Supplemental Table 1 Homologous Analysis of Transcript-Derived Fragments (Tdfs) Expressed

Supplemental Table 4 Homologous Analysis of transcript-derived fragments (TDFs) expressed between the embryonic and non-embryonic callus No. Primer Size Accumulation Sequence similarity Accession no. E comb. (bp) value NC C

Metabolism 1 M7/P2 115 + 3-hydroxyisobutyryl-CoA NM_001156818 4e-51 hydrolase/ catalytic (Zea mays) 2 M10/E8 222 + 2-oxo acid dehydrogenase XM_002274443 3e-18 (Vitis vinifera) 3 M11/P15 176 + omega-6 fatty acid desaturase NM_001155650 4e-79 (Zea mays) 4 M11/E3 315 + arabinogalactan protein NM_001155433 3e-102 (Zea mays) Cell Growth/Division 5 M6/P13 280 + callose synthase AY177665.1 2e-80 (Hordeum vulgare) 6 M9/P8 421 + glycosyl transferase family 1 NM_129577 8e-30 protein (Arabidopsis thaliana) 7 M1/E3 468 + glucan synthase FJ853604 7e-107 (Hordeum vulgare) 8 M3/P8 215 + Galactosyl galactosyl xylosyl NM_001158001 4e- protein 3-beta-glucuronosyl 105 transferase (Zea mays) 9 M6/P4 142 + kinesin heavy chain like BAB03114 8e-60 protein (Arabidopsis thaliana) Energy production and conversion 10 M7/E8 199 + ATP-dependent helicase NM_120949 5e-28 (Arabidopsis thaliana) 11 M7/E5 190 + NADH dehydrogenase EU956079 1e-91 (Zea mays) 12 M5/P5 364 + NADH dependent Glutamate AB008845 2e-131 Synthase (Oryza sativa) 13 M6/E4 186 + phospholipid-transporting XM_002517828 2e-25 ATPase (Ricinus communis) Transcription 14 M6/P8 299 + DNA binding protein NM_001158320.1 7e-149 (Zea mays) 15 M3/P8 513 + WRKY9 (Oryza sativa) AY341850 2e-96 16 M1/P12 280 + SAR DNA binding protein AB015431 4e-56 (Oryza sativa) 17 M11/P8 229 + transcription factor APF I EU961488 1e-93 (Zea mays) 18 M11/P14 373 + AP2 domain transcription EF659468 2e-48 factor (Zea mays) 19 M11/E3 385 + gypsy/Ty3-type AF050455 6e-157 retrotransposon Tekay (Zea mays) Protein synthesis/Degradation 20 M9/P8 323 + chloroplast phytoene synthase AY455286 7e-54 (Y1) gene (Zea mays) 21 M10/E6 323 + glycine cleavage system H NM_001159198 1e-77 protein (Zea mays) 22 M10/E7 206 + 22 kDa alpha zein gene AF090447 3e-100 cluster (Zea mays) 23 M10/E1 294 + chaperonin (Zea mays) EU969028 6e-42 24 M7/P5 274 + ubiquitin fusion protein EU967205 5e-17 (Zea mays) 25 M3/E5 220 + minichromosome NM_001111819 2e-103 maintenance protein (Zea mays) 26 M3/P16 272 + aspartic proteinase NM_001153734 2e-15 nepenthesin-2 (Zea mays) 27 M1/P4 356 + caspase/ cysteine-type NM_100097 4e-20 endopeptidase (Vitis vinifera) 28 M1/P8 397 + nucleotide binding protein NM_001158880 0 (Zea mays) Transporters 29 M9/P6 339 + importin beta-like protein Y15226 9e-110 (Oryza sativa) 30 M9/P8 246 + transposon protein (Zea mays) NM_001155502 3e-114 31 M10/E7 172 + protein transport protein NM_111590 3e-24 Sec24 (Arabidopsis thaliana) Cell structure 32 M11/E6 350 + dnaJ protein (Zea mays) AF053468.1 9e-174 33 M10/E5 192 + LHY protein (Zea mays) NM_001138057 6e-90 34 M7/E6 445 + B73 chloroplast (Zea mays) AY928077.1 0 35 M3/P4 392 + USP family protein NM_001155721 0 (Zea mays) 36 M7/P2 226 + TPD1 (Zea mays) NM_001159242 4e-107 Signal transduction 37 M6/P2 322 + 26S proteasome regulatory AB070259 2e-24 particle non-ATPase subunit (Oryza sativa) 38 M10/E5 338 + GTP-binding proteinTypA BAB08691 5e-88 (Arabidopsis thaliana) 39 M1/P8 385 + Metallopeptidase (Zea mays) NM_001157773 0 40 M10/E3 230 + chloroplast purple acid FJ974008 1e-56 phosphatase isoform (Zea mays) 41 M5/E4 290 + zinc finger protein AB001886 2e-21 (Oryza sativa) 42 M6/P2 302 + ARF for GTP-ase activating EU970929 6e-74 protein (Zea mays) 43 M7/P7 117 + guanine nucleotide-exchange AF262215 2e-41 protein (Oryza sativa) 44 M7/P2 268 + 1-associated receptor kinase 1 XM_002519849.1 6e-10 precursor (Ricinus communis) 45 M7/P11 116 + protein binding protein NM_001157731 2e-24 (Zea may) Stress/Disease/Defence 46 M6/P11 286 + Glutathione-regulated XM_00251829 8e-34 potassium-efflux system protein kefB (Ricinus communis) 47 M9/P5 424 + respiratory burst oxidase AY603975 2e-75 protein B (Oryza sativa) 48 M5/P11 470 + retrotransposon and repetitive AY038013 2e-44 DNA linked to receptor kinase gene (Oryza sativa) 49 M5/P2 344 + HSP protein (Zea mays) NM_001177009 8e-168 50 M11/P14 410 + 14-3-3-like protein EU965250 0 (Zea mays) Function Unknown Protein, Hypothetical and Unclassified Protein 51 M11/P10 364 + F-box domain containing NM_001157934 4e-134 protein (Zea mays) 52 M7/P10 298 + ORMDL family protein EU966520 2e-148 (Zea may) 53 M5/P8 440 + Putative Coatomer subunit XM_002515297 2e-120 beta (Ricinus communis) 54 M9/E3 203 + Sorghum bicolor hypothetical XM_002466510.1 1e-91 protein, mRNA 55 M9/E7 264 + Populus trichocarpa clone AC217570.1 0.93 POP028-M02, complete sequence 56 M9/E6 311 + Sorghum bicolor clone SB- AC196829.2 0.008 BBc0050H06, complete sequence 57 M9/E1 264 + Brassica rapa subsp, AC189271.2 0.27 pekinensis clone KBrB023L08, complete sequence 58 M9/P12 306 + Zea mays hypothetical protein NM_001148518.1 2e-98 LOC100274140, mRNA 59 M9/P11 248 + Oryza sativa Japonica Group AP004553.2 6e-47z genomic DNA, chromosome 8, BAC clone 60 M9/P8 211 + Zea mays contig09160, EZ073523.1 7e-52 mRNA sequence 61 M10/E8 346 + Zea mays clone BT017158.1 2e-143 EL01N0368A12, mRNA sequence 62 M10/P3 291 + Zea mays clone 275336 EU964030.1 5e-138 phosphopantothenate-cysteine ligase mRNA 63 M10/P5 338 + Zea mays full-length cDNA BT066928.1 6e-169 clone ZM_BF0108B05 mRNA, complete cds 64 M10/P7 339 + Zea mays LOC542221 NM_001111832.1 9e-167 (cl122_1), mRNA 65 M10/P7 193 + Zea mays full-length cDNA BT087913.1 3e-93 clone ZM_BFb0306G16 mRNA, complete cds 66 M10/P8 191 + Zea mays contig53594, EZ052473.1 2e-90 mRNA sequence 67 M10/P10 234 + Zea mays clone 274630 EU963967.1 2e-102 hypothetical protein mRNA, complete cds 68 M10/P12 273 + Zea mays clone contig644, BT016811.1 6e-130 mRNA sequence 69 M10/P11 255 + Zea mays LOL3 NM_001154268.1 7e-97 (LOC100281350), mRNA sequence 70 M10/P11 314 + Zea mays hypothetical protein NM_001149370.1 5e-157 LOC100275233 mRNA sequence 71 M10/P6 221 + Zea mays clone contig09160, EZ073523.1 7e-52 mRNA sequence 72 M11/E2 192 + Zea mays full-length cDNA BT040345.1 1e-92 clone ZM_BFc0084J06 mRNA, complete cds 73 M11/E3 176 + Zea mays full-length cDNA BT065938.1 5e-84 clone ZM_BFb0034G11 mRNA, complete cds 74 M11/E5 166 + Zea mays hypothetical protein NM_001143107.1 6e-70 LOC100216702 mRNA sequence 75 M11/E5 212 + Zea mays clone 391409 EU948954.1 2e-103 mRNA sequence 76 M11/P6 313 + Sorghum bicolor hypothetical XM_002468125.1 3e-140 protein, mRNA 77 M11/P7 213 + Zea mays hypothetical protein NM_001151604.1 5e-104 LOC100278276 mRNA sequence 78 M11/P10 234 + Zea mays hypothetical protein NM_001151604.1 2e-102 LOC100278276 mRNA sequence 79 M11/P10 450 + Zea mays clone 1393829 EU953254.1 0.0 mRNA sequence 80 M11/P12 217 + Sorghum bicolor hypothetical XM_002454857.1 3e-38 protein, mRNA 81 M11/P12 309 + Zea mays hypothetical protein NM_001152329.1 6e-156 LOC100279308 mRNA sequence 82 M11/P16 157 + Zea mays hypothetical protein NM_001148300.1 9e-74 LOC100279308 mRNA sequence 83 M11/P16 161 + Sorghum bicolor hypothetical XM_002466002.1 3e-74 protein, mRNA 84 M7/E6 168 + Zea mays hypothetical protein NM_001149663.1 5e-77 LOC100275614 mRNA sequence 85 M7/P2 307 + Zea mays full-length cDNA BT085895.1 1e-19 clone ZM_BFc0078D04 mRNA, complete cds 86 M7/P8 118 + Human DNA sequence from CT824642.1 0.35 clone XX-HCC1954_40J06, complete sequence 87 M7/P11 155 + Sorghum bicolor hypothetical XM_002468236.1 8e-05 protein, mRNA 88 M7/P12 165 + Zea mays clone contig56668, EZ055546.1 4e-78 mRNA sequence 89 M7/P16 244 + Zea mays clone contig48809, EZ113148.1 7e-110 mRNA sequence 90 M5/E2 138 + Zea mays hypothetical protein NM_001148439.1 2e-63 LOC100274060 mRNA sequence 91 M5/E5 181 + Zea mays full-length cDNA BT041729.2 3e-75 clone ZM_BFb0040G12 mRNA, complete cds 92 M1/E3 694 + Zea mays clone 379753 EU948536.1 0.0 mRNA sequence 93 M1/P12 363 + Zea mays full-length cDNA BT054470.1 0.0 clone ZM_BFc0076M12 mRNA, complete cds 94 M3/P2 188 + Zea mays full-length cDNA BT070006.1 9e-88 clone ZM_BFb0367E17 mRNA, complete cds 95 M3/P10 148 + Sorghum bicolor hypothetical XM_002451497.1 4e-59 protein, mRNA 96 M6/P9 108 + Zea mays hypothetical protein NM_001152213.1 9e-53 LOC100279189 mRNA sequence 97 M6/P11 164 + Zea mays hypothetical protein NM_001174666.1 8e-75 LOC100381884 mRNA sequence 98 M6/P11 230 + Zea mays full-length cDNA BT061295.1 1e-106 clone ZM_BFb0132C02 mRNA, complete cds 99 M10/E3 192 + Zea mays full-length cDNA BT040345.1 1e-92 clone ZM_BFc0084J06 mRNA, complete cds 100 M10/E5 243 + Zea mays clone contig15518, EZ079879.1 3e-43 mRNA sequence 101 M11/E3 283 + Zea mays hypothetical protein AY112622.1 1e-32 LOC100279189 mRNA sequence