logFC > 2)