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Bioresources and Bioprocessing

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
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