Table 2.
Known and novel sugarcane microRNA candidates.
| Number | miRNA familya | No. transcripts (TPM) from inactive bud (0 DAP)b | No. transcripts (TPM) from active bud (2 DAP)b | Annotationc |
|---|---|---|---|---|
| Known miRNAs | ||||
| 1 | miR156 | 2.5 | 5.8 | miRbase, EST |
| 2 | miR159* | 100244.6 | 46877.7 | miRbase, EST |
| 3 | miR160* | 31.5 | 227.8 | miRbase |
| 4 | miR162* | 88.5 | 117.7 | miRbase |
| 5 | miR164* | 6.1 | 34.6 | miRbase |
| 6 | miR166* | 912.6 | 2224.2 | miRbase, EST (CN607727)d |
| 7 | miR167* | 7.8 | 11.5 | miRbase, EST |
| 8 | miR168* | 1157.1 | 3937 | miRbase, EST |
| 9 | miR169* | 6.6 | 3.7 | miRbase, EST |
| 10 | miR171* | 22.4 | 450.8 | miRbase |
| 11 | miR172 | 1.2 | 3.3 | miRbase |
| 12 | miR319* | 2584.1 | 766.8 | miRbase, EST |
| 13 | miR393 | 7.8 | 4.7 | miRbase |
| 14 | miR394 | 8.7 | 14.0 | miRbase |
| 15 | miR395 | 3.0 | 7.5 | miRbase |
| 16 | miR396 | 91.0 | 74.9 | miRbase, EST |
| 17 | miR397* | 0.0 | 6.8 | miRbase |
| 18 | miR398* | 0.0 | 5.4 | miRbase |
| 19 | miR399 | 5.5 | 1.6 | miRbase |
| 20 | miR408* | 0.8 | 9.1 | miRbase, EST |
| 21 | miR444* | 0.5 | 6.8 | miRbase, EST |
| 22 | miR444b.2* | 0.9 | 3.5 | miRbase, EST |
| 23 | miR444d.3* | 2.3 | 6.8 | miRbase, EST |
| 24 | miR529 | 18.2 | 20.6 | miRbase |
| 25 | miR827* | 27.6 | 150.4 | miRbase, EST |
| 26 | miR1878* | 39.9 | 10.3 | miRbase |
| Novel miRNA candidates | ||||
| 1 | miRcand1* | 30.6 | 1.2 | EST (CA257509)d |
| 2 | miRcand2* | 29.4 | 530.6 | EST (CA222602)d |
a microRNAs with an asterisk showed significant differential expression (P <0.01) using the Bonferroni-corrected P value of Fisher’s exact test.
b The normalized expression of transcripts per million (TPM) was obtained by the following formula: (total read count of each miRNA/total count of high-quality small RNA reads)×1 000 000. The normalized values were rounded to the nearest tenth.
c Annotation of the reads based on miRbase version17 and/or matching with EST sequences.
d Identified in this work.