Table 1

Expression analysis of Papaya Micro RNAs
MiR ID qPCR fold change Deep sequencing reads per million
Flower Leaves PRSV infected leaves Flower Leaves PRSV infected leaves
1 cpa-MIR156/57a 1.00 1.46 2.70 132.68 2426.48 1093.61
2 cpa-MIR156/57b 1.00 0.09 0.03 132.47 815.04 540.48
3 cpa-MIR159a 1.00 0.80 0.05 441.84 805.61 0.00
4 cpa-MIR159b 1.00 0.06 0.03 0.00 0.00 0.67
5 cpa-MIR159/319 1.07 0.00 0.00
6 cpa-MIR160 1.00 0.18 0.46 19.32 16.08 11.32
cpa-MIR160* 1.00 0.32 27.34 0.00 0.00 191.11
7 cpa-MIR164 1.00 0.10 0.25 229.94 114.05 77.69
8 cpa-MIR165/166a†† 1.00 1.20 0.70 16800.30 29790.48 21150.36
9 cpa-MIR165/166b†† 4096.54 8447.99 6703.93
11 cpa-MIR165/166c†† 0.00 161.8 0.00
10 cpa-MIR166b* 1.00 0.47 29.51 0.00 0.00 456.35
cpa-MIR166c* 0.00 83.60 0.00
12 cpa-MIR167a††† 1.00 1.17 2.30 171.54 155.63 35.74
13 cpa-MIR167b††† 60.11 650.83 176.68
14 cpa-MIR167c††† 17.60 4725.63 1581.26
cpa-MIR167* 1.00 1.13 0.46 0.00 168.50 0.00
15 cpa-MIR169 1.00 0.19 0.26 0.00 0.00 0.44
16 cpa-MIR170/71 1.00 0.41 0.69 22.97 94.32 35.96
17 cpa-MIR172 1.00 0.07 0.13 5.58 0.00 0.00
18 cpa-MIR390 1.00 0.48 1.14 428.53 0.00 0.00
cpa-MIR390* 1.00 0.12 0.31 0.00 0.00 8.88
19 cpa-MIR393 1.00 0.57 0.43 1.50 0.00 0.00
cpa-MIR393* 1.00 0.42 6.79 0.00 0.00 11.10
20 cpa-MIR394 1.00 0.70 0.57 167.67 202.80 116.31
21 cpa-MIR395 1.00 1.36 0.54 0.00 1.50 7.10
22 cpa-MIR396 1.00 2.63 0.15 0.00 55.74 0.00
cpa-MIR396* 1.00 0.72 5.25 79.01 0.00 1021.03
23 cpa-MIR408 1.00 0.11 0.15 9.23 0.00 0.00
cpa-MIR408* 1.00 0.16 12.41 0.00 4.07 45.72
24 cpa-MIR535 1.00 0.51 0.23 292.63 686.85 348.48
25 cpa-MIR-novel_01 1.00 0.60 0.71 13.31 30.87 9.10
26 cpa-MIR-novel_02 1.00 0.15 1.43 225.86 69.46 3595.35
27 cpa-MIR-novel_03 1.00 0.22 30.76 8.37 8.15 19.31
28 cpa-MIR-novel_04 1.00 0.19 0.36 3.01 6.43 3.33
29 cpa-MIR-novel_05 1.00 0.20 0.82 110.14 134.84 21.75
30 cpa-MIR-novel_06 1.00 0.11 0.52 54.10 40.52 0.00
cpa-MIR-novel_06* 1.00 0.19 284.64 0.00 0.00 108.10
31 cpa-MIR-novel_07 1.00 0.15 4.12 3.44 0.00 1.55
32 cpa-MIR-novel_08 1.00 0.22 0.16 0.00 1.29 0.00
33 cpa-MIR-novel_09a 1.00 0.30 0.29 0.00 0.64 0.00
34 cpa-MIR-novel_09b 1.00 0.45 0.44 0.00 13.51 29.30
35 cpa-MIR-novel_10 1.00 2.15 1.67 71.71 0.00 0.00
36 cpa-MIR-novel_11 1.00 0.73 0.44 57.75 0.00 0.00
37 cpa-MIR-novel_12 1.00 0.02 0.14 37.36 0.00 0.00
38 cpa-MIR-novel_13 1.00 0.53 0.63 6.44 0.00 0.00
39 cpa-MIR-novel_14 1.00 0.28 0.00 5.37 0.00 0.00
40 cpa-MIR-novel_15 1.00 0.29 0.28 4.29 0.00 0.00
41 cpa-MIR-novel_16 1.00 0.28 0.56 3.01 0.00 0.00
42 cpa-MIR-novel_17 1.00 0.00 0.51 2.58 0.00 0.00
43 cpa-MIR-novel_18 1.00 0.87 2.52 2.58 0.00 0.00
44 cpa-MIR-novel_19 1.00 0.24 0.65 2.58 0.00 0.00
45 cpa-MIR-novel_20 Not detected by qPCR 4.07 0.00 0.00
46 cpa-MIR-novel_21 1.00 0.29 0.24 2.36 0.00 0.00
47 cpa-MIR-novel_22 1.00 1.69 0.29 2.15 0.00 0.00
48 cpa-MIR-novel_23 1.00 0.28 0.19 2.15 0.00 0.00
49 cpa-MIR-novel_24 1.00 0.13 0.00 0.00 12.22 0.00
50 cpa-MIR-novel_25 1.00 0.14 0.00 0.00 9.00 0.00
51 cpa-MIR-novel_26 1.00 0.37 0.48 0.00 5.57 0.00
52 cpa-MIR-novel_27 1.00 1.00 0.10 0.00 4.07 0.00
53 cpa-MIR-novel_28 Not detected by qPCR 0.00 2.36 0.00
54 cpa-MIR-novel_29 1.00 0.04 0.11 0.00 3.22 0.00
55 cpa-MIR-novel_30 1.00 0.42 0.22 0.00 3.00 0.00
56 cpa-MIR-novel_31 1.00 0.21 0.88 0.00 2.79 0.00
57 cpa-MIR-novel_32 1.00 0.17 0.40 0.00 2.14 0.00
58 cpa-MIR-novel_33 1.00 6.94 5.25 0.00 0.00 6.66
59 cpa-MIR-novel_34 1.00 0.00 2.06 0.00 0.00 6.66
60 cpa-MIR-novel_35 0.00 1.00 3.60¥ 0.00 0.00 2.44

qPCR fold change is normalized on initial RNA input, the sequencing expression level was normalized on per million reads of respective library.

†,††,††† - The sequences can not be distinguished by stem-loop primers, so tested together for qPCR.

¥ - normalized on leaf expression level since no expression detected on flower.

Aryal et al.

Aryal et al. BMC Genomics 2012 13:682   doi:10.1186/1471-2164-13-682

Open Data