Skip to main content

Advertisement

Table 4 Glycosyl hydrolase (GH) transcripts in C1A cellulosome under different growth conditions

From: Transcriptomic analysis of lignocellulosic biomass degradation by the anaerobic fungal isolate Orpinomyces sp. strain C1A

CAZyme family Grown on Number of genes Total expression level (corrected FKPM)a Cellulosomal expression as the percentage of overall expression
Cellulosomal transcripts Non-cellulosomal transcripts Cellulosomal transcripts Non-cellulosomal transcripts
GH2 Glucose 1 1 5.92 0 100
Alfalfa 1 1 8.56 0 100
Energy cane 1 1 1.3 0 100
Corn stover 1 1 1.05 0 100
Sorghum 1 1 4.12 0 100
GH3 Glucose 2 17 314.9 399.47 44.08
Alfalfa 2 17 242.54 431.09 36.01
Energy cane 2 17 351.98 698.8 33.5
Corn stover 2 16 652.1 2852.93 18.6
Sorghum 2 17 446.42 948.41 32.01
GH5 Glucose 17 30 726.01 149.18 82.95
Alfalfa 16 34 483.4 302.36 61.52
Energy cane 15 34 607.37 343 63.91
Corn stover 16 34 804.65 275.4 74.5
Sorghum 19 34 556.98 287.72 65.94
GH6 Glucose 5 17 238.21 1561.09 13.24
Alfalfa 6 18 281.87 2983.09 8.63
Energy cane 6 18 495.5 3366.11 12.83
Corn stover 6 18 615.54 6341.22 8.85
Sorghum 6 18 473.62 3898.85 10.83
GH8 Glucose 1 2 113.21 4.35 96.3
Alfalfa 1 2 30.34 1.85 94.25
Energy cane 1 2 30.81 2.12 93.56
Corn stover 1 2 13 0.32 97.6
Sorghum 1   99.22 12.6 88.73
GH9 Glucose 9 21 340.63 267.28 56.03
Alfalfa 9 21 529.3 357.95 59.66
Energy cane 9 20 686.42 730.46 48.45
Corn stover 9 20 1124.22 1068.22 51.28
Sorghum 9 20 931.39 1276.62 42.18
GH10 Glucose 9 28 1339.11 1008.83 57.03
Alfalfa 9 28 1121.04 1565.45 41.73
Energy cane 9 28 927.74 1002.55 48.06
Corn stover 9 28 1300.71 1188.28 52.26
Sorghum 9 28 1167.53 2315.29 33.52
GH11 Glucose 5 23 194.91 1293.61 13.09
Alfalfa 5 23 96.62 910.9 9.59
Energy cane 5 24 110.25 1808.23 5.75
Corn stover 5 23 171.18 1808.46 8.65
Sorghum 5 24 175.12 6065.55 2.81
GH26 Glucose 5 6 136 0.35 99.74
Alfalfa 4 7 127.33 39.9 76.14
Energy cane 4 7 56.67 16.98 76.94
Corn stover 4 7 88 6.95 92.68
Sorghum 4 7 35.69 10.54 77.19
GH43 Glucose 4 31 318.72 392.93 44.79
Alfalfa 4 31 433.95 388.55 52.76
Energy cane 4 32 251.13 214.52 53.93
Corn stover 4 31 285.36 209.19 57.7
Sorghum 4 32 298.46 448.81 39.94
GH45 Glucose 6 16 602.8 2371.52 20.27
Alfalfa 6 16 377.34 2276.56 14.22
Energy cane 6 16 322.7 1659 16.28
Corn stover 6 16 420.71 1233.16 25.44
Sorghum 8 16 343.55 1971.77 14.84
GH48 Glucose 15 17 3094.01 515.24 85.72
Alfalfa 14 16 1715.18 213.22 88.94
Energy cane 14 16 2345.99 241.14 90.68
Corn stover 14 16 3980 9.36 99.77
Sorghum 16 16 1622.43 455.19 78.09
GH74 Glucose 3 4 50 0.3 99.4
Alfalfa 3 4 87.66 6.92 92.68
Energy cane 3 4 53.55 12.03 81.66
Corn stover 3 4 59.07 5.68 91.23
Sorghum 3 4 23.3 8.22 73.92
GH95 Glucose 1 1 35.79 0 100
Alfalfa 1 1 39.09 0 100
Energy cane 1 1 21.54 0 100
Corn stover 1 1 16.34 0 100
Sorghum 1 1 37.22 0 100
GH115 Glucose 1 4 89 0.4 99.55
Alfalfa 1 4 21.09 6.42 76.66
Energy cane 1 4 6.09 1.17 83.83
Corn stover 1 4 2.55 0.01 99.72
Sorghum 1 4 4.41 1.66 72.7
GH124 Glucose 1 3 35.19 34.88 50.22
Alfalfa 1 3 41.2 47.86 46.26
Energy cane 1 3 56.3 61.68 47.72
Corn stover 1 3 98.51 79.55 55.33
Sorghum 1 3 43.06 60.28 41.67
  1. aCorrected FPKM values normalized by the library size, as calculated using the estimateDispersions function in the R package DESeq [44]