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Table 5 Potential miRNA target genes regulated during barley seed development

From: miRNA regulation in the early development of barley seed

EST

smRNAs with perfect offset

Degradome

ID

Closest homolog

Sp.

E-score

Cat.

Family

nb

RPM-A

RPM-B

RPM-C

RPM-A

RPM-B

RPM-C

 

Transcription factors

           

U21_18652

APETALA2-like protein

tae

0.E + 00

I

miR172

3

14.78

58.87

58.84

1.64

0.63

0.36

U21_19162

CBF (NF-YA2 homolog)

osa

8.E-80

I

miR169

2

4.10

1.49

0.78

1.02

0.30

1.60

U21_13817

CBF (NF-YA5 homolog)

osa

4.E-29

I

miR169

4

7.66

5.54

5.68

3.84

1.16

0.71

U21_8533

CBF (NF-YA9 homolog)

tae

5.E-40

II

miR169

2

4.10

1.49

0.78

7.38

2.41

3.48

U21_9757

NAC

osa

1.E-126

I

miR164

20

324.78

560.70

314.03

0.72

0.83

0.82

U21_3667

GAMyb protein

hvu

0.E + 00

I

miR159

5

6.44

4.46

3.35

6.07

6.84

2.28

U21_18637

SPL16

osa

6.E-83

I

miR156

77

4418.37

8965.97

7953.70

1.48

0.03

0.21

U21_19856

SPL18

osa

2.E-52

I

miR156

77

4418.37

8965.97

7953.70

2.00

1.06

0.14

U21_13717

DOF1

tae

1.E-154

II

pot-miRNA

3

25.59

29.03

35.61

0.39

0.00

0.00

 

Chloroplast functions

           

U21_4432

RNP-A, chloroplastic

osa

1.E-112

II

pot-miRNA

1

1.37

1.08

0.77

1.18

0.17

0.00

U21_495

Carbonic anhydrase, chloro.

osa

1.E-115

III

pot-miRNA

1

1.64

1.08

1.16

0.26

0.40

1.56

U21_40749

Chlorophyll a-b binding prot.

tae

3.E-40

II

pot-miRNA

3

3.28

1.22

1.55

0.00

0.40

0.00

U21_1307

Ferredoxin, chloroplastic

tae

1.E-54

III

pot-miRNA

2

2.33

1.08

1.03

91.01

112.87

75.62

U21_6135

PGlcT

ath

9.E-40

I

pot-miRNA

1

0.41

0.68

0.10

0.53

8.32

8.46

 

Phytohormone signalling

           

U21_11104

VP1/ABI3

osa

4E-90

III

miR516

2

2.05

6.08

6.19

0.00

0.00

0.78

U21_48909

ABI8

tae

1E-71

III

pot-miRNA

5

15.06

15.53

22.71

0.00

0.20

0.00

U21_9888

GA 3-oxidase 1

hvu

0.E + 00

I

pot-miRNA

7

145.90

168.22

129.92

0.00

0.23

0.14

U21_9040

GID1

hvu

1E-133

II

pot-miRNA

8

3.83

37.94

114.57

0.49

0.07

0.00

U21_7409

TIR1

osa

9.E-231

III

miR393

1

0.14

0.81

0.90

3.64

4.26

2.52

U21_12845

ARF1 (AtARF6-like)

osa

1.E-119

I

miR167

37

1424.78

2234.51

2583.93

3.91

1.82

2.63

U21_8147

ARF2 (AtARF6-like)

osa

8.E-176

I

miR167

37

1424.78

2234.51

2583.93

3.91

1.82

2.63

U21_19718

ARF3 (AtARF6-like)

osa

1.E-116

I

miR167

37

1424.78

2234.51

2583.93

3.91

1.82

2.63

U21_1664

ARF4 (AtARF2-like)

osa

5.E-302

II

tasiR-ARFs

8

299.60

129.61

36.00

0.82

0.13

0.00

U21_19004

ARF5 (AtARF3-like)

osa

1E-56

II

tasiR-ARFs

8

299.60

129.61

36.00

0.26

0.20

0.00

U21_24760

ARF6 (AtARF3-like)

tae

1E-119

II

tasiR-ARFs

8

299.60

129.61

36.00

1.12

0.50

0.00

U21_26602

ARF7 (AtARF3-like)

tae

1E-124

III

tasiR-ARFs

3

49.68

14.18

4.39

3.25

0.43

0.64

U21_22467

ACC oxidase

osa

1E-24

II

pot-miRNA

1

2.05

2.16

0.90

0.00

0.17

0.00

 

Defence response

           

U21_18842

OsMLA10-like

osa

1E-47

I

miR5071

23

651.63

537.46

257.39

0.98

0.40

0.00

U21_23305

OsMLA1-like

osa

1E-72

III

pot-miRNA

4

35.31

28.76

22.19

3.97

0.86

1.17

  1. List of 29 of the 96 potential miRNA targets identified in this study. The left part of the table shows ESTs predicted to be regulated through miRNA-mediated cleavage, their category of confidence (cat.), and their associated function according to homology with the closest annotated gene from one of the following species (sp.): Hordeum vulgare (hvu), Triticum aestivum (tae), Oriza sativa (osa) or Arabidopsis thaliana (ath). Genes are arranged by functional group indicated by the headings in the closest homolog column. The middle part of the table shows the number (nb) of smRNAs matching the target with a perfect offset, the sum of their reads (in RPM) in each library and to which family they belong (pot-miRNA indicates when no match was found to a known or new miRNA identified in this study). The right part shows the number of degradome sequences (in RPM) resulting from the cleavage. The grey boxes indicate when the number of reads was significantly higher than the threshold.
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BMC Plant Biology

ISSN: 1471-2229

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