Dynamic changes in transcriptome and cell wall composition underlying brassinosteroid-mediated lignification of switchgrass suspension cells

Rao, Xiaolan; Shen, Hui; Pattathil, Sivakumar; Hahn, Michael G.; Gelineo-Albersheim, Ivana; Mohnen, Debra; Pu, Yunqiao; Ragauskas, Arthur J.; Chen, Xin; Chen, Fang; Dixon, Richard A.

doi:10.1186/s13068-017-0954-2

Biotechnology for Biofuels and Bioproducts

Table 1 Expression of switchgrass genes involved in cell wall development

From: Dynamic changes in transcriptome and cell wall composition underlying brassinosteroid-mediated lignification of switchgrass suspension cells

Gene information			Expression information
Microarray Probe	PvGene	Clade/Gene	Cluster	0 h	Induced				Non-induced		Compare
Microarray Probe	PvGene	Clade/Gene	Cluster	0 h	6 h	1 Day	3 Days	7 Days	1 Day	7 Days	1 Day	7 Days
Expansin
AP13ITG71529_at	Pavir.Aa00711	α-Expansin	4	260	1176	3260	2120	1002	2025	737	1	0
KanlowCTG26349_s_at	Pavir.Aa00711	α-Expansin	4	185	572	1927	942	603	1215	397	1	0
AP13ITG57935_at	Pavir.Aa00840	β-Expansin	5	3692	3666	134	71	40	16,793	8354	− 1	0
AP13CTG27439_s_at	Pavir.Ia02285	β-Expansin	5	2721	5043	2475	440	346	13636	6467	− 1	0
CESA
AP13.12059.m00001_s_at	Pavir.Ca01073	OsCESA1	2	1771	6165	4553	3517	2713	3351	2759	0	0
AP13CTG00607_s_at	Pavir.Ba01088	OsCESA3	4	1160	2574	2285	3019	1894	1391	1362	0	0
AP13CTG25870_s_at	Pavir.J35010	OsCESA8		2702	4804	3832	4513	3535	3877	3669	0	0
KanlowCTG12907_s_at	Pavir.J30974	OsCESA4	16	51	30	98	94	114	58	65	1	1
KanlowCTG34110_at	Pavir.Ib00804	OsCESA7	0	8	11	9	10	9	9	8	0	0
AP13CTG25049_s_at	Pavir.Bb02205	OsCESA9	0	52	44	56	52	66	56	56	0	0
KanlowCTG15421_s_at	Pavir.Ea00385	OsCESA1	15	1795	1003	1622	2469	1176	1956	1810	0	0
OTHSWCTG06249_s_at		OsCESA5	7	820	904	1810	803	1300	939	1094	1	0
AP13CTG06255_s_at	Pavir.J12858	OsCESA2	16	917	549	827	1418	774	941	868	0	0
COBRA
AP13CTG00322_s_at	Pavir.Ia00526	COB	2	3061	6252	5466	3902	3750	4715	3158	0	0
AP13ITG43381_at	Pavir.Ia00525	COB	5	1771	2628	697	164	697	3370	4215	0	− 1
Cellulose-like synthases
AP13CTG01955_at	Pavir.Ia02025	CSLA	16	204	201	246	269	213	411	224	0	0
AlamoCTG01742_s_at	Pavir.Ib01792	CSLA	12	86	145	279	474	394	207	233	0	1
AP13CTG06284RC_s_at	Pavir.Ia00426	CSLC	13	350	151	187	161	144	228	133	0	0
AP13CTG27051_s_at	Pavir.Fa01312	CSLC	5	133	251	39	25	32	147	98	− 1	0
KanlowCTG19494_s_at	Pavir.Fb00422	CSLF	5	335	304	327	150	134	154	125	1	0
KanlowCTG37527_s_at	Pavir.Ba00688	CSLF	0	164	212	199	147	190	202	174	0	0
Callose synthesis
KanlowCTG45113_s_at	Pavir.Aa00017	Callose synthase	16	215	100	551	879	379	241	233	1	0
AP13ITG74190RC_at	Pavir.Ib02063	Callose-binding	11	64	83	178	116	66	57	48	1	0
Cell wall precursor
KanlowCTG00021_s_at	Pavir.Ia00394	UGD	1	2487	8192	2541	1710	2633	4416	2852	0	0
AP13CTG07489_at	Pavir.Ea03089	UXS	2	416	1017	583	537	605	637	637	0	0
KanlowCTG22514_s_at	Pavir.Ea03089	UXS	0	530	1003	872	820	780	614	813	1	0
AP13CTG10419_s_at	Pavir.Gb00500	UXE	1	792	1820	696	695	809	927	934	0	0
AP13CTG28681_s_at	Pavir.Ba03802	UXE	3	186	396	335	329	488	374	300	0	1
AP13CTG00023_s_at	Pavir.Gb00638	UXT	4	63	249	409	338	1273	72	156	1	1
KanlowCTG06720_s_at	Pavir.Ia00627	UXT	2	695	1531	855	1053	1227	588	666	1	1
AP13CTG08328RC_s_at	Pavir.Ab02692	UER	5	1017	969	566	639	474	2925	1380	− 1	0
Arabinoxylan (AX) and glucuronoarabinoxylan (GAX) synthesis (backbone)
AP13CTG08590_s_at	Pavir.J27018	IRX9	3	280	635	729	481	563	627	441	0	0
AP13ITG73683_s_at	Pavir.Ib01337	IRX9	5	461	385	195	116	124	469	345	− 1	− 1
AlamoCTG02760_s_at	Pavir.Ea01094	IRX9L	12	136	139	207	370	362	87	174	1	1
AP13ITG60236_at	Pavir.Ea01094	IRX9L	16	194	153	292	666	548	148	227	1	1
AP13ITG74502_x_at	Pavir.J37721	IRX14L	1	221	2740	402	234	121	513	208	0	0
KanlowCTG18373_s_at	Pavir.J06597	IRX14L	1	4068	5793	3770	2684	3800	3711	4190	0	0
AP13CTG44601_s_at	Pavir.Ea03872	IRX10	2	388	3191	1018	714	930	609	896	0	0
AP13CTG03198_s_at	Pavir.J03056	IRX10	2	443	3104	851	809	882	1413	1262	− 1	− 1
Arabinoxylan (AX) and glucuronoarabinoxylan (GAX) synthesis (side chain)
AP13ITG71461_at	Pavir.Aa01690	GUX	3	74	274	261	122	419	184	226	0	0
KanlowCTG10196_x_at	Pavir.J03459	GUX	1	135	419	170	165	135	353	303	0	0
AP13CTG04376_s_at	Pavir.Aa01745	XAX1	5	146	236	85	73	64	330	217	− 1	0
AP13ITG43704_at	Pavir.Ea01415	XAT1	13	136	29	19	15	20	73	53	− 1	0
AP13.12340.m00010_s_at	Pavir.Da01068	XAT1	0	179	147	173	190	146	212	227	0	− 1
PF02458 (candidates for forming the ester linkages in GAX)
AP13CTG59034RC_at	Pavir.Gb00939		12	22	34	103	280	171	27	30	0	1
AP13ITG73138_at	Pavir.Fa02187		5	190	143	60	27	106	68	135	0	0
KanlowCTG26994RC_at	Pavir.Aa01433		12	73	138	256	626	354	98	105	1	1
AP13ITG72773_s_at	Pavir.Eb00373		13	1226	269	126	89	117	509	311	− 1	0
Pectin biosynthesis
AP13CTG05511_s_at	Pavir.Ba00640	ARAD1	1	79	95	65	80	75	131	80	− 1	0
AP13CTG06439_at	Pavir.Aa00624	GALS1	4	114	422	512	481	490	212	186	1	1
AP13CTG14035_at	Pavir.J20866	RGXT4	4	129	211	228	254	217	291	219	− 1	0
AP13ITG63440_at	Pavir.J14339	RGXT4	4	120	209	247	280	235	304	239	0	0
AP13CTG02428_s_at	Pavir.Ba01601	GAUT1	0	1418	1296	1565	1607	1332	1562	1462	0	0
AP13CTG18174_at	Pavir.Ba00237	GAUT7	2	118	331	247	232	125	447	315	− 1	− 1
KanlowCTG43804_at	Pavir.Fb01281	GAUT4	16	90	77	138	150	95	206	162	− 1	− 1
AP13CTG09682_s_at	Pavir.Ab01751	GAUT8	5	609	755	369	449	225	573	371	− 1	− 1
Pectin esterases
AP13ITG41170_at	Pavir.Ea01491	PME	5	699	484	73	80	72	104	97	0	0
AP13CTG29622_at	Pavir.Ia02028	PME	13	55	13	7	9	26	12	12	0	0
AP13ITG67053RC_at	Pavir.Eb02306	PAE	5	83	92	27	15	10	602	200	− 1	0
AP13CTG10801RC_at	Pavir.Ba00334	PAE	9	838	495	289	407	78	852	353	− 1	0
KanlowCTG09579_s_at	Pavir.Eb04062	PAE	1	174	290	170	167	145	280	180	− 1	0
Wall structural protein
AP13CTG23898_at	Pavir.J33924	AGP13	5	923	976	127	126	121	774	399	− 1	0
AP13ITG74104_at	Pavir.J33924	AGP13	5	120	158	13	13	16	174	67	− 1	− 1
AP13ITG53973_s_at	Pavir.Eb02706	FLA	1	315	1924	529	352	111	188	146	1	0

Expression values at each data point represent the mean of three biological replicates. Cluster represents the expression groups of filtered genes in induced samples defined by self-organizing map (SOM) method (Fig. 6a). Differential expression genes between induced and non-induced samples on 1 and 7 days were identified by the linear model in LIMMA [84]; − 1 (represented by bold italic), significant lower expression in induced samples than in non-induced samples, 1 (represented by italic), significant higher expression in induced samples than in non-induced samples, 0, no change between induced and non-induced samples

Back to article page

ISSN: 2731-3654

Contact us

General enquiries: journalsubmissions@springernature.com