1 SUPLEMENTARY MATERIAL 2 1) Comparative analysis of the different differential expression methods applied to the 3 transcriptome of Vanilla planifolia Jacks. 4 5 6 7 8 9 10 11 12 13 14 2dpi 10dpi 15 16 Supplemental Figure S1. Venn diagram showing the comparison of the differentially 17 expressed unigenes obtained with the methods DESeq2, EdgeR, NOISeq, and DESeq. At the 18 center of the diagram we observed that the EdgeR method comprises the great majority of 19 genes determined by the other methods. The right panel corresponds to 2 dpi, while the left 20 panel corresponds to 10 dpi. 21 22 23 24 25 26 2) Global expression profiles in response to infection caused by Fusarium 27 oxysporum f. sp. vanillae in vanilla. 28 . 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 2dpi 10dpi 51 Supplemental Figure S2. Heat map that contrasts the global vanilla response to 52 Fusarium oxysporum f. sp. vanillae. On the right we observe the early response 53 (2dpi); while in the left panel it presents the response to 10dpi. All differentially 54 expressed unigenes are included. 55 56 3) Expression profiles related to biotic stress, in the late response (10dpi) of 57 vanilla to Fusarium oxysporum f. sp. vanillae 58 59 60 61 62 63 64 65 66 67 68 69 70 71 Supplemental Figure S3. Heat map indicating the expression profiles of the annotated DEG 72 unigenes, corresponding to 10dpi. The numbers in the figure correspond to different 73 categories of gene ontology, as described below: 25 C1-metabolism, 11 lipid metabolism, 3 74 minor CHO metabolism, 13 amino acid metabolism, 16 secondary metabolism, 26 misc, 17 75 hormone metabolism, 30 signalling, 31 cell, 23 nucleotide metabolism, 27 RNA, 28 DNA, 76 33 development, 24 Biodegradation of Xenobiotics, 18 Co-factor and vitamine metabolism, 77 35 not assigned, 34 transport, 29 protein, 20 stress, 2 major CHO metabolism, 10 cell wall. 78 79 80 81 4) Expression profiles related to biotic stress, in the late response (10dpi) of 82 vanilla to Fusarium. 83 84 85 86 87 88 89 90 91 92 93 94 95 96 Supplemental Figure S4. In the present figure, generated with the Mapman software, the 97 expression profiles of the annotated unigenes related to biotic stress in the plants (plant- 98 pathogen interaction), in the late response, to the 10dpi, of vanilla before Fusarium. 99 100 101 102 103 104 105 5) STRING network of genes differentially expressed at 10 dpi in the vanilla 106 response to Fusarium. 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 Supplemental Figure S5. Protein-protein interactions were plotted in STRING by entering 125 the TAIR codes of all genes differentially expressed in the vanilla transcriptome in response 126 to Fusarium at 10 dpi. The colored bubbles correspond to different proteins present in 127 Arabidopsis. The thickness of the edge corresponds positively to the confidence of the 128 interactio 129 130 1) Main categories of gene ontology corresponding to the transcripts of the early 131 response (2 dpi) of vanilla before Fusarium. GO term Ontology Description Number Reference p-value FDR GO:0006412 P translation 74 1445 2.90E-41 2.10E-38 GO:0034645 P Celular macromolecule biosynthetic process 93 3661 6.50E-29 1.90E-26 GO:0009058 P biosynthetic process 110 5118 7.90E-29 1.90E-26 GO:0009059 P macromolecule biosynthetic process 93 3685 1.00E-28 1.90E-26 GO:0044249 P cellular biosynthetic process 107 4925 2.80E-28 4.00E-26 GO:0019538 P protein metabolic process 94 4009 1.10E-26 1.30E-24 GO:0010467 P gene expression 90 3962 1.80E-24 1.90E-22 GO:0044267 P cellular protein metabolic process 84 3487 2.70E-24 2.40E-22 GO:0044238 P primary metabolic process 140 8995 4.00E-24 3.20E-22 GO:0043170 P macromolecule metabolic process 117 7127 6.60E-21 4.70E-19 GO:0008152 P metabolic process 147 10614 1.40E-20 9.10E-19 GO:0044260 P cellular macromolecule metabolic process 107 6447 4.40E-19 2.60E-17 GO:0044237 P cellular metabolic process 124 8722 3.40E-17 1.90E-15 GO:0009987 P cellular process 147 11684 1.60E-16 8.30E-15 GO:0042254 P ribosome biogenesis 21 241 2.70E-16 1.30E-14 GO:0022613 P ribonucleoprotein complex biogenesis 21 253 6.60E-16 3.00E-14 GO:0044085 P cellular component biogenesis 23 571 4.40E-11 1.80E-09 GO:0003735 F structural constituent of ribosome 63 494 4.20E-57 1.40E-54 GO:0005198 F structural molecule activity 63 659 5.20E-50 8.30E-48 GO:0008135 F translation factor activity, nucleic acid 11 181 1.20E-07 1.30E-05 binding GO:0003746 F translation elongation factor activity 6 38 6.10E-07 4.90E-05 GO:0022626 C cytosolic ribosome 62 336 4.60E-65 1.00E-62 GO:0044445 C cytosolic part 58 360 1.00E-57 1.10E-55 GO:0033279 C ribosomal subunit 58 389 5.50E-56 4.10E-54 GO:0005840 C ribosome 63 524 1.20E-55 6.50E-54 GO:0030529 C ribonucleoprotein complex 63 703 2.00E-48 8.80E-47 GO:0043232 C intracellular non-membrane-bounded 69 1040 3.70E-45 1.20E-43 organelle GO:0043228 C non-membrane-bounded organelle 69 1040 3.70E-45 1.20E-43 GO:0005829 C cytosol 64 912 3.90E-43 1.10E-41 GO:0022625 C cytosolic large ribosomal subunit 36 162 3.20E-40 7.70E-39 GO:0015934 C large ribosomal subunit 36 225 1.10E-35 2.40E-34 GO:0044422 C organelle part 80 2562 3.30E-30 6.00E-29 GO:0044446 C intracellular organelle part 80 2561 3.20E-30 6.00E-29 GO:0032991 C macromolecular complex 70 2180 7.00E-27 1.20E-25 GO:0022627 C cytosolic small ribosomal subunit 22 130 1.20E-22 1.80E-21 GO:0015935 C small ribosomal subunit 22 164 1.10E-20 1.60E-19 GO:0044444 C cytoplasmic part 106 6289 2.30E-19 3.20E-18 GO:0005737 C cytoplasm 109 6822 2.80E-18 3.70E-17 GO:0005730 C nucleolus 20 209 2.70E-16 3.20E-15 GO:0043229 C intracellular organelle 112 8149 4.40E-14 4.90E-13 GO:0005622 C intracellular 125 9671 4.40E-14 4.90E-13 GO:0043226 C organelle 112 8155 4.70E-14 4.90E-13 GO:0031981 C nuclear lumen 22 374 1.00E-13 1.00E-12 GO:0044424 C intracellular part 120 9302 2.70E-13 2.60E-12 GO:0043233 C organelle lumen 24 539 2.20E-12 1.90E-11 GO:0070013 C intracellular organelle lumen 24 539 2.20E-12 1.90E-11 GO:0044428 C nuclear part 24 543 2.50E-12 2.10E-11 GO:0031974 C membrane-enclosed lumen 24 546 2.80E-12 2.30E-11 GO:0044464 C cell part 152 15217 1.80E-08 1.30E-07 GO:0005623 C cell 152 15217 1.80E-08 1.30E-07 GO:0016020 C membrane 56 4068 7.70E-07 5.60E-06 132 Supplemental Table 1. List of the main functional categories, determined with the 133 AgriGO 2.0 software, to which the annotated transcripts belong, which show 134 differential expression at 2 dpi, in the vanilla transcriptome in response to Fusarium 2) Top 100 list of transcripts expressed (up-regulated) at 2 dpi in the vanilla transcriptome, in response to Fusarium. Name logFc TRINITY_DN89410_c0_g1_i1|CDS1,AT1G64550.1,"AT1G64550.1 | ATGCN3, GCN3 | general control non- 12.7703632 repressible 3 TRINITY_DN104321_c0_g1_i1|CDS1 AT5G36950.1 AT5G36950.1|DegP10|DegPprotease10 11.1087838 TRINITY_DN83426_c0_g1_i1|CDS1,AT1G18610.1,AT1G18610.1 | Galactose oxidase/kelch repeat superfamily 10.4627113 protein TRINITY_DN54807_c0_g2_i1|CDS1,AT5G60390.3,AT5G60390.3 | GTP binding Elongation factor Tu family 10.1980704 protein TRINITY_DN6978_c0_g1_i1|CDS1,AT1G69100.1,AT1G69100.1 | Eukaryotic aspartyl protease family protein 10.1743963 TRINITY_DN63794_c0_g1_i3|CDS1, AT3G22590.1,"AT3G22590.1 | PHP, CDC73 | PLANT HOMOLOGOUS 10.014206 TO PARAFIBROMIN TRINITY_DN75904_c0_g1_i1|CDS1,AT4G00680.1,AT4G00680.1 | ADF8 | actin depolymerizing factor 8 9.88375811 TRINITY_DN91577_c0_g1_i1|CDS1,AT5G66720.1,AT5G66720.1 | Protein phosphatase 2C family protein 9.82955438 TRINITY_DN29703_c0_g1_i2|CDS1 AT4G00900.1 AT4G00900.1|ECA2,ATECA2|ER-typeCa2+-ATPase2 9.64577056 TRINITY_DN66086_c0_g1_i2|CDS1,AT1G10760.1,"AT1G10760.1 | SEX1, SOP1, SOP, GWD1, GWD | 9.57132483 Pyruvate phosphate dikinase, PEP/pyruvate binding domain TRINITY_DN65143_c0_g1_i1|CDS1,AT4G01210.1,AT4G01210.1 | glycosyl transferase family 1 protein 9.34292421 TRINITY_DN90514_c0_g1_i1|CDS1,AT3G02260.1,"AT3G02260.1 | BIG, DOC1, TIR3, UMB1, ASA1, LPR1, 9.30763592 CRM1 | auxin transport protein (BIG) TRINITY_DN65916_c0_g1_i2|CDS1,AT1G10095.1,AT1G10095.1 | Protein prenylyltransferase superfamily 9.28687646 protein TRINITY_DN18150_c0_g1_i1|CDS1 AT3G15720.1 AT3G15720.1|Pectinlyase-likesuperfamilyprotein 9.21071873 TRINITY_DN45207_c1_g1_i1|CDS1 AT5G58420.1 AT5G58420.1|RibosomalproteinS4(RPS4A)familyprotein 9.13507978 TRINITY_DN74463_c0_g1_i1|CDS1,AT4G16370.1,"AT4G16370.1 | ATOPT3, OPT3 | oligopeptide transporter 9.11594149 TRINITY_DN10093_c0_g2_i1|CDS1 AT1G06080.1 AT1G06080.1|ADS1|delta9desaturase1 9.10695891 TRINITY_DN89649_c0_g1_i1|CDS1,AT4G35840.1,AT4G35840.1 | RING/U-box superfamily protein 9.07751021 TRINITY_DN97412_c0_g1_i1|CDS1,AT1G18610.1,AT1G18610.1 | Galactose oxidase/kelch repeat superfamily 9.02973479 protein TRINITY_DN64271_c0_g1_i1|CDS1,AT2G24820.1,AT2G24820.1 | TIC55-II | translocon at the inner envelope 9.0048794 membrane of chloroplasts 55-II TRINITY_DN89945_c0_g1_i1|CDS1,AT3G04400.1,AT3G04400.1 | emb2171 | Ribosomal protein L14p/L23e 8.93054813 family protein TRINITY_DN41912_c0_g2_i1|CDS1 AT1G13950.1 AT1G13950.1|EIF-5A,ELF5A-1,ATELF5A- 8.91277437 1,EIF5A|eukaryoticelongationfactor5A-1 TRINITY_DN97075_c0_g1_i1|CDS1,AT5G02960.1,AT5G02960.1 | Ribosomal protein S12/S23 family protein 8.88831654 TRINITY_DN47565_c0_g2_i1|CDS1 AT3G60245.1 AT3G60245.1|Zinc-bindingribosomalproteinfamilyprotein 8.83080173 TRINITY_DN69294_c0_g1_i1|CDS1,AT5G15520.1,AT5G15520.1 | Ribosomal protein S19e family protein 8.74353089 TRINITY_DN66456_c0_g1_i5|CDS1,AT2G34780.1,"AT2G34780.1 | EMB1611, MEE22 | maternal effect 8.71800884 embryo