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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
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
  1. 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
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