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Table 2 Differential expressed genes in high IA producing strains

From: Itaconic acid degradation in Aspergillus niger: the role of unexpected bioconversion pathways

A 2logR values RPKM values
Locus tag Old locus tag Annotation TargetP AB1.13 AB1.13 CAD AB1.13 #49B CitB#99 AB1.13 AB1.13 CAD AB1.13 #49B CitB#99
ANI_1_1474074 An08g10920 Citrate synthase (CitB) Cytosol 0.02 0.04 − 0.05 11.40 3.05 3.10 2.87 10,838.65
cadA (A. terreus)   Cis-aconitate decarboxylase Cytosol 0.05 10.62 9.47 10.72 3.54 6887.96 3116.06 7417.64
ANI_1_1906104 An12g05750 MFS phosphate transporter PM 0.13 1.02 10.28 10.55 1.09 2.87 2375.80 2852.93
hph (S. hindustanus) Hygromycin B 4-O-kinase Cytosol 0.23 0.17 8.84 10.04 0.94 0.86 759.61 1743.36
mttA (A. terreus)   Putative mitochondrial tricarboxylite transporter Mito − 0.18 0.18 8.46 9.86 0.19 0.54 477.02 1257.78
mfsA (A. terreus)   Putative major facilitator superfamily transporter A PM 0.07 1.44 7.49 9.19 0.30 2.36 222.56 721.88
amdS (A. nidulans)   Acetamidase A Cytosol 0.00 8.57 7.57 7.90 0.37 517.76 259.47 325.00
ANI_1_2022014 An01g14940 Phospholipase C PLC-C Secreted 0.06 0.08 4.99 7.18 8.40 8.53 286.39 1310.11
ANI_1_1486074 An08g11030 3-Phytase B Secreted − 0.03 0.21 5.94 6.99 27.36 32.28 1771.34 3663.34
ANI_1_2368024 An02g02840 Sialidase Secreted − 0.05 0.06 7.22 6.81 0.21 0.30 184.78 139.52
ANI_1_236084 An09g02180 Lipase Secreted/Mito − 0.34 − 0.30 3.96 6.78 2.43 2.55 67.01 479.51
ANI_1_1848144 An16g06190 Metabolite transport protein GIT1 PM 0.04 0.73 6.80 6.46 6.81 11.62 846.83 669.87
ANI_1_166144 An16g01340 Glyoxalase domain-containing protein 5 Mito/Cytosol 0.24 4.70 5.70 6.20 16.28 379.47 761.69 1080.98
ANI_1_248124 An14g01550 Acid phosphatase Secreted − 0.16 − 0.27 4.91 5.89 4.20 3.82 174.16 345.29
ANI_1_1500104 An12g02320 Short-chain dehydrogenase/reductase Cytosol 0.01 3.07 4.70 5.65 2.33 26.63 84.56 164.88
ANI_1_1330084 An09g03700 Hypothetical protein Secreted − 0.14 0.10 4.05 5.64 0.46 0.72 25.72 79.39
ANI_1_460094 An11g03340 Alpha-amylase A type-1/2 Secreted − 0.12 0.33 1.56 5.52 12.80 17.81 43.27 683.63
ANI_1_542164 An18g04140 Acid phosphatase Secreted 0.04 0.07 4.04 5.50 1.42 1.45 37.62 104.94
ANI_1_1576144 An16g02440 Phytase-like Secreted − 0.03 0.04 4.27 5.48 3.98 4.23 97.10 226.06
ANI_1_260144 An16g01850 BYS1 domain protein Secreted − 0.64 − 0.16 2.35 5.30 9.22 13.19 79.91 623.78
ANI_1_1250124 An14g02660 NPP1 domain protein Secreted 0.12 0.24 4.08 5.29 3.11 3.48 63.27 147.19
ANI_1_2836024 An02g08830 Histone transcription regulator 3 Nucleus 0.00 0.09 − 0.03 5.15 9.48 10.11 9.28 371.63
ANI_1_652114 An13g01750 Acid phosphatase Secreted 0.06 0.10 4.67 5.13 70.73 72.83 1754.06 2422.06
ANI_1_1440124 An14g04660 Aromatic ring-opening dioxygenase, catalytic LigB subunit Cytosol/Mito/Per 0.13 0.32 0.32 5.13 2.59 3.10 3.09 113.67
ANI_1_1432064 An07g00760 Putative itaconyl-CoA transferase (ictA) Mito 0.32 3.27 3.92 5.06 13.07 108.35 170.34 375.89
ANI_1_1812184 An04g04240 Phosphate transporter PM 0.27 1.05 4.83 4.99 2.94 5.74 91.74 102.55
ANI_1_126034 An03g01120 Aromatic-amino-acid aminotransferase Nucleus − 0.34 3.62 4.24 4.98 29.79 478.24 735.44 1226.92
ANI_1_246114 An13g01760 Oligopeptide transporter PM 0.33 0.46 2.43 4.97 1.30 1.51 8.88 56.23
ANI_1_1908104 An12g05810 Multicopper oxidase Secreted 0.04 0.20 4.33 4.76 0.18 0.31 21.98 30.01
ANI_1_2118064 An07g09220 Putative itaconyl-CoA hydratase (ichA) Mito − 0.11 2.78 4.04 4.71 7.32 60.28 146.61 232.65
ANI_1_1324074 An08g09850 Acid phosphatase Secreted − 0.18 − 0.36 3.70 4.58 128.06 112.96 1896.57 3490.63
ANI_1_1520134 An15g04760 Glycosyl hydrolase family 71 protein Secreted − 0.29 − 0.82 2.21 4.57 1.58 0.79 13.68 74.04
ANI_1_2122184 An04g08320 MFS monocarboxylate transporter PM 0.17 0.49 1.25 4.46 7.11 9.16 16.14 158.52
ANI_1_3198024 An02g13080 Phenylacetate-coenzyme A ligase Cytosol − 0.28 − 0.51 0.35 4.28 0.27 0.08 0.96 28.87
ANI_1_1430064 An07g00750 Fungal transcription factor Nucleus/Mito 0.02 3.04 3.73 4.28 0.52 11.37 19.01 28.19
ANI_1_820034 An03g06550 Glucoamylase Secreted 0.13 − 0.02 1.76 4.18 243.81 218.86 756.84 4054.75
ANI_1_1020134 An15g07520 Phosphoglycerate mutase family protein Cytosol − 0.20 − 0.60 4.75 4.18 12.67 9.31 420.93 282.80
ANI_1_1810184 An04g04230 Phosphate transporter (reannotated) Nucleus/Cytosol − 0.18 0.33 4.60 4.17 4.67 7.06 154.52 114.01
ANI_1_294044 An05g02340 Extracellular dihydrogeodin oxidase/laccase Secreted − 0.08 − 0.07 4.48 4.11 0.44 0.44 32.96 25.14
ANI_1_864144 An16g06510 Trans-aconitate 2-methyltransferase (tmtA) Cytosol 0.08 0.73 2.40 4.08 12.71 20.51 67.34 218.46
ANI_1_342114 An13g02590 Sugar transporter PM − 0.01 0.28 2.16 4.06 3.21 4.16 18.01 69.60
ANI_1_1098184 An04g06920 Alpha-glucosidase Secreted 0.00 − 0.33 0.57 4.04 174.34 138.54 258.87 2884.10
ANI_1_1820094 An11g03450 Small secreted protein Secreted 0.33 1.68 2.25 4.02 58.07 149.69 222.30 763.49
ANI_1_330024 An02g02480 MFS phosphate transporter PM − 0.20 1.65 3.18 4.02 3.12 13.82 41.86 75.60
ANI_1_762014 An01g05900 Cytochrome P450 Secreted − 0.13 − 0.10 3.86 4.00 0.63 0.66 24.97 27.63
ANI_1_1778074 An08g02590 GPI anchored protein Secreted − 0.06 0.21 3.26 4.00 10.62 13.07 115.12 192.81
B 2logR values RPKM values
Locus tag Old locus tag Annotation TargetP AB1.13 AB1.13 CAD AB1.13 #49B CitB99 AB1.13 AB1.13 CAD AB1.13 #49B CitB99
ANI_1_542134 An15g03800 Hydrophobin Secreted 0.06 − 0.55 − 2.13 − 8.78 981.57 641.93 213.11 1.14
ANI_1_1416134 An15g04010 Hypothetical protein Nucleus 0.27 − 0.20 − 5.87 − 7.79 288.73 208.03 3.11 0.09
ANI_1_92174 An10g00820 Oxaloacetate acetylhydrolase Cytosol − 0.13 − 0.81 − 2.61 − 7.51 1803.48 1122.69 323.44 9.81
ANI_1_220174 An10g00800 Purine nucleoside permease Secreted − 0.13 − 0.33 − 2.72 − 6.47 375.32 326.25 61.40 3.64
ANI_1_1046034 An03g01450 Major Facilitator Superfamily PM − 0.20 − 0.83 − 2.49 − 6.29 73.83 47.18 14.31 0.10
ANI_1_1062034 An03g01590 Arginine permease PM 0.13 0.41 − 2.09 − 6.08 243.24 295.39 51.56 2.30
ANI_1_964034 An03g00580 Cytochrome P450 monooxygenase Mito − 0.29 − 1.86 − 3.52 − 6.00 228.74 76.05 23.45 3.39
ANI_1_966034 An03g00590 Trichodiene synthase Tri5 Cytosol − 0.31 − 2.27 − 4.02 − 5.87 94.11 23.35 6.27 1.01
ANI_1_170034 An03g01460 1-Aminocyclopropane-1-carboxylate oxidase Cytosol − 0.10 − 0.86 − 2.52 − 5.43 114.81 67.35 20.61 1.88
ANI_1_1914064 An07g06460 C-7 hydroxycephem methyltransferase Cytosol − 0.26 − 0.32 − 4.38 − 5.28 36.47 35.03 1.16 0.16
ANI_1_182034 An03g01540 FAD dependent oxidoreductase Secreted/Cytosol 0.05 − 0.42 − 1.58 − 5.26 78.94 56.69 24.80 1.02
ANI_1_1770144 An16g05290 Purine-cytosine permease PM − 0.05 0.00 − 1.13 − 5.22 838.03 867.97 395.45 22.38
ANI_1_990084 An09g00660 OPT oligopeptide transporter protein PM 0.01 0.10 − 0.27 − 5.09 279.04 298.75 230.29 7.20
ANI_1_2008094 An11g05190 Type 1 glutamine amidotransferase Cytosol − 0.02 0.24 − 1.25 − 5.06 70.06 84.12 29.32 1.16
ANI_1_1366064 An07g00170 Hypothetical protein Secreted 0.37 0.34 − 1.87 − 5.04 56.14 54.96 11.10 0.35
ANI_1_1572014 An01g11640 Ammonium transporter PM 0.22 0.03 − 1.36 − 5.02 222.82 195.30 74.16 4.91
ANI_1_1862104 An12g05440 Urea active transporter 1 PM − 0.15 − 0.26 − 2.63 − 5.01 68.04 63.09 11.38 1.38
ANI_1_2238104 An12g09660 Phosphoribosyl transferase Cytosol 0.64 0.85 − 1.49 − 4.94 126.25 145.43 27.94 1.66
ANI_1_1456124 An14g04760 Male sterility domain containing protein Cytosol 0.26 − 0.49 − 2.51 − 4.91 258.07 152.77 36.93 6.18
ANI_1_708024 An02g05060 Hypothetical protein Secreted − 0.03 − 1.15 − 1.98 − 4.81 810.00 371.87 208.67 28.41
ANI_1_2764024 An02g08200 Short-chain dehydrogenase/reductase Cytosol 1.05 2.54 − 0.64 − 4.80 308.27 867.28 94.68 4.34
ANI_1_2236104 An12g09640 Uracil-regulated protein 1 Cytosol 0.44 0.67 − 0.72 − 4.80 107.20 125.82 47.45 1.86
ANI_1_46014 An01g00370 Aspartic endopeptidase (AP1) Nucleus 0.10 − 0.18 − 1.58 − 4.79 1351.68 1115.18 422.54 44.77
ANI_1_1054034 An03g01520 12-oxophytodienoate reductase Mito − 0.03 − 1.01 − 1.20 − 4.71 42.16 20.82 18.17 0.68
ANI_1_1850094 An11g03640 OPT oligopeptide transporter family PM − 0.11 − 0.52 − 0.49 − 4.71 104.23 78.34 79.93 3.35
ANI_1_1990074 An08g05320 Short-chain dehydrogenase/reductase Cytosol − 1.43 − 1.61 − 3.15 − 4.70 16.50 14.51 4.33 0.82
ANI_1_474154 An17g01540 GABA permease PM 0.07 0.26 − 2.34 − 4.67 85.82 98.28 15.40 2.26
ANI_1_1748104 An12g04260 NAD dependent epimerase/dehydratase Mito 1.23 2.79 − 2.00 − 4.66 69.28 206.65 6.50 0.19
ANI_1_726064 An07g05830 Formamidase Cytosol − 0.03 0.02 − 0.57 − 4.58 267.27 276.94 184.40 10.45
ANI_1_3344014 An01g14400 Cercosporin toxin resistance protein CRG1 Cytosol 0.04 0.02 − 2.87 − 4.56 63.05 62.21 7.56 1.65
ANI_1_176044 An05g01410 Acyl-CoA oxidase Mito − 0.30 − 0.96 − 2.25 − 4.55 178.03 111.60 45.07 8.38
ANI_1_568054 An06g02150 DUF3328 protein Secreted 0.11 0.34 − 4.28 − 4.55 48.49 57.10 1.36 0.96
ANI_1_1554124 An14g05980 MFS transporter PM 0.01 0.48 − 3.43 − 4.54 29.12 40.79 1.78 0.29
ANI_1_1048034 An03g01470 d-galactonate transporter PM − 0.07 − 1.24 − 2.35 − 4.52 37.53 16.20 6.96 0.76
ANI_1_806074 An08g05670 Nitrate transporter PM 0.13 1.08 − 1.66 − 4.44 44.15 86.17 12.00 0.90
ANI_1_3376014   Fe(II)/2-oxoglutarate (2OG) oxygenase Cytosol − 0.17 − 0.07 − 1.01 − 4.38 97.28 104.78 54.14 4.31
ANI_1_1340084 An09g03750 MAC/Perforin domain Cytosol 0.10 0.11 − 2.61 − 4.37 22.58 22.73 2.58 0.06
ANI_1_1514034 An03g06020 4-Carboxymuconolactone decarboxylase Cytosol 0.19 − 0.43 − 1.29 − 4.31 5568.62 3603.74 1987.79 245.12
ANI_1_2954014 An01g09970 Surface layer protein Cytosol 0.37 − 0.03 − 1.62 − 4.29 66.37 50.05 16.01 1.67
ANI_1_2450014 An01g03790 Urea active transporter 1 PM − 0.05 − 0.17 − 0.10 − 4.29 116.82 107.59 113.28 5.27
ANI_1_616114 An13g01470 Laminin gamma 3 Secreted − 0.15 − 1.01 − 2.79 − 4.27 110.93 60.59 16.95 5.42
ANI_1_1456104 An12g01910 Phytase Secreted − 0.04 − 0.95 − 4.39 − 4.26 30.69 15.78 0.55 0.70
ANI_1_142174 An10g00180 Cupin_like Cytosol/Mito 0.34 − 0.10 − 1.24 − 4.24 424.35 310.92 140.90 16.72
ANI_1_1362014 An01g09980 Asp-hemolysin Secreted 0.32 − 0.14 − 1.07 − 4.21 347.94 252.51 132.21 14.06
ANI_1_878114 An13g03990 Nucleobase-cation-symport-1 (NCS1) transporter PM − 0.08 0.15 − 2.27 − 4.21 30.66 36.14 5.91 0.81
ANI_1_2456094   S-adenosylmethionine-dependent methyltransferase   0.08 − 0.27 − 3.01 − 4.20 69.27 54.39 7.29 2.63
ANI_1_2086074 An08g07010 DUF3445 protein Mito 0.00 − 0.25 − 2.44 − 4.17 37.07 31.01 6.01 1.11
ANI_1_212174   Nitrilase   − 0.38 − 0.59 − 2.64 − 4.12 18.92 16.23 3.15 0.49
ANI_1_1828184 An04g04370 Phenylalanine ammonia-lyase PM 0.17 − 0.10 − 2.11 − 4.11 277.24 229.84 56.44 13.37
ANI_1_76154 An17g00640 Zinc-binding alcohol dehydrogenase domain-containing protein cipB Cytosol 1.04 2.86 − 2.13 − 4.11 119.10 425.44 12.36 2.40
ANI_1_1094134 An15g00280 Polysaccharide deacetylase Cytosol 0.00 − 0.07 − 0.98 − 4.08 204.72 194.38 102.72 11.10
ANI_1_1144084 An09g01920 FAD binding domain protein Secreted 0.75 2.11 − 1.49 − 4.04 39.96 103.97 7.67 0.48
ANI_1_294064 An07g02310 Glutathione S-transferase Ure2-like protein Cytosol 0.01 − 0.86 − 2.83 − 4.02 187.81 102.94 25.42 10.62
  1. (A) Genes upregulated in high IA producing conditions. Cutoff of 2logR values of 4.00 or higher was held. (B) Genes downregulated in high IA producing conditions. Cutoff of 2logR values of − 4.00 was held