Table 3

Validation of miRNAs identified by parameterized miRDeep.

miRNA Family

miRNA name

Confirmation by RACE

Seedling RPM

If identified by parameterized miRDeep

Reads aligned

Star (count)

miR156

zma-MIR156d

14111.2

✔

5932

1

miR156

zma-MIR156l

12645.91

✔

1659

1

miR160

zma-MIR160b

✔

292.65

miRNA overlapping with CDS

miR162

zma-MIR162

✔

2.74

poor abundance of reads

miR166

zma-MIR166d

314.6

✔

328

1

miR166

zma-MIR166k

✔

6.52

miRNA homologous to CDS

miR166

zma-MIR166m

✔

49.75

miRNA homologous to CDS

miR167

zma-MIR167b

✔

2860.25

✔

17402

1

miR167

zma-MIR167c

✔

2872.95

✔

72684

0

miR168

zma-MIR168a

10364.43

✔

32179

1

miR169

zma-MIR169f

1234.4

✔

3371

0

miR171

zma-MIR171f

✔

15483.87

✔

78

1

miR171

zma-MIR171m

4.12

✔

508

1

miR172

zma-MIR172b

134.49

✔

81

1

miR390

zma-MIR390b

2220.41

✔

6504

1

miR394

zma-MIR394a

✔

4.46

MiRNA overlapping with CDS

miR396

zma-MIR396f

849.46

✔

2503

1

miR396

zma-MIR396g

43.23

miRNA homologous to CDS

miR397

zma-MIR397b

556.13

✔

1628

1

miR399

zma-MIR399h

43.23

✔

129

1

miR399

zma-MIR399i

90.57

✔

272

0

miR529

zma-MIR529

359.2

✔

1050

1

miR827

zma-MIR827

711.89

miRNA overlapping with CDS

Unclassified

?

-

334

0

The candidates were compared against a recently discovered set of miRNAs, from chromosome 5 of maize, expressed in seedlings [14]. The data in third and fourth columns are from [14], while those in last two columns are from current study. The cases missed out by parameterized miRDeep appeared mainly due to a filter which discarded reads mapped to coding sequences (CDS). Even chance homology of a miRNA, either complete or at least in mature/star region, to any CDS can result into the miRNA being unidentified. RPM: Reads Per Million.

Thakur et al. BMC Genomics 2011 12:108   doi:10.1186/1471-2164-12-108