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Table 1 T. reesei RUT-C30 and A. niger N402 transcriptome studies using different carbon sources and growth conditions

From: Comparative transcriptome analysis reveals different strategies for degradation of steam-exploded sugarcane bagasse by Aspergillus niger and Trichoderma reesei

Species

Carbon source

Pre-treatment

Time-course

Technology

Total number of CAZymes genes upregulated

Reference

T. reesei QM9414

Cellulose, sophorose and glucose

-

24, 48 and 72 h, cellulose; 24 and 48 h, glucose; 2, 4 and 6 h, sophorose

RNA-seq (Illumina HiSeq 2000)

21, sophorose; 25, cellulose; 17, glucosea

42

T. reesei NG14 and RUT-C30

Lactose and glucose

-

1, 3, 6 and 24 h, microarray; 1, 6 and 24 h, RNA-Seq

Microarray and RNA-seq (Illumina HiSeq 2000)

29, T. reesei NG 14; 26, T. reesei RUT C30b

46

T. reesei QM6a

Wheat straw and glucose (control)

Ball milling

Wheat straw 24 h vs. glucose 48 h

RNA-seq (SOLiD 4)

33, wheat strawc

40

T. reesei QM9414

Wheat straw, lactose and glucose (control)

Grinding and acid thermochemical

50 h, wheat straw; 28 h, lactose

Microarray

40, wheat straw; 7, lactose;

41

T. reesei RUT-C30

Ground bagasse (BO); steam-exploded bagasse (BS); enzymatically hydrolysed(BE); steam-exploded wheat straw(WH); steam-exploded spruce (SP); oat spelt xylan (XO); birch xylan (XB); avicel cellulose 1%(AV1); avicel cellulose 0.75% (AV0.75); sophorose (SO)

Ground (bagasse), enzymatically hydrolsed (bagasse), steam-exploded (spruce, wheat straw, bagasse)

Lignocellulosic substrate 6, 17, 41 and 65 h

Microarray

87 (BO), 98 (BS), 124 (BE), 82 (WH), 51 (SP), 68 (XO), 94 (XB), 58 (AV1), 43 (AV0.75), 57 (SO)

43

A. niger N402

Willow and glucose

Ball milling

Willow 24 h vs. glucose 48 h

RNA-seq (SOLiD 5500)

107, willowd

31

A. niger N402

Wheat straw

Ball milling

Glucose 48 h + wheat straw 6 and 24 h

RNA-seq (SOLiD 5500)

64, wheat straw

33

A. niger N402

Wheat straw and glucose (control)

Ball milling

24 h, wheat straw

RNA-seq (SOLiD 4)

191, wheat straw d

32

A. niger N402

Sugarcane bagasse (SB) and fructose (control)

Steam-exploded

Fructose 24 h + SEB 6, 12 and 24 h

Microarray

67, SB

34

  1. aTotal RNA of the different time points of the same carbon source was pooled and sequenced; b It was not cited how many CAZymes were induced in RNA-seq data, thus we considered as upregulated genes with log2 ratio > 1 at least in one time point; c Considering only the CAZy genes with fold change > 20; d Considering only genes having fold change values > 2