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Table 3 Summary information of known miRNA families and their transcript abundance identified in all libraries

From: Identification of miRNAs involved in fruit ripening in Cavendish bananas by deep sequencing

miRNA family

No.of members

miRNA reads

Normalized reads

Fold Change

CK

ET

1-MCP

CK

ET

1-MCP

Log2 (ET/CK)

Log2 (1-MCP/CK)

Log2 (ET/1-MCP)

Conserved miRNA

         

 miR156

9

455

9460

147

107.20

1049.83

55.39

3.29

−0.95

4.24

 miR157

2

16

1584

46

3.77

175.78

17.33

5.54

2.20

3.34

 miR159

9

38786

103380

48416

9138.35

11472.62

18242.38

0.33

1.00

−0.67

 miR160

3

28

111

80

6.60

12.32

30.14

0.90

2.19

−1.29

 miR162

2

832

8566

398

196.03

950.61

149.96

2.28

−0.39

2.66

 miR164

4

100

271

60

23.56

30.07

22.61

0.35

−0.06

0.41

 miR165

1

5

70

6

1.18

7.77

2.26

2.72

0.94

1.78

 miR166

9

2303

60599

1615

542.61

6724.99

608.51

3.63

0.17

3.47

 miR167

7

997

4609

684

234.90

511.48

257.72

1.12

0.13

0.99

 miR168

3

1743

10209

1448

410.67

1132.95

545.58

1.46

0.41

1.05

 miR169

3

2

0

3

0.47

0.01

1.13

ND

ND

ND

 miR171

9

22

90

6

5.18

9.99

2.26

0.95

−1.20

2.14

 miR172

9

133

689

61

31.34

76.46

22.98

1.29

−0.45

1.73

 miR319

6

84317

264863

69638

19865.89

29393.23

26238.49

0.57

0.40

0.16

 miR390

4

8

34

7

1.88

3.77

2.64

1.00

0.48

0.52

 miR393

2

304

1008

14

71.63

111.86

5.27

0.64

−3.76

4.41

 miR394

1

38

45

26

8.95

4.99

9.80

−0.84

0.13

−0.97

 miR395

4

62

66

50

14.61

7.32

18.84

−1.00

0.37

−1.36

 miR396

9

13214

47358

9078

3113.34

5255.56

3420.45

0.76

0.14

0.62

 miR397

1

1

0

0

0.24

0.01

0.01

ND

ND

ND

 miR398

4

26

44

13

6.13

4.88

4.90

−0.33

−0.32

0.00

 miR399

3

28

11

12

6.60

1.22

4.52

−2.43

−0.55

−1.89

 miR408

3

27

80

26

6.36

8.88

9.80

0.48

0.62

−0.14

 miR528

1

40

209

24

9.42

23.19

9.04

1.30

−0.06

1.36

 miR529

1

964

2429

552

227.13

269.56

207.98

0.25

−0.13

0.37

 miR530

1

0

0

1

0.01

0.1

0.38

ND

ND

ND

 miR827

1

0

1

0

0.01

0.11

0.01

ND

ND

ND

 miR858

2

62

58

60

14.61

6.44

22.61

−1.18

0.63

−1.81

 miR845

2

1

0

2

0.24

0.01

0.75

ND

ND

ND

Non-conserved miRNA

       

 miR829

1

1

2

0

0.24

0.22

0.01

ND

ND

ND

 miR418

1

0

1

0

0.01

0.11

0.01

ND

ND

ND

 miR1432

1

0

1

0

0.01

0.11

0.01

ND

ND

ND

 miR1511

1

3

3

2

0.71

0.33

0.75

ND

ND

ND

 miR1887

1

1

0

0

0.24

0.01

0.01

ND

ND

ND

 miR4995

1

11

8

9

2.59

0.89

3.39

−1.55

0.39

−1.93

 miR5368

1

27

63

22

6.36

6.99

8.29

0.14

0.38

−0.25

 miR5632

1

1

0

0

0.24

0.01

0.01

ND

ND

ND

 miR5658

1

1

2

0

0.24

0.22

0.01

ND

ND

ND

 miR6300

1

94

94

115

22.15

10.43

43.33

−1.09

0.97

−2.05

  1. Normalized reads formula: normalized read count = (actual miRNA count / total count of clean reads) × 1,000,000. The clean reads in CK, ET and 1-MCP library are 4,244,311, 9,011,022 and 2,654,040 respectively (Table 2). After normalization, if the normalized read count of a given miRNA is zero, the expression value is set to 0.01 for further analysis, and if the read count of a given miRNA was less than five in both libraries, differential expression analysis was not performed owing to their too low expression level and replaced it with ND
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BMC Genomics

ISSN: 1471-2164

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