RNA-sequencing reveals the complexities of the transcriptional response to lignocellulosic biofuel substrates in Aspergillus niger

Steven T Pullan; Paul Daly; Stéphane Delmas; Roger Ibbett; Matthew Kokolski; Almar Neiteler; Jolanda M van Munster; Raymond Wilson; Martin J Blythe; Sanyasi Gaddipati; Gregory A Tucker; David B Archer

doi:10.1186/s40694-014-0003-x

Table 4 Expression of genes relevant to the non-CAZy response of A. niger to willow

From: RNA-sequencing reveals the complexities of the transcriptional response to lignocellulosic biofuel substrates in Aspergillus niger

Gene ID			RPKM			Fold change ^b Willow 24 h/glucose 48 h	p- value Willow 24 h/glucose 48 h
ATCC 1015	CBS513.88	Gene name (if any) and annotation ^a (abbreviated)	Glucose 48 h	Willow 24 h	Willow 24 h + Glucose 5 h	Fold change ^b Willow 24 h/glucose 48 h	p- value Willow 24 h/glucose 48 h
Esterases & Lipases
TID_173684	An02g09690	Ortholog(s) have role in fatty acid catabolic process	0.50	21.96	0.22	98.05	<0.01
TID_51662	An09g00120	fae A, Feruloyl esterase	0.00	13.01	0.06	N/A	<0.01
TID_50877	An13g01880	Triacylglycerol lipase	0.00	0.98	0.00	N/A	<0.01
TID_210730	An16g01880	lipanl, Lysophospholipase	0.36	62.07	0.72	379.56	<0.01
TID_54865	N/A	N/A	0.02	27.43	0.16	2713.67	<0.01
This Study	An03g06560	Triacylglycerol lipase	0.00	0.05	0.00	N/A	0.65
TID_53620	An16g03700	Has domain(s) with predicted hydrolase activity	0.05	11.07	14.25	531.54	<0.01
Surface-interacting Proteins
TID_128530	An07g03340	hyp1, Hydrophobin	4.21	2.30	4.92	1.09	1.00
This Study	An08g09880	Putative hydrophobin	1.40	6.33	5.62	9.53	<0.01
TID_188224	An09g00840	Putative cell wall galactomannoprotein	1.31	721.16	2.13	1075.30	<0.01
TID_54125	An18g02730	Ortholog of A. nidulans FGSC A4: AN3257	0.12	3.36	0.73	59.77	<0.01
Enzymes of Carbon and Nitrogen Metabolism
TID_51997	An01g03740	D-xylose reductase	0.25	27.73	0.25	242.13	<0.01
TID_52460	An02g13750	Ortholog(s) have extracellular region localization	2.60	35.39	6.74	28.40	<0.01
TID_40496	An15g02410	Has domain(s) with predicted nucleotide binding activity	3.71	2.98	4.41	1.72	0.59
TID_40740	An15g05990	Has domain(s) with predicted nucleotide binding..activity	0.25	0.48	0.23	3.69	0.60
TID_56084	An11g10890	Aldose 1-epimerase	2.37	10.48	0.50	9.75	<0.01
Transporters
TID_56643	An12g09270	Putative lactose permease	0.12	38.20	1.72	676.84	<0.01
TID_38375	An08g04040	transmembrane transporter activity	0.53	7.98	0.84	32.31	<0.01
TID_55668	An06g00560	transmembrane transporter activity	0.19	24.08	0.30	263.55	<0.01
TID_180069	An07g02540	transmembrane transporter activity	0.10	2.05	0.75	43.05	<0.01
TID_197549	An02g08230	transmembrane transporter activity	0.26	18.83	0.09	146.66	<0.01
TID_54095	An18g01700	transmembrane transporter activity	0.09	2.83	0.15	65.55	<0.01
TID_54838	An13g03110	Has domain(s) with predicted role in transmembrane transport	0.35	5.77	0.11	34.61	<0.01
Others
TID_120161	An18g05500	Ortholog(s) have extracellular region localization	0.64	16.86	0.14	56.34	<0.01
TID_42809	An18g03380	Ortholog(s) have IgE binding activity	0.13	4.23	1.31	69.84	<0.01
TID_180489	An07g00070	Protein of unknown function	2.84	1.66	2.29	1.21	1.00
TID_53013	An11g07040	Ortholog of A. niger ATCC 1015 : 53013-mRNA	0.07	8.61	0.10	233.95	<0.01
TID_43786	An12g02560	N/A	0.13	0.18	0.17	3.20	0.92

^aThe annotations here are for the A. niger CBS513.88 strain from the AspGD database [44].
^bThe fold changes were calculated by the DESeq statistical analysis package using the normalised read counts.

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