Table 1.
Predicted precursor genes and potential targets of detected tomato miRNAs and miRNA*s
| Genea | Predicted precursorb | Gene ID | Predicted target gened |
| sly-miR156d | sly-MIR156dc | LE_HBa0125A23_SP6_300719 | SPL2 (SGN-U#324312) |
| sly-miR156a–c | sly-MIR156b | C02HBa0194N24.1 | SPL3 (SGN-U#317176) |
| sly-miR156a–c | sly-MIR156c | C02SLe0022J22.1 | SPL3 (SGN-U#317176) |
| sly-miR159 | sly-MIR159 | C03HBa0029M12.1 | GAMyb-like1 (EF175474) |
| sly-miR162 | sly-MIR162 | SL_EcoRI0035M01_T7_295421 | |
| sly-miR166a | sly-MIR166a | C06HBa0073H07.1 | REV (SGN-U#321033) |
| sly-miR166b/sly-miR166b* | sly-MIR166b | C08HBa0005L01.1 | REV (SGN-U#321033) |
| sly-miR167 | sly-MIR167 | C06HBa0028D14.1 | ARF8 (SGN-U#327976) |
| sly-miR168/sly-miR168* | sly-MIR168c | C12HBa0067C22.2 | AGO1 (SGN-U#338285) |
| sly-miR171a | sly-MIR171a | C02HBa0060J03.2 | SCL6 (SGN-U#333058) |
| sly-miR171b/sly-miR171b* | sly-MIR171b | C02HBa0167J21.2 | SCL6 (SGN-U#333058) |
| sly-miR171c/sly-miR171c* | sly-MIR171c | C12HBa0090D09.1 | SCL6 (SGN-U#333058) |
| sly-miR171d | sly-MIR171d | C12HBa0146I19.1 | SCL6 (SGN-U#333058) |
| sly-miR319 | sly-MIR319 | LE_HBa0015P16_SP6_130147 | TCP (SGN-U#324434) |
| sly-miR396/sly-miR396* | sly-MIR396c | C12HBa0211M21.1 | Transcription activator GRL1 (SGN-U#323341) |
| sly-miR403 | sly-MIR403 | SL_EcoRI0010F07 | PAZ domain-containing protein (SGN-U#315036) |
| sly-miR390 | C07HBa0229H10.2 | PP2C (SGN-U#325391) | |
| sly-miR164 | C07HBa0179K09.1 | CUC2 (SGN-U#326326) |
b
The predicted precursor structures are indicated in Fig. S1
c
Precursor genes that are first predicted in this study
d
SPL: squamosa promoter-binding protein-like; REV: homeodomain-leucine zipper protein Revoluta; ARF: auxin-responsive factor; AGO: argonaute protein; SCL: scarecrow-like transcription factor; PP2C: protein phosphatase 2C; CUC2: cup-shaped cotyledon CUC2