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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