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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

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