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Table 1 Drought responsive precursor miRNAs with their candidate target genes and their expression patterns

From: Transcriptome profiling of drought responsive noncoding RNAs and their target genes in rice

Gene ID

aRPKM

bLog2 Ratio

cMature miRNA/target sequence

dPARE sequence

PARE libraries

C

d1

d2

d3

1d/C

2d/C

3d/C

  

eA

fB

gC

hD

Inducible miRNAs/targets

 miR-399k

119,291

99,410

1,530,906

3,519,097

−0.26

3.68

4.88

3′-GCCCCGUUUAAAGGAAACCGU-5′

     

 Os05g0557700-01

25,889

23,611

8,802

9,104

−0.13

−1.56

−1.51

737-CUGGGCAAAUCUCCUUUGGCA-757

TCCTTTGGCAAAATACCTAT

0

0

1

1

 miR-415

234,165

109,765

160,988

1,529,388

−1.09

−0.54

2.71

3′-GACGAGACGAAGACAAGACAA-5′

     

  Os04g0550200-01

9,337

2,36

1,749

273

−1.98

−2.42

−5.10

789-UUACUCUGCUUCUGCUCUGUU-809

CTGCTCTGTTCTCTTTCTTC

0

0

0

1

  Os10g0500500-01

13,806

11,519

7,428

3,613

−0.26

−0.89

−1.93

976-UGCUCUGCAUUUCUUCUGUU-995

TTCTTCTGTTACTCATTCGA

0

2

0

0

 miR-168a

329,822

678,870

1,513,995

981,069

0.11

1.27

0.64

3′-AGGGCUAGACGUGGUUCGCU-5′

     

  Os02g0831600-01

5,715

5,283

1,584

687

−0.11

−1.85

−3.06

446-UCCCGAGCUGCGCCAAGCAA-465

CGCCAAGCAATAATGGAAGC

0

0

2

7

  Os03g0687000-02

11,281

10,412

3,293

1,896

−0.12

−1.78

−2.57

1807-UCAUGAUCUGCGCCAAGUGG-1826

CGCCAAGTGGTACAGGTTCA

0

0

0

1

  Os03g0687000-01

9,006

8,713

2,571

1,591

−0.05

−1.81

−2.50

1905-UCAUGAUCUGCGCCAAGUGG-1924

CGCCAAGTGGTACAGGTTCA

0

0

0

1

 miR-821c

27,730

47,537

376,336

364,452

0.78

3.76

3.72

3′-AGUUGAAAAAACAACUACUGAA-5′

     

  Os10g0412600-01

14,944

16,110

4,884

334

0.11

−1.61

−5.48

685-UGAACUUUUUUAUUGGUGAUUC-706

TTGGTGATTCCCTCTAATGT

0

0

0

1

 miR-171f-3p

8,297

82,972

107,863

207,429

3.32

3.70

4.64

3′-CUAUAACCGUGCCGAGUUAGU-5′

     

  Os09g0555600-01

2,031

1,926

380

60

−0.08

−2.42

−5.07

1488-GGUAUUGGCAUUGCUCAAUUA-1508

TGCTCAATTATGGGCTAAAG

0

0

0

1

 miR-816

150,534

95,795

301,069

136,849

−0.65

1.00

−0.14

3′-CAACAUCAUUUUAUACAGUG-5′

     

  Os01g0338100-00

1,722

1,227

701

534

−0.49

−1.30

−1.69

277-AUUGUUGUAGAAUAUGUCAC-296

AATATGTCACTGACCTGGTC

0

0

0

1

 miR-166c-5p

16,860

50,580

25,290

42,150

1.58

0.58

1.32

3′-GAGCCUGGUCUGUUGUAAGG-5′

     

  Os03g0823100-01

41,418

36,220

21,357

6,526

−0.19

−0.96

−2.67

784-CUUGGACCAGCCAAUAUUUU-803

CCAATATTTTCCTTCTATTT

0

0

1

1

 miR-166c-3p

16,860

50,580

25,290

42,150

1.58

0.58

1.32

3′-CCCUUACUUCGGACCAGGCU-5′

     

  Os12g0612700-01

667

751

573

121

0.17

−0.22

−2.47

874-UGGGAUGAAGCCUGGUCCGG-893

CCTGGTCCGGATTCCATTGG

0

0

53

73

 miR-167g

-

25,701

89,953

12,850

-

-

-

3′-GUCUAGUACGACCGUCGAAGU-5′

     

 miR-167b

6,465

 

19,394

12,929

- -

1.58

1.00

3′-UCUAGUACGACCGUCGAAGU-5′

     

  Os06g0129100-01

21,789

14,688

2,477

275

−0.57

−3.14

−6.31

1085-UGUUCAUGCCGGCAGCUUCA-1104

GGCAGCTTCAGGCTCCAGGT

0

0

0

10

  Os07g0481400-01

10,354

8,139

4,789

1,387

−0.35

−1.11

−2.90

2770-UAGAUCAUGCUGACAGCCUCA-2790

GACAGCCTCAAAACAATTGA

0

0

1

6

 miR-159b

11,210

67,260

67,260

-

2.58

2.58

-

3′-GUCUCGAGGGAAGUUAGGUUU-5′

     

  Os06g0605600-01

3,381

3,623

4,557

934

0.10

0.43

−1.86

403-UAGAGCUCCCUUCACUCCAAU-423

TCACTCCAATATCCCAACTA

0

3

0

16

  Os03g0683866-00

5,268

5,001

4,429

1,662

−0.07

−0.25

−1.66

1320-UAAAGCUGCCUUCAGUCCAGA-1340

TCAGTCCAGAATATGGGCTT

0

0

0

1

 miR-159f

5,605

11,210

28,025

-

1.00

2.32

- -

3′-AUCUCGAGGGAAGUUAGGUUC-5′

     

  Os06g0605600-01

3,381

3,623

4,557

934

0.10

0.43

−1.86

403-UAGAGCUCCCUUCACUCCAAU-423

TCACTCCAATATCCCAACTA

0

3

0

16

 miR-169f

-

6,198

43,389

198,351

- -

- -

- -

3′-AUCCGUUCAGUAGGAACCGAU-5′

     

  Os02g0776400-01

1,807

1,507

469,

60

−0.26

−1.94

−4.91

983-UAGGCAAUUCAUCCUUGGCUU-1003

TCCTTGGCTTAAGTTTCATG

6

5

6

66

  Os03g0411100-01

12,413

14,677

4,257

2,061

0.24

−1.54

−2.59

1242-UGGCAAUUCAUCCUUGGCUU-1261

TCCTTGGCTTATGAAGTATC

28

42

37

156

 miR-156i

-

-

23,416

23,416

- -

- -

- -

3′-CACGAGUGAGAGAAGACAGU-5′

     

  Os06g0663500-00

3,829

3,070

3,323

867

−0.32

−0.20

−2.14

749-GUGCUCUCUCUCUUCUGUCA-768

TCTTCTGTCAGCTAGTTCAA

0

5

1

35

  Os02g0174100-01

2,114

2,279

1,071

564

0.11

−0.98

−1.95

2221-GUGCUCUCUCUCUUCUGUCA-2240

TCTTCTGTCATCTAGTTCTT

0

2

0

11

  Os02g0139400-01

13,403

16,632

13,100

1,392

0.31

−0.03

−3.27

1869-AUGCUCUCUCUCUUCUGUCA-1888

TCTTCTGTCAATCGATTCAG

0

5

25

34

Repressible miRNAs / targets

 miR-530

1,433,087

241,496

231,823

84,299

−1.77

−2.63

−4.09

3′-AUCCACGUCCACGUUUACGU-5′

     

  Os04g0603200-01

28,344

24,091

55,324

69,156

−0.23

0.96

1.29

653-CAGAUGAAGGUGCAAAUGCA-672

TGCAAATGCAGGAGCTGTAA

0

0

0

1

  Os03g0296700-02

334

434

534

568

0.38

0.68

0.77

440-UGGAUGCUGGUGCAGAUGCA-459

TGCAGATGCACCGTTCTGAT

0

0

1

0

 miR-399e

169,670

107,160

17,860

8,930

−0.66

−3.25

−4.25

3′-CCCGUUUAGAGG-AAACCGU-5′

     

  Os04g0415000-01

5,599

8,625

25,400

18,132

0.62

2.18

1.70

491-GGGCAAUUCUCCGUUUGGCA-510

CCGTTTGGCAGAAGATCAAC

0

0

0

1

 miR-156f

1,501,297

1,370,996

657,172

436,226

−0.13

−1.19

−1.78

3′-CACGAGUGAGAGAAGACAGU-5′

     

 miR-156d

1,070,078

1,159,932

1,110,921

130,697

0.12

0.05

−3.03

3′-CACGAGUGAGAGAAGACAGU-5′

     

 miR-156g

136,247

364,020

657,790

19,159

0.09

−0.45

−1.91

3′-CACGAGUGAGAGAAGACAGU-5′

     

 miR-156j

351,247

364,020

657,790

19,159

0.05

0.91

−4.20

3′-CACGAGUGAGAGAAGACAGU-5′

     

  Os01g0922600-01

1,610

2,024

20,929

4,295

0.33

3.70

1.42

620-GUGCUCUCUCUCUUCUGUCA-639

TCTTCTGTCAGACAACCCCA

0

0

2

19

  Os09g0507100-00

42

75

941

950

0.83

4.47

4.49

1034-GUGCUCUCUCUCUUCUGUCA-1053

TCTTCTGTCATCCCCGGCCA

0

0

2

1

 miR-815a

25,391

-

12,696

12,696

-

−1.00

−1.00

3′-GGUUAGAGGAGUUAGGGGAA-5′

     

 miR-815c

511,525

531,986

225,071

71,613

0.06

−1.18

−2.84

3′-GGUUAGAGGAGUUAGGGGAA-5′

     

  Os08g0465800-01

9,970

9,526

61,668

74,744

−0.07

2.63

2.91

1896-CCAAUCUCCUUCCUCCUCUU-1915

TCCTCCTCTTTTTAATCTCT

0

0

0

1

 miR-159a

395,153

360,286

96,851

65,859

−0.13

−2.03

−2.58

3′-UCUCGAGGGAAGUUAGGUUU-5′

     

  Os03g0331700-02

7,076

3,394

22,641

50,780

−1.06

1.68

2.84

1513-UGAGUUCCCUUCAUUCCAAA-1532

TCATTCCAAAAGCTTAATTG

0

0

0

1

 miR-393b

151,675

175,623

127,726

31,932

0.21

−0.25

−2.25

3′-UAGUUACGCUAGGGAAACCU-5′

     

  Os05g0150500-00

5,537

4,773

20,300

36,796

−0.21

1.87

2.27

1556-GACAAUGCGAUCCCUUUGGA-1575

TCCCTTTGGATGTCGTCGTG

16

18

88

655

 miR-528

227,512

287,384

23,949

-

0.34

−3.25

-

3′-GAGGAGACGUACGGGGAAGGU-5′

     

  Os07g0570550-00

290

522

1,334

1,566

0.85

2.20

2.43

180-CUCCUCUGC-UGCCCCUUCCA-199

GCCCCTTCCATGGCGCCCGC

0

0

205

0

 miR-166d

92,729

33,720

84,299

16,860

−1.46

−0.14

−2.46

3′-CCCUUACUUCGGACCAGGCU-5′

     

  Os03g0640800-01

1,189

1,224

4,376

8,977

0.04

1.88

2.92

956-UGGGAUGAAGCCUGGUCCGG-975

CCTGGTCCGGATTCCATTGG

0

0

53

73

  Os10g0480200-02

1,638

1,282

2,956

3,158

−0.35

0.85

0.95

922-UGGGAUGAAGCCUGGUCCGG-941

CCTGGTCCGGATTCGTTTGG

0

3

12

179

  1. aRPKM, Reads Per Kilobase of transcript per Million mapped reads; blog2 ratio, log2(drought treatment / control); cbases underlined indicated potential cleavage sites; dPARE sequence matching to cleavage products, starting between base 10 and 11 from the 5′ end of the predicted miRNA pairing; eA (SC938), PARE library of rice wild type seedling degradome, GSM455938 (GEO Accession number); fB (INF939), PARE library of rice wildtype inflorescence degradome, GSM455939; gC (INF9311a), PARE library of rice inflorescence (93-11) wildtype degradome, GSM476257; hD (NPBs), PARE library of rice 3-week-old seedlings wildtype degradome, GSM434596 [29]