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Table 3 Conserved maize miRNA targets identified by degradome sequencing in this study

From: Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing

miRNAa

Target gene

Location of the target site

Repeat normalized read abundance (category)b

Target gene annotationc

Other degradome evidence

5′-RACE or genetic experiment

   

I

II

III

IV

   

miR156

GRMZM2G156621

CDS

2.50 (3)

3.50 (2)

39.00 (2)

 

SBP-box transcription factor#

[26]

N

miR156

GRMZM2G067624

3′-UTR

18.00 (2)

46.50 (2)

51.50 (2)

97.00 (2)

SBP-box transcription factor#

[26, 28]

N

miR156

GRMZM2G163813

CDS/3′-UTR

3.33 (2)

17.67 (2)

  

SBP-box transcription factor#

[26, 28]

N

miR156

GRMZM2G113779

3′-UTR

18.00 (2)

4.00 (2)

86.00 (2)

352.00 (0)

SBP-box transcription factor

[28]

N

miR156

GRMZM2G126827

CDS

2.50 (3)

3.50 (2)

39.00 (2)

 

SBP-box transcription factor#

[26]

N

miR156

GRMZM2G318882

5′-UTR

0.03 (1)

   

SBP-box transcriptionfactor

N

N

miR156

GRMZM2G136158

CDS

0.03 (1)

   

SBP-box transcription factor

N

N

miR156

GRMZM2G460544

CDS

  

2.00 (3)

 

SBP-box transcription factor#

[26, 28]

N

miR156

GRMZM5G878561

CDS

  

6.50 (3)

7.50 (0)

SBP-box transcription factor

[26]

N

miR156

GRMZM2G307588

CDS

  

2.00 (3)

 

SBP-box transcription factor#

[26, 28]

N

miR156

GRMZM2G371033

CDS

  

6.50 (1)

7.50 (0)

SBP-box transcription factor

[26]

N

miR156

GRMZM2G160917

CDS/3′-UTR

  

2.00 (3)

 

SBP-box transcription factor#

[26, 28]

N

miR156

GRMZM2G126018

CDS

  

2.00 (2)

 

SBP-box transcription factor#

[28]

N

miR159

GRMZM2G139688

CDS

76.00 (2)

169.00 (0)

86.00 (2)

3.00 (2)

MYB domain transcription factor#

[26, 28]

N

miR159

GRMZM2G038195

CDS

2.5 (2)

 

5.50 (2)

 

Metallophosphoesterase#

N

N

miR159

GRMZM2G093789

CDS

 

0.67 (3)

  

MYB domain transcription factor#

[28]

N

miR159

GRMZM2G167088

CDS

 

2.00 (2)

 

0.33 (4)

MYB domain transcription factor#

N

N

miR159

GRMZM2G416652

CDS

 

2.00 (2)

 

0.33 (4)

Homeodomain-like#

N

N

miR159

GRMZM2G028054

CDS

 

24.00 (2)

  

MYB domain transcription factor#

[26, 28]

N

miR159

GRMZM2G075064

CDS

 

0.67 (2)

  

MYB domain transcription factor#

N

N

miR159

GRMZM2G423833

CDS

 

0.67 (3)

  

MYB domain transcription factor#

[28]

N

miR159

GRMZM2G089361

CDS

   

1.33 (3)

TCP Transcription factor#

[26]

N

miR159

GRMZM2G387828

CDS

   

4.00 (1)

unknown

N

N

miR160

GRMZM2G005284

CDS

2.00 (1)

2.00 (2)

  

Auxin response factor#

N

N

miR160

AC207656.3_FGT002

CDS

6.50 (0)

18.00 (2)

  

Auxin response factor#

[26]

N

miR160

GRMZM2G159399

CDS

8.5 (2)

23.00 (2)

 

1.00 (4)

Auxin response factor#

[26, 28]

N

miR160

GRMZM5G808366

CDS

10.00 (0)

3.00 (2)

32.00 (1)

 

Auxin response factor

N

N

miR160

GRMZM2G153233

CDS

24.00 (0)

68.00 (0)

37.00 (0)

1.00 (4)

Auxin response factor#

[26, 28]

N

miR160

GRMZM2G390641

CDS

 

2.33 (0)

5.00 (2)

 

Auxin response factor#

[26]

N

miR160

GRMZM2G081406

CDS

 

2.33 (3)

5.00 (3)

 

Auxin response factor#

[26, 28]

N

miR162

GRMZM2G040762

CDS

   

1.00 (4)

DICER-LIKE1

N

N

miR164

GRMZM2G457630

5′-UTR

 

2.50 (0)

  

No apical meristem (NAM) protein

N

N

miR164

GRMZM2G370846

3′-UTR

  

2.33 (1)

 

No apical meristem (NAM) protein

N

N

miR164

GRMZM2G370850

3′-UTR

  

2.33 (1)

 

No apical meristem (NAM) protein

N

N

miR164

GRMZM2G393433

CDS

  

2.50 (3)

 

Helix-loop-helix DNA-binding#

[28]

N

miR164

GRMZM2G163975

CDS

-

-

2.50 (1)

-

Helix-loop-helix DNA-binding#

N

N

miR166

GRMZM2G109987

CDS

0.6 (3)

2.40 (2)

15.80 (2)

27.80 (2)

bZIP transcription factor (rld1)#

[28]

N

miR166

GRMZM2G042250

CDS

 

2.00 (2)

15.75 (2)

17.00 (2)

bZIP transcription factor (rld2)#

[28]

N

miR166

GRMZM2G469551

CDS

  

25.50 (2)

28.00 (0)

bZIP transcription factor#

[26]

N

miR166

GRMZM2G123644

CDS

   

0.60 (2)

unknown

[26]

N

miR166

GRMZM2G336718

CDS

   

0.60 (2)

unknown

[26]

N

miR166

GRMZM2G055957

3′-UTR

   

9.50 (0)

unknown

[26, 28]

N

miR166

GRMZM2G178102

CDS

   

0.60 (3)

bZIP transcription factor#

[26, 28]

N

miR166

GRMZM2G003509

CDS

   

0.60 (2)

bZIP transcription factor#

[26, 28]

N

miR167

GRMZM2G028980

CDS

 

77.00 (0)

  

Auxin response factor#

[26]

N

miR167

GRMZM2G089640

CDS

 

74.00 (0)

 

40.50 (0)

Auxin response factor#

[26, 30]

N

miR167

GRMZM2G078274

CDS

  

6.60 (2)

147.80 (0)

Auxin response factor#

[26, 30]

N

miR167

GRMZM2G475882

CDS

  

6.60 (2)

 

Auxin response factor#

[26, 28]

N

miR169

GRMZM5G829103

3′-UTR

32.00 (2)

1923.40 (0)

24.60 (2)

3.40 (2)

CCAAT-binding transcription factor

[26, 28]

N

miR169

GRMZM2G165488

3′-UTR

7.25 (2)

2804.25 (0)

8.25 (2)

1.25 (2)

CCAAT-binding transcription factor#

[26, 28, 30]

[30]

miR169

GRMZM2G037630

3′-UTR

12.00 (2)

13.00 (2)

 

2.00 (2)

CCAAT-binding transcription factor

[26, 28]

N

miR169

GRMZM2G000686

3′-UTR

3.60 (2)

21.80 (0)

2.70 (2)

0.10 (4)

CCAAT-binding transcription factor#

[26, 28]

N

miR169

GRMZM5G853836

3′-UTR

21.00 (2)

50.00 (2)

27.50 (2)

 

unknown

[26, 28]

N

miR169

GRMZM5G857944

3′-UTR

129.67 (0)

139.00 (0)

67.33 (0)

16.00 (0)

CCAAT-binding transcription factor

[26, 28]

N

miR169

GRMZM2G038303

3′-UTR

17.00 (2)

4.00 (2)

23.00 (0)

12.00 (0)

CCAAT-binding transcription factor#

[28, 30]

N

miR169

GRMZM5G849099

3′-UTR

4.00 (2)

   

unknown

N

N

miR169

GRMZM2G409430

CDS

3.50 (0)

   

unknown

N

N

miR169

GRMZM2G091964

3′-UTR

138.67 (2)

257.33 (0)

27.00 (2)

99.33 (0)

CCAAT-binding transcription factor#

[26, 28, 30]

[30]

miR169

GRMZM2G078124

CDS/3′-UTR

 

1.00 (2)

  

Molluscan rhodopsin C-terminal tail#

[28, 30]

[30]

miR171

GRMZM2G418899

CDS

1.80 (2)

80.40 (0)

4.60 (2)

0.60 (2)

GRAS transcription factor#

[26, 29]

N

miR171

GRMZM2G037792

CDS

1.80 (3)

80.40 (0)

4.60 (3)

0.60 (3)

GRAS transcription factor#

[26, 28, 29]

[25]

miR171

GRMZM5G825321

CDS

1.80 (2)

80.40 (0)

4.60 (3)

0.60 (2)

GRAS transcription factor

[26, 28]

N

miR171

GRMZM2G110579

CDS

0.33 (4)

35.67 (2)

2.67 (3)

1.67 (2)

GRAS transcription factor

[26, 28]

N

miR171

GRMZM2G098800

CDS

1.80 (2)

29.67 (0)

2.67 (3)

1.67 (2)

GRAS transcription factor#

[26, 28, 29]

N

miR172

GRMZM2G176175

CDS

1.40 (3)

9.20 (0)

6.40 (0)

1.80 (0)

AP2 transcription factor (sid1)#*

[28, 30]

[32, 33]

miR172

GRMZM5G862109

CDS/3′-UTR

1.40 (3)

80.20 (2)

8.73 (2)

1.80 (2)

AP2 transcription factor (ids1)#*

[28]

[32, 33]

miR172

GRMZM2G138676

CDS

0.20 (4)

   

AP2 transcription factor

N

N

miR172

GRMZM2G174784

CDS/3′-UTR

1.00 (3)

3.00 (2)

15.00 (2)

 

AP2 transcription factor#

[28]

N

miR172

GRMZM2G076602

CDS

 

10.00 (0)

13.00 (0)

 

AP2 transcription factor#

[30]

N

miR172

GRMZM5G879527

3′-UTR

   

2.50 (0)

AP2 transcription factor

N

N

miR172

GRMZM2G160730

3′-UTR

   

0.50 (4)

Glossy15#*

[28, 30]

[36]

miR319

GRMZM2G412073

CDS

4.00 (3)

   

unknown#

N

N

miR319

GRMZM2G028054

CDS

5.00 (2)

2.00 (2)

 

7.33 (2)

MYB domain transcription factor#

[26, 28]

N

miR319

GRMZM2G180568

CDS

 

3.00 (0)

17.00 (1)

 

unknown

N

N

miR319

GRMZM2G020805

CDS

 

1.00 (4)

  

unknown

[26, 28]

N

miR319

GRMZM2G089361

CDS

 

5.00 (2)

8.33 (0)

88.00 (0)

TCP Transcription factor#

[26, 28, 30]

N

miR319

GRMZM2G115516

CDS

 

5.00 (2)

8.33 (2)

88.00 (0)

TCP Transcription factor#

[26, 28]

N

miR319

GRMZM2G109843

CDS

   

53.33 (0)

MYB domain transcription factor

[30]

N

miR319

GRMZM2G056612

CDS

   

70.33 (0)

TCP Transcription factor

N

N

miR319

GRMZM2G015037

CDS

   

0.33 (4)

MYB domain transcription factor

[26]

N

miR319

AC205574.3_FG006

CDS

   

0.33 (4)

TCP Transcription factor

[28]

N

miR390

GRMZM2G124744

3′-UTR

 

35.33 (0)

  

Inorganic pyrophosphatase

[28]

N

miR390

GRMZM2G155490

3′-UTR

  

56.00 (0)

 

unknown#

N

N

miR390

GRMZM5G806469

3′-UTR

  

13.00 (2)

 

unknown

[28]

N

miR390

GRMZM2G304745

CDS

  

16.00 (1)

 

Leucine-rich repeat#

N

N

miR393

GRMZM2G135978

CDS

 

7.00 (2)

10.00 (2)

 

Transport inhibitor response 1-like

[26, 28]

N

miR394

GRMZM2G119650

CDS

3.00 (3)

20.00 (2)

 

3.00 (2)

Cyclin-like F-box#

[26]

[28]

miR394

GRMZM2G064954

CDS

 

18.00 (2)

14.00 (2)

13.00 (2)

Cyclin-like F-box#

[26, 30]

N

miR395

GRMZM2G149952

CDS

 

1.00 (4)

  

ATP-sulfurylase#

[26, 28, 30]

N

miR396

GRMZM2G018414

CDS

2.50 (2)

  

447.50 (0)

Glutamine-Leucine-Glutamine#

N

N

miR396

GRMZM2G099862

CDS

5.00 (2)

 

2.25 (3)

30.75 (0)

Glutamine-Leucine-Glutamine#

[30]

N

miR396

GRMZM2G098594

CDS

1.00 (2)

  

0.33 (3)

Glutamine-Leucine-Glutamine#

N

N

miR396

GRMZM2G119359

CDS

1.00 (3)

  

0.33 (3)

Glutamine-Leucine-Glutamine

N

N

miR396

GRMZM2G478709

CDS

8.00 (2)

0.50 (4)

4.00 (3)

 

SKI-interacting protein SKIP#

N

N

miR396

GRMZM2G124566

CDS

 

0.33 (4)

  

Growth-regulating factor#

N

N

miR396

GRMZM2G045977

CDS

 

0.33 (4)

  

Growth-regulating factor#

N

N

miR396

GRMZM2G041223

CDS

 

0.33 (4)

  

Putative growth-regulating factor 6#

[30]

N

miR396

GRMZM2G129147

CDS

 

0.33 (4)

  

Growth-regulating factor (GDF5)#

[30]

N

miR396

GRMZM2G178261

CDS

 

0.50 (3)

  

Growth-regulating factor 1 (GDF1)#

[28, 30]

N

miR396

GRMZM2G443903

CDS

 

0.50 (3)

  

K Homology#

[30]

N

miR396

GRMZM2G033612

CDS

  

16.00 (2)

637.00 (0)

Glutamine-Leucine-Glutamine

N

N

miR397

GRMZM2G094699

CDS

  

5.00 (2)

 

unknown

N

N

miR398

AC234183.1_FGT002

CDS

   

17.00 (0)

unknown

N

N

miR399

GRMZM2G153087

CDS

1.00 (4)

   

PHD finger protein

N

N

miR399

GRMZM2G082384

CDS

  

2.25 (3)

 

Mrp, conserved site;ATPase-like

N

N

miR529

GRMZM2G318882

5′-UTR

0.03 (1)

   

SBP-box transcription factor

N

N

miR529

GRMZM2G136158

CDS

0.03 (1)

0.04 (1)

0.01 (1)

0.001 (1)

SBP-box transcription factor

N

N

miR529

GRMZM2G031501

5′-UTR

0.20 (4)

   

unknown

[26, 30]

N

miR529

GRMZM5G878561

CDS

 

1.50 (3)

 

1.50 (2)

SBP-box transcription factor

[26]

N

miR529

GRMZM2G031983

5′-UTR

 

0.04 (1)

0.01 (1)

 

SBP-box transcription factor

N

N

miR529

GRMZM2G371033

CDS

 

1.50 (3)

 

1.50 (2)

SBP-box transcription factor

[26]

N

miR529

GRMZM2G163813

CDS/3′-UTR

 

0.33 (4)

  

SBP-box transcription factor#

[26]

N

miR529

GRMZM2G149022

CDS

  

0.01 (1)

 

unknown

N

N

miR529

GRMZM2G084947

5′-UTR

  

0.01 (1)

 

unknown

N

N

miR529

GRMZM2G169121

3′-UTR

  

0.01 (1)

 

unknown

N

N

miR529

GRMZM2G062052

5′-UTR

  

0.01 (1)

 

ZCN19 protein

N

N

miR529

GRMZM2G148074

5′-UTR

  

0.01 (1)

 

Transcription factor, K-box

N

N

miR529

GRMZM2G031870

5′-UTR

  

0.01 (1)

 

SBP-box transcription factor

N

N

miR529

GRMZM2G096234

3′-UTR

  

0.01 (1)

 

Non-specific lipid-transfer protein

N

N

miR529

GRMZM2G141955

5′-UTR

  

0.01 (1)

 

SBP-box transcription factor

N

N

miR529

AC233899.1_FGT004

5′-UTR

  

0.01 (1)

 

homeodomain-leucine zipper transcription factor

N

N

miR529

GRMZM2G165355

CDS

  

0.01 (1)

 

zinc finger protein 7

N

N

miR529

GRMZM2G131280

3′-UTR

   

0.001 (1)

SBP-box transcription factor

N

N

TAS3

GRMZM2G056120

CDS

0.50 (3)

1.25 (3)

11.25 (2)

5.00 (2)

DNA binding

N

N

TAS3

GRMZM5G874163

3′-UTR

0.50 (3)

1.58 (2)

11.25 (2)

5.00 (2)

DNA binding

N

N

TAS3

GRMZM2G437460

CDS

 

11.00 (2)

8.50 (2)

0.50 (4)

Auxin response factor

N

N

TAS3

GRMZM2G030710

CDS

  

1287.00 (0)

1.00 (4)

DNA binding

N

N

  1. aMiRNA data from miRBase 19.0. bCalculation based on the method in Addo-Quaye et al.[47],. cGene annotations fromB73 RefGen_v2 (release 5b. 60 in February 2011). *validated in Zhai et al; Zhao et al. [28, 30], #Predicted by Zhang et al. [17]. Abbreviation: tpm, transcripts per million; CDS, coding sequence; UTR, untranslated region; siRNA, small interfering RNA.