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Table 2 Expression of genes involved in carbohydrate hydrolytic pathway

From: Transcriptomic analysis of Aspergillus niger strains reveals the mechanism underlying high citric acid productivity

Gene ID (1015) Gene ID (513.88) Predicted function (homolog and organism)a FPKM-10 h FPKM-40 h Fold changeb
S1 S3 S2 S1 S3 S2 S1/S3 (10 h) S1/S2 (10 h) S1/S3 (40 h) S1/S2 (40 h)
220039 An04g09890 agsA, GH13, alpha-amylase, alpha-1,3 glucan synthases 85.31 3.70 69.89 18.92 84.01 41.45 4.52 − 2.15 − 1.13
20924 An02g13240 agdC, GH13, alpha-amylase, (A. parasiticus glcA) 94.33 6.81 34.64 9.80 27.69 25.98 3.79 1.44 − 1 − 1,79
4000142 No amyA, GH13, alpha-amylase, catalytic region 314.72 7.81 364.47 10,173.90 196.30 8128 5.33 5.69
6.225.1 An15g07800 agtC, GH 13, alpha-amylase, catalytic region 18.68 0.88 2.99 4.99 43.02 0.24 4.40 2.64   4.37
80803 An14g04190 gbeA, glycoside hydrolase GH 13, 1,4-alpha-glucan-branching enzyme 80.46 10.18 19.34 15.07 58.91 53.08 2.98 2.05 − 1.96 − 1.81
140568 An03g06560 Glycoside hydrolase GH15, glucan-1,4-alpha-glucosidase with starch-binding domain 2003.34 36.57 1922.03 7633.04 293.32 8669.53 5.77 4.7
1.137.1 An01g10930 agdC, glycoside hydrolase, GH31, alpha/beta-glucosidase 325.56 65.10 122.57 99.21 41.37 405.03 2.32 1.41 1.26 − 2.03
170127 An04g06920 agdA, glycoside hydrolase, GH 31, alpha-glucosidase 2116.14 213.84 860.88 1651.11 241.73 1790.41 3.30 1.29 2.77
180456 An16g06800 Glycoside hydrolase, GH 5, endoglucanase A 505.16 93.65 557.327 104.11 77.28 449.4 2.43 − 2.11
190032 An03g00940 Glycoside hydrolase, GH 10, endo-1,4-beta-xylanase F1 1100.38 0.45 1.12 108.75 1.64 18.16 11.24 9.96 6.05 2.58
11115 An01g00780 xynB, glycoside hydrolase, GH 11, endo-1,4-beta-xylanase 218.08 13.44 5.87 191.03 0.45 29.15 4.02 5.22 8.74 2.71
80523 An14g02760 eglA, glycoside hydrolase GH 12, endoglucanase A 460.75 1.92 10.67 85.96 4.34 375.94 7.9 5.43 4.3 − 2.12
10876 An01g03340 Glycoside hydrolase GH 12, xyloglucanase 25.10 7.61 52.69 255.83 6.47 47.62 1.72 − 1.05 5.3 2.42
6000593 An15g07760 Glycoside hydrolase, GH 26, mannan endo-1,4-beta-mannosidase E 316.29 62.32 63.14 11.45 1.10 9.46 2.34 2.32 3.37
22004 An02g11150 aglB, glycoside hydrolase, GH 27, alpha-galactosidase B 59.76 6.19 41.36 618.92 1.10 248.35 3.27 9.14 1.32
20338 An02g04900 Glycoside hydrolase, GH 28, endopolygalacturonase C 698.14 21.98 362.65 458.52 16.00 307.35 4.99 4.84
90046 An12g08280 inuE, glycoside hydrolase, GH 32, inulinase 224.97 14.74 52.39 8.03 0.50 3.50 3.93 2.1 4.01 1.19
17000028 An04g06990 Glycoside hydrolase, GH 47,1, 2-alpha-mannosidase 62.66 14.20 92.03 47.61 125.33 99.55 2.14 − 1.40
30627 An08g05230 Glycoside hydrolase, GH 61, endoglucanase-4 468.30 6.76 19.19 13.28 8.30 30.59 6.11 4.61 − 1.20
6.376.1 An15g04900 Glycoside hydrolase, GH 61, endo-beta-1,4-glucanase D 130.324 6.08 1.30 0.59 1.07 2.03 4.42 6.65 − 1.79
190140 An03g00960 axhA, Glycoside hydrolase, GH 62, alpha-l-arabinofuranosidase 648.17 1.98 3.37 563.18 1.59 66.70 8.36 7.59 8.47 3.08
210054 No Chitinase 1761.52 48.82 494.28 513.94 728.75 1145.75 5.17 1.83 − 1.15
10199 An01g12440 Chitin-binding, domain 3 367.96 15.93 29.17 333.84 7.89 39.68 4.52 3.65 5.4 3.07
140158 An03g04190 Chitinase 213.33 20.54 283.81 347.27 212.54 617.82 3.37
13.203.1 An04g04670 cfcC, GH18, Chitinase 150.49 18.23 56.79 96.25 162.39 119.70 3.04 1.4
10106 An01g12450 bxgA, chitinase 245.54 37.36 83.58 465.89 7.44 205.65 2.72 1.55 5.97 1.18
80155 An14g01840 Chitinase 494.65 192.43 679.08 3093.6 1858.9 2445.76 1.36
  1. “–” denotes genes with no differences at transcriptional level, fold change ≤ 1. Some of the genes have small differences, but have a decisive impact on CA production. We also used fold change as an indicator
  2. “No” denotes that sequence was not mapped to the genome sequence assembly of A. niger strain CBS 513.88
  3. a Description of gene or closest homolog (BLASTP)
  4. b Fold change of differentially expressed (FDR < 0.05, FPKM ≥ 50 in A. niger YX-1217 at time 10 h or time 40 h) genes based on a comparison of transcription levels at YX-1217/ATCC 1015 (designated as S1/S3) (10 h), YX-1217/YX-1217G (designated as S1/S2) (10 h), YX-1217/ATCC 1015 (designated as S1/S3) (40 h), and YX-1217/YX-1217G (designated as S1/S2) (40 h), respectively