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Table 6 Information of DEGs overlapped in IME vs. ME at three stages that are possibly involved in embryogenic callus formation and DEGs for qRT-PCR

From: De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)

Category ID Annotation qRT-PCR Overlapped between stages in IMEs not in MEs Bio- process
Bio-processes-involved genes (BPGs) comp120922_c0 Indole-3-glycerol phosphate lyase, chloroplastic; indole synthase    response to stimulus;in multi-organism process
comp129240_c0 Cellulose synthase   
comp129268_c1 Mobile element transfer protein; POT family   
comp128278_c0 Cellulose synthase    reproductive process
comp127468_c0 S-locus glycoprotein family yes   in multi-organism process; reproductive process
comp115979_c0 beta-expansin TaEXPB2 [Triticum aestivum]    in multi-organism process; reproductive process; reproduction
comp122548_c0 Expansin-B6 [Triticum urartu]   
comp124996_c0 Expansin EXPB8 [Triticum aestivum]   
comp126585_c2 Expansin-B18   
comp131969_c0 Expansin EXPB9 [Triticum aestivum]   
comp123173_c0 Aldose reductase [Triticum urartu]    response to stimulus; reproductive process
comp133735_c0 Multicopper oxidase;; Laccase-19   yes
comp139514_c1 RNA recognition motif; Glycine-rich RNA-binding protein   
comp117215_c0 Salt tolerant protein [Triticum aestivum]    response to stimulus
comp118386_c0 hypothetical protein F775_08244 [Aegilops tauschii]   
comp122412_c0 Pathogenesis-related protein / dehydrase and lipid transport   
comp123242_c0 predicted protein [Hordeum vulgare subsp. vulgare]   
comp124683_c0 NmrA-like family; NADH(P)-binding; Isoflavone reductase-like protein   
comp125897_c0 GDSL/SGNH-like Acyl-Esterase family; Protein ESKIMO 1   
comp127496_c0 Glutaredoxin; Monothiol glutaredoxin-S5 (Rice)   
comp129379_c0 AnnexinD4 [Aegilops tauschii]   
comp129891_c0 Pirin-like protein   
comp130209_c0 Cytochrome P450   
comp131119_c0 DREPP plasma membrane polypeptide; Salt stress root protein Yes  
comp131357_c0 short chain dehydrogenase;11-beta-hydroxysteroid dehydrogenase 1B   
comp132259_c0 Glycosyl transferases group 1; Sucrose synthase 1   
  comp132259_c1 Sucrose synthase 2 [Triticum urartu]   
comp132409_c0 Glycosyl hydrolases family 17   
comp132805_c0 Glycogenin-2 [Triticum urartu]   
comp134609_c0 ATPase family associated with various cellular activities   
comp135852_c0 Multicopper oxidase;; Putative laccase-5 (Rice)   
comp137996_c3 Fructan 6-exohydrolase [Triticum aestivum]   
comp138064_c0 Ethylene insensitive 3   
comp138118_c0 Senescence-associated protein   
comp140305_c0 Universal stress protein family   
comp140523_c1 Glycosyl hydrolases family 18; Xylanase inhibitor protein 1   
comp141536_c0 Aconitase family (aconitate hydratase) Yes Yes
comp141781_c0 hypothetical protein TRIUR3_11299 [Triticum urartu]   
comp142326_c1 RRM in Demeter;Transcriptional activator DEMETER Yes  
Unknown genes that overlapped between stages in IMEs not in MEs comp120934_c0 Xyloglucan endotransglucosylase/hydrolase (XTH) protein 22 Yes Yes  
comp126349_c0 Xyloglucanendo-transglycosylase (XET) C-terminus Yes Yes  
comp128901_c0 Root cap Yes Yes  
comp128978_c0 Cortical cell-delineating protein Yes Yes  
comp134128_c0 U-box domain;E3 ubiquitin-protein ligase Yes Yes  
comp136525_c0 glycerol-3-phosphate acyltransferase 2 Yes Yes  
comp142930_c0 Reverse transcriptase Integrase core domain;gag-polypeptide of LTR copia-type Yes Yes  
Overlapped TFs comp127465_c1 YABBY Yes   
comp131637_c0 bHLH Yes   
comp134166_c0 bZIP Yes   
comp118204_c0 MIKC    
comp131990_c0 LSD    
comp140577_c0 G2-like    
comp125594_c0 ERF   Yes  
comp126788_c0 ERF Yes Yes  
comp128506_c0 ERF Yes   
comp129826_c0 NAC    
Overlapped SSEGs comp111117_c0 Disease resistance protein    
comp123801_c0 Disease resistance protein    
comp136600_c0 Disease resistance protein    
comp78404_c0 Disease resistance protein    
comp131631_c0 Disease resistance protein    
comp132305_c0 zinc finger    
comp132823_c2 zinc finger Yes   
comp136499_c1 zinc finger    
comp136627_c0 zinc finger    
comp124435_c0 LTP    
comp141004_c1 LTP    
comp146809_c0 LTP Yes   
comp126873_c0 LEA    
comp113034_c0 LEA    
comp113890_c0 LEA    
comp129476_c0 LEA Yes   
comp131074_c0 LEA    
comp131947_c0 LEA    
comp136871_c0 LEA    
comp117547_c0 Calcium-dependent    
comp120829_c0 Calcium-dependent    
comp121468_c3 Calcium-dependent    
comp122478_c2 GST    
comp134985_c3 GST    
comp162414_c0 Auxin-induced protein    
comp125890_c1 Peroxidase    
comp126327_c4 Peroxidase    
comp128155_c1 Peroxidase    
comp129605_c0 Peroxidase    
comp129803_c0 Peroxidase   Yes  
comp130824_c1 Peroxidase Yes   
comp130824_c2 Peroxidase    
comp138541_c1 Peroxidase    
comp140208_c0 HSP    
comp124012_c0 Germin-like protein Yes   
DEGs not overlapped that for qRT-PCR comp116720_c1 Heat shock 70 kDa protein Yes   
comp125045_c0 Oleosin 16 kDa Yes   
comp125097_c0 Zinc finger CCCH domain-containing protein Yes   
comp125797_c0 Auxin-induced protein 1 Yes   
comp127206_c0 WAT1-related protein Yes   
comp128173_c1 GDSL esterase/lipase At2g40250 (Precursor) Yes   
comp128869_c0 B3 domain-containing protein Yes   
comp131743_c0 Yes   
comp133896_c0 Desiccation-related protein Yes   
comp134203_c0 Cytochrome P450 71C3 Yes   
comp137615_c0 Antimicrobial peptide 2d (Precursor) Yes