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Table 1 Sequence diversity, Tajima's D and HKA test results

From: Sequence variation and selection of small RNAs in domesticated rice

Small RNA

O. sativa

O. rufipogon

Target

Candidate Status

 

Indicasubgroup

Japonicasubgroup

     
 

N

D

HKA- P

N

D

HKA- P

N

D

HKA- P

  

MIR164e

21

-1.90*

0.101

21

1.18

0.285

10

-1.04

0.447

NAC

Putative

MIR390

25

-1.21

0.106

20

-0.09

0.014

11

-1.23

0.257

TAS3

Putative

MIR395a-b

27

-1.56

NA

21

-1.94*

NA

11

-1.49

NA

APS/AST

Putative

TAS3a2

28

-1.86*

0.029

24

-0.85

0.158

10

-1.35

0.503

ARF

Putative

AK120922

25

0.26

0.003

18

-1.77

0.055

11

-2.05*

0.250

Unknown

ND

MIR164a

25

1.54

0.129

22

-1.31

0.215

11

-0.84

0.433

Unknown

ND

MIR164c

23

-0.51

0.167

23

-0.63

0.297

8

0.47

0.294

NAC

ND

MIR164d

25

-0.48

0.147

21

-1.29

0.260

12

-1.54

0.464

NAC

ND

MIR166f

29

-1.02

0.161

23

-0.81

0.342

10

-0.20

0.419

HD-ZIP

ND

MIR395i-k

25

0.98

0.106

18

-0.52

0.248

9

-0.60

0.245

APS/AST

ND

MIR396f

21

-0.54

0.089

20

0.76

0.288

10

-0.68

0.470

GRL

ND

MIR399a

27

0.35

0.099

24

-0.68

0.278

14

1.21

0.403

PT

ND

MIR399d

23

-2.37*

0.107

22

-0.87

0.002

12

-2.04*

0.255

PT

ND

MIR399i

22

-0.95

0.102

22

-1.08

0.196

11

-1.03

0.442

PT

ND

MIR440

25

0.04

0.097

20

-0.57

0.137

14

-1.58

0.339

Unknown

ND

MIR443

29

0.15

0.148

21

-1.57

0.274

9

-0.39

0.301

Unknown

ND

MIR1318

22

0.34

0.078

21

-0.65

0.227

12

-0.45

0.439

Unknown

ND

MIR1432

26

0.20

0.081

22

-1.30

0.176

10

0.57

0.382

EF

ND

MIR1862d

21

0.71

0.113

20

-0.14

0.270

9

-1.88*

0.394

NAC

ND

MIR1867

24

-1.21

0.094

24

-1.11

0.280

10

-0.94

0.493

Unknown

ND

  1. N, number of accessions sequenced D:Tajima' D; HKA-P: P value of multi-locus HKA test; NA: not available; NAC, NAC domain transcription factor; TAS3, ta-siRNA gene using miR390 as the processing guide; APS, ATP-sulfurylase; AST, sulfate transcription factor; ARF, Auxin response factor; HD-ZIP, homeodomain leucine-zipper transcription factor; GRL, GRL transcription factor; PT: Phosphate transporter; EF: EF hand proteins; ND, not determined. The significant (P < 0.05) test results were labeled bold and * (for Tajima's D results). For details, also see Additional file 3.