Transcriptional landscape of Aspergillus nigerat breaking of conidial dormancy revealed by RNA-sequencing

Novodvorska, Michaela; Hayer, Kimran; Pullan, Steven T; Wilson, Raymond; Blythe, Martin J; Stam, Hein; Stratford, Malcolm; Archer, David B

doi:10.1186/1471-2164-14-246

BMC Genomics

Table 1 Selection of differentially expressed genes at T0-T1 generated by GeneChips and RNA-seq

From: Transcriptional landscape of Aspergillus nigerat breaking of conidial dormancy revealed by RNA-sequencing

Gene	Verified/putative function	Fc¹↑up/↓down	RPKM T0	RPKM T1	RPKM Fc ↑up/↓down
	Gluconeogenesis/glyoxylate cycle
An04g05300	fructose bisphosphatase (A. nidulans acuG)	↓ 31.39	71.07	11.66	↓ 6.09
An11g02550	phosphoenolpyruvate carboxykinase (A. nidulans acuF)	↓ 80.62	37.27	2.88	↓ 12.94
An01g09270	isocitrate lyase (A. nidulans acuD)	↓ 20.47	627.18	93.74	↓ 6.69
An15g01860	malate synthase (A. nidulans acuE)	↓ 40.61	28.52	3.68	↓ 7.75
An12g01990	acyl-CoA synthetase	↓ 2.04	16.85	3.29	↓ 5.12
An07g09190	acyl-CoA synthetase	↓ 6.07	23.8	10.77	↓ 2.20
An08g04990	carnitine acetyl transferase (A. nidulans facC)	↓ 20.74	107.81	10.2	↓ 10.56
An08g06580	facB, acetate regulatory DNA binding protein	↓ 2.09	16.27	0.99	↓ 16.43
	*Metabolism of alternative carbon sources*
An13g00480	triacylglycerol lipase	↓ 17.13	10.83	0.36	↓ 30.08
An09g05120	triacylglycerol lipase	↓ 5.09	11.84	0.81	↓ 14.62
An02g04680	lipase	↓ 4.93	19.39	4.46	↓ 4.35
An07g04200	triacylglycerol lipase	↓ 3.32	123.82	6.02	↓ 20.57
An18g06580	triacylglycerol lipase	↓ 3.21	58.96	3.63	↓ 16.24
An16g05570	aspartate aminotransferase	↓ 11.93	31.74	1.9	↓ 16.70
An14g01190	arginase	↓ 4.86	37.15	1.4	↓ 26.53
An15g03260	threonine aldolase*	↓ 2.09	9.41	8.47	↓ 1.11
	*Fermentation/glycolysis*
An02g06820	pyruvate decarboxylase	↓ 17.56	111.28	6.39	↓ 17.41
An08g01520	alcohol dehydrogenase	↓ 194.72	247.83	2	↓ 123.91
An12g09950	alcohol dehydrogenase	↓ 118.28	92.97	0.62	↓ 149.95
An04g02690	alcohol dehydrogenase	↓ 35.46	163.73	21.91	↓ 7.47
An17g01530	adhA, alcohol dehydrogenase	↓ 21.35	71.04	5.21	↓ 13.63
An09g03140	alcohol dehydrogenase	↓ 11.59	132.35	3.76	↓ 35.19
An16g05420	glucose-6-phosphate isomerase	↓ 11.61	23.29	2.44	↓ 9.54
An02g14380	hxkA, hexokinase	↓ 6.26	24.59	5.16	↓ 4.76
An18g01670	pfkA, 6-phosphofructokinase	↓ 64.25	42.44	12.52	↓ 3.38
An02g07470	fructose-bisphosphate aldolase	↓ 22.15	242.31	13.33	↓ 18.17
An08g02260	pgkA, phosphoglycerate kinase	↓ 19.01	32.17	15.68	↓ 2.05
An02g03830	creA, catabolite repressor	↑ 2.57	4.43	30.22	↑ 6.82
An02g03540	hexose transport protein	↑ 42.48	33.08	523.81	↑ 15.83
	*GABA shunt*
An10g00090	glutamate dehydrogenase	↓ 89.12	246.31	3.87	↓ 63.64
An15g04770	glutamate decarboxylase	↓ 63.83	62.34	2.3	↓ 27.10
An08g08840	glutamate decarboxylase	↓ 5.74	16.85	3.14	↓ 5.36
An17g00910	GABA transaminase	↓ 4.63	7.63	0	n/a
An14g02870	succinic semialdehyde dehydrogenase	↓ 31.91	274.43	2.34	↓ 117.27
	*TCA cycle*
An08g05580	isocitrate dehydrogenase	↑ 2.71	10.85	69.17	↑ 6.37
An18g06760	isocitrate dehydrogenase	↑ 3.17	55.23	354.46	↑ 6.41
An04g04750	oxoglutarate dehydrogenase	↑ 2.23	22.9	109.76	↑ 4.79
An17g01670	succinyl-CoA synthetase	↑ 5.36	24.29	128.98	↑ 5.31
	*Metabolism of internal carbohydrates*
An01g09290	neutral trehalase (A. nidulans treB)	↓ 5.01	719.2	58.5	↓ 12.29
An08g10510	tpsA, trehalose-6-phosphate synthase	↓ 48.49	124.99	2.69	↓ 46.46
An07g08710	tpsB, trehalose-6-phosphate synthase	↓ 2.00	22.52	12.47	↓ 1.80
An11g10990	trehalose-6-phosphate phosphatase	↓ 2.82	73.39	39.34	↓ 1.86
An03g02430	mannitol dehydrogenase	↓ 14.61	74.76	31.38	↓ 2.38
An02g05830	mpdA, mannitol-1-phosphate dehydrogenase	↓ 2.96	34.05	6.03	↓ 5.64
An04g04890	glycerol kinase	↓ 24.53	209.95	50.67	↓ 4.14
An08g00210	glycerol-3-phosphate dehydrogenase	↓ 16.76	80.42	25.23	↓ 3.18
An14g04920	tpiA, triose-phosphate-isomerase	↓ 29.26	72.81	4.87	↓ 14.95
An16g01830	gpdA, glyceraldehyde-3 phosphate dehydrogenase	↓ 14.75	107.99	19.98	↓ 5.40
An07g05790	osmoregulator (S. cerevisiae SGD1)	↑ 11.18	3.14	96.62	↑ 30.7
	*Nitrogen metabolism*
An14g02720	neutral amino acid transporter	↑ 13.44	3.02	313.74	↑ 103.89
An15g07550	neutral amino acid transporter	↑ 2.59	32.67	398.48	↑ 12.20
An16g05880	neutral amino acid transporter	↑ 37.51	14.66	907.29	↑ 61.89
An03g05360	neutral amino acid transporter	↑ 3.97	5.05	127.9	↑ 25.33
An04g09420	neutral amino acid transporter	↑ 58.88	0	126.15	n/a
An17g00860	translation initiation factor (A. fumigatus cpcC)	no change²	45.91	60.85	↑ 1.32
An01g07900	cpcA, transcription factor	↑ 3.55	18.59	123.24	↑ 6.62
An01g08850	transcription factor (A. nidulans cpcB)	↑ 3.86	23.52	530.23	↑ 22.54
An11g06180	transcription factor (A. nidulans prnA)	↑ 2.59	20.6	101.93	↑ 4.94
An11g06160	proline oxidase (A. nidulans prnD)	↑ 5.49	25.16	248.82	↑ 9.88
An11g06150	proline permease (A. nidulans prnB)	↑ 2.10	0	9.34	n/a
An11g06140	proline utilisation protein (A. nidulans prnC)	↑ 3.67	1.68	70.97	↑ 42.24
An12g08960	areA, transcription factor	no change²	23.9	12.21	↓ 1.95
An11g00450	nitrate transport protein	↑ 79.28	8.41	909.98	↑ 108.20
An08g05610	niaD, nitrate reductase	↑ 5.51	2.19	22.31	↑ 10.18
An08g05640	niiA, nitrite reductase*	↑ 2.61	7.34	7.97	↑ 1.08
An18g02330	transcription factor (A. nidulans nirA)	present T0, absent T1	45.17	15.7	↓ 2.88
An04g00990	gdhA, NADP-dependent glutamate dehydrogenase	↑ 9.61	48.66	1066.53	↑ 21.91
An03g05590	uracil transporter	↑ 28.54	14.71	384.05	↑ 26.11
An11g04340	uracil transporter	↑ 9.43	2.43	28.05	↑ 11.54
An07g01950	uracil transporter (A. nidulans uapC)	↓ 8.95	69.95	1.51	↓ 46.32
An01g08050	uaY, transcription factor	↓ 5.75	57.87	15.15	↓ 3.82
An14g03370	allantoinase*	↑ 27.48	7.64	16.23	↑ 2.12
	*Mitochondria/respiration*
An12g01480	Aminoacyl-tRNA biosynthesis	↑ 2.85	20.41	36.35	↑ 1.78
An08g02450	ATP synthase complex assembly	↑ 2.63	4.82	51.51	↑ 10.69
An15g01710	atp7, F1Fo-ATP synthase	↑ 2.29	31.59	265.5	↑ 8.40
An01g10880	F1Fo-ATP synthase	↑ 4.53	13.27	427.48	↑ 32.21
An11g04370	cytochrome b5	↑ 65.60	4.32	84.98	↑ 19.67
An02g04330	cytochrome C oxidase	↑ 5.29	0.72	140.73	↑195.46
An08g08720	cytochrome C peroxidase	↑ 11.09	11.03	148.09	↑13.43
An14g00240	holocytochrome-c synthase	↑ 2.50	16.53	48.96	↑ 2.96
An02g12620	mitochondrial respiratory chain complex IV	↑ 5.93	25.57	238.28	↑ 9.32
An08g04150	mitochondrial ribosomal protein	↑ 9.46	7.78	316.39	↑ 40.67
An15g05790	mitochondrial RNA polymerase	↑ 2.56	122.85	236.49	↑ 1.93
An04g02550	mitochondrial translation elongation factor	↑ 33.29	13.97	1080.27	↑ 77.33
An01g10190	mitochondrial transport protein	↑ 41.01	14.25	555.87	↑ 39.01
An08g04240	NADH:ubiquinone reductase	↑ 16.45	4.44	470.4	↑ 105.94
An02g12510	plasma membrane H(+)-ATPase pmaA	↑ 65.65	24.33	1271.65	↑ 52.27
An04g05220	ubiquinol-cytochrome C reductase	↑ 2.95	13.09	213.13	↑ 16.28

Fc¹ = Fold change based on GeneChip data.
No change² = fold change < 2.
The RPKM values shown are from the combined mapping scores of two distinct biological samples at each time point. Three statistical significance tests were applied to changes in gene expression measured by RNA-seq, the Likelihood Ratio Test [53], Fisher’s Exact Test [54], and an MA-plot-based method with Random Sampling model [52]. All changes in gene transcription, between T0 and T1, listed for RNA-seq data scored a p-value of < 0.001 for all three statistical tests, other than those genes highlighted with a *.

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