Table 1.
Target of banana known miRNAs (or families)a
| miRNA | Target | ASb | Categoryc | Reads at the cleavage site (tpb)d | Target annotation |
|---|---|---|---|---|---|
| Conserved targets for known miRNAs | |||||
| miR156 | Achr6T36010 | 3 | 0 | 722.4 | Putative Squamosa promoter-binding-like protein 12 |
| Achr10T23280 | 1 | 0 | 214.0 | Putative Squamosa promoter-binding-like protein 12 | |
| Achr5T21990 | 1 | 0 | 240.8 | Putative Squamosa promoter-binding-like protein 12 | |
| Achr10T02970 | 1 | 0 | 989.9 | Putative Squamosa promoter-binding-like protein 12 | |
| Achr3T11170 | 1.5 | 0 | 124.9 | Putative Squamosa promoter-binding-like protein 17 | |
| Achr5T25090 | 1.5 | 0 | 133.8 | Putative Squamosa promoter-binding-like protein 18 | |
| Achr7T22940 | 1.5 | 0 | 2060.1 | Putative Squamosa promoter-binding-like protein 16 | |
| Achr8T25550 | 1.5 | 0 | 124.9 | Putative Squamosa promoter-binding-like protein 17 | |
| miR159 | Achr2T12990 | 3.5 | 0 | 693.8 | Putative Transcription factor PCF6 |
| Achr4T22960 | 3.5 | 0 | 292.5 | Putative Transcription factor PCF6 | |
| Achr4T31520 | 3.5 | 0 | 194.4 | Putative Transcription factor PCF6 | |
| Achr5T02530 | 3.5 | 0 | 881.1 | Putative Transcription factor PCF6 | |
| Achr7T01160 | 3.5 | 0 | 881.1 | Putative Transcription factor PCF6 | |
| Achr5T06660 | 3 | 0 | 160.5 | Putative Transcription factor TCP4 | |
| Achr8T19990 | 3 | 0 | 454.8 | Putative Transcription factor TCP4 | |
| Achr10T0102 | 3 | 0 | 481.6 | Putative Transcription factor TCP4 | |
| miR160 | Achr6T18900 | 1.5 | 0 | 321.1 | Putative Auxin response factor 22 |
| Achr9T29480 | 1.5 | 0 | 695.6 | Putative Auxin response factor 17 | |
| Achr11T00640 | 2 | 0 | 27,825.2 | Auxin response factor 18 | |
| Achr5T18540 | 2 | 0 | 13,029.7 | Auxin response factor 18 | |
| Achr5T14630 | 2 | 0 | 4053.4 | Auxin response factor 18 | |
| Achr5T03960 | 2 | 0 | 6822.5 | Auxin response factor 18 | |
| Achr4T18240 | 2 | 0 | 4080.1 | Auxin response factor 18 | |
| Achr8T18930 | 2 | 0 | 3852.7 | Auxin response factor 18 | |
| miR164 | Achr3T23360 | 3 | 0 | 936.4 | Putative NAC domain-containing protein |
| Achr9T27530 | 3.5 | 0 | 1337.7 | no apical meristem protein, putative | |
| Achr9T26140 | 2 | 0 | 6207.1 | NAC domain-containing protein | |
| Achr9T10210 | 2 | 0 | 20,347.1 | NAC domain-containing protein | |
| miR167 | AchrUn_randomT06470 | 3.5 | 0 | 5468.7 | Auxin response factor 12 |
| Achr11T25770 | 4 | 0 | 5415.2 | Auxin response factor 6 | |
| Achr3T23290 | 4 | 0 | 5281.4 | Auxin response factor 17 | |
| Achr5T00590 | 4 | 0 | 4535.0 | Auxin response factor 17 | |
| Achr5T26580 | 4 | 0 | 5281.4 | Auxin response factor 6 | |
| Achr5T02450 | 4 | 0 | 4454.7 | Auxin response factor 6 | |
| miR168 | Achr3T27070 | 4 | 0 | 1150.5 | Protein argonaute 1B |
| miR171 | Achr4T07190 | 3 | 0 | 165,720.2 | Putative Scarecrow-like protein 15 |
| Achr3T29970 | 3 | 0 | 8802.4 | Putative Scarecrow-like protein 15 | |
| Achr4T03460 | 3 | 0 | 508.3 | Putative Scarecrow-like protein 15 | |
| Achr5T20860 | 2 | 0 | 1551.8 | Putative Scarecrow-like protein 6 | |
| miR393 | Achr6T20580 | 3 | 0 | 4666.5 | Transport inhibitor response 1-like protein |
| Achr6T16510 | 3 | 0 | 3424.6 | Transport inhibitor response 1-like protein | |
| Achr6T08000 | 3 | 0 | 4882.8 | Transport inhibitor response 1-like protein | |
| Achr9T01140 | 3 | 0 | 4693.3 | Transport inhibitor response 1-like protein | |
| AchrUn_randomT10710 | 2 | 0 | 3917.4 | Transport inhibitor response 1-like protein | |
| Achr10T12000 | 2 | 0 | 3244.0 | Transport inhibitor response 1-like protein | |
| miR396 | Achr3T15140 | 2.5 | 0 | 615.4 | growth regulating factor protein, putative |
| Achr7T27480 | 2.5 | 0 | 615.4 | growth-regulating factor, putative | |
| miR535 | Achr10T02970 | 4 | 0 | 989.9 | Putative Squamosa promoter-binding-like protein 12 |
| Achr4T05720 | 4 | 0 | 695.6 | Putative Squamosa promoter-binding-like protein 12 | |
| Non-conserved targets for known miRNAs | |||||
| miR156 | Achr10T05030 | 3.5 | 2 | 240.8 | CCR4-NOT transcription factor, putative, expressed |
| miR164 | AchrUn_randomT19770 | 3 | 0 | 20,775.2 | Hypothetical protein |
| Achr11T02240 | 4 | 4 | 13.4 | Probable aquaporin TIP1–1 | |
| Achr8T12920 | 4 | 4 | 13.4 | Probable aquaporin TIP1–1 | |
| miR396 | Achr5T20170 | 4 | 1 | 267.5 | Hypothetical protein |
| Achr8T26530 | 2.5 | 0 | 615.4 | metalloendopeptidase/ metallopeptidase/ zinc ion binding protein, putative | |
| miR528 | AchrUn_randomT22730 | 3.5 | 0 | 1172.8 | Putative Polyphenol oxidase A1, chloroplastic |
| AchrUn_randomT25220 | 3.5 | 4 | 8.9 | Putative Polyphenol oxidase A1, chloroplastic | |
| Achr8T34370 | 2.5 | 2 | 615.4 | Polyphenol oxidase, chloroplastic | |
| miR530 | Achr2T17590 | 1 | 0 | 2354.4 | Hypothetical protein |
| miR535 | Achr4T12470 | 4 | 0 | 668.9 | Putative uncharacterized protein |
| miR828 | Achr2T17960 | 3 | 0 | 107.0 | Hypothetical protein |
a A detailed list was included in Additional file 1: Table S5. b The alignment score (AS) threshold was set to 4 for known miRNAs. c Category 0: > 1 raw read at the position, abundance at position is equal to the maximum on the transcript, and there is only one maximum on the transcript. Category 1: > 1 raw read at the position, abundance at position is equal to the maximum on the transcript, and there is more than one maximum position on the transcript. Category 2: > 1 raw read at the position, abundance at position is less than the maximum but higher than the median for the transcript. Category 3: > 1 raw read at the position, abundance at position is equal to or less than the median for the transcript. Category 4: only 1 raw read at the position. d Reads at the cleavage site were normalized to transcripts per billion (tpb)