Table 5.
miRNA targets identified in the degradome libraries generated from three alfalfa genotypes. #Mis. is number of mismatches on the miRNA complementary site; Valid reads is Reads corresponding to the expected cleavage site; Total reads is Total reads mapped to the cDNA of the gene; Percent is Percent reads at the expected cleavage site
| genotypes | miRNA id# | Target gene | #Mis. | Valid reads | Total reads | Percent | Target gene annotation |
|---|---|---|---|---|---|---|---|
| Altet-4 | miR156e | Medtr7g028740.2 | 0 | 4 | 23 | 17.4 | squamosa promoter-binding-like protein |
| Altet-4 | miR156a | Medtr7g444860.1 | 0 | 2 | 28 | 7.1 | squamosa promoter-binding-like protein |
| Altet-4 | miR156a | Medtr3g099080.1 | 0 | 1 | 3 | 33.3 | squamosa promoter-binding 13A-like protein |
| Altet-4 | miR159b | Medtr8g042410.1 | 2.5 | 1 | 16 | 6.3 | MYB transcription factor |
| Altet-4 | miR160c | Medtr2g094570.3 | 1 | 4 | 21 | 19.1 | auxin response factor 1 |
| Altet-4 | miR164d | Medtr2g064470.1 | 1 | 2 | 34 | 5.9 | NAC transcription factor-like protein |
| Altet-4 | miR164d | Medtr8g058330.1 | 2 | 5 | 49 | 10.2 | protein transporter Sec61 subunit alpha-like protein |
| Altet-4 | miR167b-5p | Medtr8g079492.3 | 4 | 4 | 62 | 6.5 | auxin response factor 2 |
| Altet-4 | miR169e-5p | Medtr2g099490.2 | 2 | 1 | 20 | 5 | CCAAT-binding transcription factor |
| Altet-4 | miR171f | Medtr0092s0100.2 | 1.5 | 5 | 24 | 20.8 | GRAS family transcription regulator |
| Altet-4 | miR172a | Medtr4g094868.3 | 1 | 1 | 13 | 7.7 | AP2 domain transcription factor |
| Altet-4 | miR172a | Medtr5g016810.2 | 1 | 1 | 18 | 5.6 | AP2 domain transcription factor |
| Altet-4 | miR172a | Medtr2g093060.3 | 0 | 4 | 17 | 23.5 | AP2-like ethylene-responsive transcription factor |
| Altet-4 | miR319d-3p | Medtr2g078200.1 | 3 | 2 | 34 | 5.9 | TCP family transcription factor |
| Altet-4 | miR319d-3p | Medtr8g463380.1 | 3 | 2 | 7 | 28.6 | TCP family transcription factor |
| Altet-4 | miR393a | Medtr1g088950.1 | 1 | 11 | 83 | 13.3 | transport inhibitor response-like protein |
| Altet-4 | miR393a | Medtr7g083610.1 | 2 | 38 | 134 | 28.4 | transport inhibitor response 1 protein |
| Altet-4 | miR395j | Medtr1g102550.1 | 1 | 1 | 76 | 1.3 | ATP sulfurylase |
| Altet-4 | miR396b-5p | Medtr1g017490.2 | 3 | 47 | 100 | 47 | growth-regulating factor |
| Altet-4 | miR396b-5p | Medtr2g041430.3 | 3 | 5 | 12 | 41.7 | growth-regulating factor-like protein |
| Altet-4 | miR396b-5p | Medtr5g027030.1 | 3 | 5 | 15 | 33.3 | growth-regulating factor |
| Altet-4 | miR396a-5p | Medtr3g052060.1 | 2 | 1 | 1 | 100 | hypothetical protein |
| Altet-4 | miR398c | Medtr4g114870.1 | 3 | 8 | 23 | 34.8 | plastocyanin-like domain protein |
| Altet-4 | miR398a-3p | Medtr8g064810.1 | 3 | 5 | 36 | 13.9 | protein disulfide isomerase (PDI)-like protein |
| Altet-4 | miR408-3p | Medtr8g089110.1 | 3 | 3 | 9 | 33.3 | basic blue-like protein |
| Altet-4 | miR408-3p | Medtr8g007020.1 | 3.5 | 5 | 73 | 6.9 | plastocyanin-like domain protein |
| Altet-4 | miR408-3p | Medtr8g007035.1 | 3.5 | 5 | 123 | 4.1 | plastocyanin-like domain protein |
| Altet-4 | miR408-5p | Medtr3g074830.1 | 3.5 | 2 | 442 | 0.5 | phosphate-responsive 1 family protein |
| Altet-4 | miR1510a-5p | Medtr2g012770.1 | 1 | 1 | 5 | 20 | disease resistance protein (TIR-NBS-LRR class) |
| Altet-4 | miR2199 | Medtr7g080780.2 | 2 | 2 | 8 | 25 | helix loop helix DNA-binding domain protein |
| Altet-4 | miR2643a | Medtr3g010590.1 | 1 | 1 | 15 | 6.7 | F-box protein interaction domain protein |
| Altet-4 | miR2643a | Medtr6g053240.1 | 3 | 2 | 4 | 50 | F-box protein interaction domain protein |
| Altet-4 | miR4414a-5p | Medtr3g117120.1 | 4 | 3 | 84 | 3.6 | BZIP transcription factor bZIP124 |
| Altet-4 | miR5213-5p | Medtr6g084370.1 | 2 | 1 | 2 | 50 | disease resistance protein (TIR-NBS-LRR class) |
| Altet-4 | miR5213-5p | Medtr6g088245.1 | 3 | 1 | 5 | 20 | disease resistance protein (TIR-NBS-LRR class) |
| Altet-4 | miR5239 | Medtr3g018680.1 | 3 | 1 | 5 | 20 | F-box/RNI superfamily protein, putative |
| Altet-4 | miR5561-3p | Medtr2g045295.1 | 3 | 1 | 4 | 25 | hypothetical protein |
| Altet-4 | miR5752b | Medtr8g066820.1 | 4 | 9 | 423 | 2.1 | PLATZ transcription factor family protein | |
| Altet-4 | miR7696a-5p | Medtr1g072130.1 | 3 | 2 | 27 | 7.4 | PHD finger protein, putative |
| Altet-4 | miR7696c-3p | Medtr3g081480.1 | 3 | 2 | 21 | 9.5 | endoplasmic reticulum vesicle transporter |
| Altet-4 | miR7696d-5p | Medtr3g112250.1 | 3.5 | 8 | 36 | 22.2 | hypothetical protein |
| Altet-4 | miR7696c-3p | Medtr4g011600.2 | 3.5 | 1 | 26 | 3.9 | sulfate transporter-like protein |
| Altet-4 | miR7696c-3p | Medtr7g085650.4 | 3.5 | 1 | 6 | 16.7 | sulfate adenylyltransferase subunit 1/adenylylsulfate kinase |
| Altet-4 | miR7701-3p | Medtr6g011380.2 | 2 | 1 | 137 | 0.7 | SPFH/band 7/PHB domain membrane-associated family protein |
| NF08ALF06 | miR156e | Medtr7g028740.2 | 0 | 14 | 36 | 38.9 | squamosa promoter-binding-like protein |
| NF08ALF06 | miR156a | Medtr7g444860.1 | 0 | 1 | 144 | 0.7 | squamosa promoter-binding-like protein |
| NF08ALF06 | miR156h-3p | Medtr7g091370.1 | 3 | 1 | 11 | 9.1 | heat shock transcription factor |
| NF08ALF06 | miR159b | Medtr8g042410.1 | 2.5 | 4 | 30 | 13.3 | MYB transcription factor |
| NF08ALF06 | miR160c | Medtr2g094570.3 | 1 | 8 | 46 | 17.4 | auxin response factor 1 |
| NF08ALF06 | miR160d | Medtr1g064430.2 | 0.5 | 3 | 24 | 12.5 | auxin response factor 1 |
| NF08ALF06 | miR160d | Medtr3g073420.1 | 0.5 | 2 | 17 | 11.8 | auxin response factor, putative |
| NF08ALF06 | miR164d | Medtr2g064470.1 | 1 | 41 | 151 | 27.2 | NAC transcription factor-like protein |
| NF08ALF06 | miR164d | Medtr8g058330.1 | 2 | 5 | 115 | 4.4 | protein transporter Sec61 subunit alpha-like protein |
| NF08ALF06 | miR167b-5p | Medtr8g079492.3 | 4 | 9 | 133 | 6.8 | auxin response factor 2 |
| NF08ALF06 | miR167a | Medtr4g076020.1 | 3.5 | 5 | 77 | 6.5 | GRAS family transcription factor |
| NF08ALF06 | miR171f | Medtr0092s0100.2 | 1.5 | 60 | 115 | 52.2 | GRAS family transcription regulator |
| NF08ALF06 | miR172a | Medtr4g094868.3 | 1 | 1 | 45 | 2.2 | AP2 domain transcription factor |
| NF08ALF06 | miR172a | Medtr5g016810.2 | 1 | 1 | 84 | 1.2 | AP2 domain transcription factor |
| NF08ALF06 | miR172a | Medtr2g093060.3 | 0 | 4 | 35 | 11.4 | AP2-like ethylene-responsive transcription factor |
| NF08ALF06 | miR172a | Medtr4g061200.4 | 1 | 1 | 28 | 3.6 | AP2-like ethylene-responsive transcription factor |
| NF08ALF06 | miR172a | Medtr7g100590.1 | 1 | 2 | 17 | 11.8 | AP2 domain transcription factor |
| NF08ALF06 | miR319d-3p | Medtr2g078200.1 | 3 | 2 | 126 | 1.6 | TCP family transcription factor |
| NF08ALF06 | miR319d-3p | Medtr8g463380.1 | 3 | 2 | 48 | 4.2 | TCP family transcription factor |
| NF08ALF06 | miR393a | Medtr1g088950.1 | 1 | 54 | 268 | 20.2 | transport inhibitor response-like protein |
| NF08ALF06 | miR393a | Medtr7g083610.1 | 2 | 472 | 771 | 61.2 | transport inhibitor response 1 protein |
| NF08ALF06 | miR393a | Medtr8g098695.2 | 4 | 1 | 46 | 2.2 | transport inhibitor response 1 protein |
| NF08ALF06 | miR396b-5p | Medtr1g017490.2 | 3 | 423 | 742 | 57 | growth-regulating factor |
| NF08ALF06 | miR396b-5p | Medtr2g041430.3 | 3 | 30 | 75 | 40 | growth-regulating factor-like protein |
| NF08ALF06 | miR396b-5p | Medtr5g027030.1 | 3 | 10 | 42 | 23.8 | growth-regulating factor |
| NF08ALF06 | miR396a-5p | Medtr3g011560.1 | 3 | 1 | 3 | 33.3 | TNP1 |
| NF08ALF06 | miR396a-5p | Medtr3g052060.1 | 2 | 3 | 11 | 27.3 | hypothetical protein |
| NF08ALF06 | miR396a-5p | Medtr8g017000.1 | 3 | 1 | 2 | 50 | Ulp1 protease family, carboxy-terminal domain protein |
| NF08ALF06 | miR398c | Medtr4g114870.1 | 3 | 14 | 49 | 28.6 | plastocyanin-like domain protein |
| NF08ALF06 | miR398a-3p | Medtr8g064810.1 | 3 | 8 | 44 | 18.2 | protein disulfide isomerase (PDI)-like protein |
| NF08ALF06 | miR408-3p | Medtr8g089110.1 | 3 | 8 | 34 | 23.5 | basic blue-like protein |
| NF08ALF06 | miR408-3p | Medtr8g007020.1 | 3.5 | 10 | 375 | 2.7 | plastocyanin-like domain protein |
| NF08ALF06 | miR408-3p | Medtr8g007035.1 | 3.5 | 10 | 675 | 1.5 | plastocyanin-like domain protein |
| NF08ALF06 | miR408-5p | Medtr3g074830.1 | 3.5 | 27 | 948 | 2.9 | phosphate-responsive 1 family protein |
| NF08ALF06 | miR482-5p | Medtr1g064430.2 | 3.5 | 1 | 24 | 4.2 | auxin response factor 1 |
| NF08ALF06 | miR530 | Medtr3g072110.1 | 2.5 | 3 | 102 | 2.9 | transmembrane amino acid transporter family protein |
| NF08ALF06 | miR1507–3p | Medtr8g036195.1 | 2 | 4 | 9 | 44.4 | NBS-LRR type disease resistance protein |
| NF08ALF06 | miR1510a-5p | Medtr7g108860.4 | 3.5 | 21 | 1061 | 2 | CS domain protein |
| NF08ALF06 | miR2199 | Medtr7g080780.2 | 2 | 1 | 26 | 3.9 | helix loop helix DNA-binding domain protein |
| NF08ALF06 | miR2643a | Medtr6g053240.1 | 3 | 25 | 33 | 75.8 | F-box protein interaction domain protein |
| NF08ALF06 | miR4414a-5p | Medtr3g117120.1 | 4 | 8 | 260 | 3.1 | BZIP transcription factor bZIP124 |
| NF08ALF06 | miR5037c | Medtr4g070550.1 | 3 | 2 | 44 | 4.6 | F-box protein interaction domain protein |
| NF08ALF06 | miR5213-5p | Medtr4g014580.1 | 1.5 | 3 | 31 | 9.7 | TIR-NBS-LRR class disease resistance protein |
| NF08ALF06 | miR5238 | Medtr3g077740.2 | 2.5 | 1 | 259 | 0.4 | pantothenate kinase |
| NF08ALF06 | miR5239 | Medtr3g018680.1 | 3 | 4 | 43 | 9.3 | F-box/RNI superfamily protein, putative |
| NF08ALF06 | miR5561-3p | Medtr2g045295.1 | 3 | 1 | 12 | 8.3 | hypothetical protein |
| NF08ALF06 | miR5752a | Medtr8g066820.1 | 4 | 13 | 936 | 1.4 | PLATZ transcription factor family protein |
| NF08ALF06 | miR7696a-5p | Medtr1g072130.1 | 3 | 4 | 259 | 1.5 | PHD finger protein, putative |
| NF08ALF06 | miR7696c-3p | Medtr3g081480.1 | 3 | 2 | 46 | 4.4 | endoplasmic reticulum vesicle transporter |
| NF08ALF06 | miR7696c-5p | Medtr7g076830.1 | 3 | 3 | 103 | 2.9 | DEAD-box ATP-dependent RNA helicase-like protein |
| NF08ALF06 | miR7696d-5p | Medtr3g112250.1 | 3.5 | 5 | 30 | 16.7 | hypothetical protein |
| NF08ALF06 | miR7696c-3p | Medtr4g011600.2 | 3.5 | 1 | 103 | 1 | sulfate transporter-like protein |
| NF08ALF06 | miR7696c-3p | Medtr7g085650.4 | 3.5 | 2 | 10 | 20 | sulfate adenylyltransferase subunit 1/adenylylsulfate kinase |
| NF08ALF06 | miR7701-3p | Medtr3g108910.1 | 2.5 | 2 | 375 | 0.5 | hypothetical protein |
| NF08ALF06 | miR7701-3p | Medtr6g011380.2 | 2 | 2 | 86 | 2.3 | SPFH/band 7/PHB domain membrane-associated family protein |
| NCES-141 | miR156e | Medtr7g028740.2 | 0 | 18 | 46 | 39.1 | squamosa promoter-binding-like protein |
| NCES-141 | miR156a | Medtr7g444860.1 | 0 | 4 | 101 | 4 | squamosa promoter-binding-like protein |
| NCES-141 | miR156a | Medtr8g096780.1 | 0 | 1 | 11 | 9.1 | squamosa promoter-binding 13A-like protein |
| NCES-141 | miR156a | Medtr3g085180.1 | 1 | 1 | 2 | 50 | squamosa promoter-binding-like protein |
| NCES-141 | miR156h-3p | Medtr7g091370.1 | 3 | 2 | 5 | 40 | heat shock transcription factor |
| NCES-141 | miR159b | Medtr8g042410.1 | 2.5 | 3 | 36 | 8.3 | MYB transcription factor |
| NCES-141 | miR160c | Medtr2g094570.3 | 1 | 12 | 37 | 32.4 | auxin response factor 1 |
| NCES-141 | miR164d | Medtr2g064470.1 | 1 | 33 | 100 | 33 | NAC transcription factor-like protein |
| NCES-141 | miR164d | Medtr8g058330.1 | 2 | 14 | 119 | 11.8 | protein transporter Sec61 subunit alpha-like protein |
| NCES-141 | miR167b-5p | Medtr8g079492.3 | 4 | 10 | 101 | 9.9 | auxin response factor 2 |
| NCES-141 | miR167a | Medtr4g076020.1 | 3.5 | 4 | 45 | 8.9 | GRAS family transcription factor |
| NCES-141 | miR167b-3p | Medtr4g124900.2 | 3.5 | 1 | 154 | 0.7 | auxin response factor 2 |
| NCES-141 | miR168a | Medtr6g477980.2 | 4 | 2 | 245 | 0.8 | argonaute protein 1A |
| NCES-141 | miR171f | Medtr0092s0100.2 | 1.5 | 36 | 70 | 51.4 | GRAS family transcription regulator |
| NCES-141 | miR172a | Medtr4g094868.3 | 1 | 2 | 50 | 4 | AP2 domain transcription factor |
| NCES-141 | miR172a | Medtr5g016810.2 | 1 | 2 | 56 | 3.6 | AP2 domain transcription factor |
| NCES-141 | miR172a | Medtr2g093060.3 | 0 | 1 | 19 | 5.3 | AP2-like ethylene-responsive transcription factor |
| NCES-141 | miR172a | Medtr4g061200.4 | 1 | 3 | 32 | 9.4 | AP2-like ethylene-responsive transcription factor |
| NCES-141 | miR319d-3p | Medtr2g078200.1 | 3 | 1 | 55 | 1.8 | TCP family transcription factor |
| NCES-141 | miR319d-3p | Medtr8g463380.1 | 3 | 1 | 26 | 3.9 | TCP family transcription factor |
| NCES-141 | miR393a | Medtr1g088950.1 | 1 | 38 | 222 | 17.1 | transport inhibitor response-like protein |
| NCES-141 | miR393a | Medtr7g083610.1 | 2 | 337 | 539 | 62.5 | transport inhibitor response 1 protein |
| NCES-141 | miR395j | Medtr1g102550.1 | 1 | 1 | 163 | 0.6 | ATP sulfurylase |
| NCES-141 | miR396b-5p | Medtr1g017490.2 | 3 | 201 | 352 | 57.1 | growth-regulating factor |
| NCES-141 | miR396b-5p | Medtr5g027030.1 | 3 | 6 | 16 | 37.5 | growth-regulating factor |
| NCES-141 | miR396b-5p | Medtr8g020560.1 | 3 | 1 | 7 | 14.3 | growth-regulating factor-like protein |
| NCES-141 | miR396a-5p | Medtr3g011560.1 | 3 | 1 | 1 | 100 | TNP1 |
| NCES-141 | miR396a-5p | Medtr8g017000.1 | 3 | 1 | 1 | 100 | Ulp1 protease family, carboxy-terminal domain protein |
| NCES-141 | miR397-5p | Medtr7g062310.1 | 1.5 | 2 | 4 | 50 | laccase/diphenol oxidase family protein |
| NCES-141 | miR398c | Medtr4g114870.1 | 3 | 8 | 21 | 38.1 | plastocyanin-like domain protein |
| NCES-141 | miR398a-3p | Medtr8g064810.1 | 3 | 47 | 89 | 52.8 | protein disulfide isomerase (PDI)-like protein |
| NCES-141 | miR398c | Medtr5g089180.1 | 3 | 4 | 19 | 21.1 | hypothetical protein |
| NCES-141 | miR408-3p | Medtr8g089110.1 | 3 | 9 | 18 | 50 | basic blue-like protein |
| NCES-141 | miR408-3p | Medtr8g007020.1 | 3.5 | 7 | 209 | 3.4 | plastocyanin-like domain protein |
| NCES-141 | miR408-3p | Medtr8g007035.1 | 3.5 | 8 | 381 | 2.1 | plastocyanin-like domain protein |
| NCES-141 | miR408-5p | Medtr3g074830.1 | 3.5 | 14 | 703 | 2 | phosphate-responsive 1 family protein |
| NCES-141 | miR482-3p | Medtr5g027900.1 | 2.5 | 1 | 19 | 5.3 | disease resistance protein (CC-NBS-LRR class) family protein |
| NCES-141 | miR530 | Medtr3g072110.1 | 2.5 | 1 | 119 | 0.8 | transmembrane amino acid transporter family protein |
| NCES-141 | miR1510a-5p | Medtr7g108860.4 | 3.5 | 17 | 746 | 2.3 | CS domain protein |
| NCES-141 | miR2643a | Medtr3g010620.1 | 1 | 2 | 72 | 2.8 | F-box protein interaction domain protein |
| NCES-141 | miR4414a-5p | Medtr3g117120.1 | 4 | 2 | 134 | 1.5 | BZIP transcription factor bZIP124 |
| NCES-141 | miR5037c | Medtr4g070550.1 | 3 | 1 | 36 | 2.8 | F-box protein interaction domain protein |
| NCES-141 | miR5213-5p | Medtr6g084370.1 | 2 | 1 | 5 | 20 | disease resistance protein (TIR-NBS-LRR class) |
| NCES-141 | miR5213-5p | Medtr4g014580.1 | 1.5 | 1 | 18 | 5.6 | TIR-NBS-LRR class disease resistance protein |
| NCES-141 | miR5213-5p | Medtr6g088245.1 | 3 | 1 | 7 | 14.3 | disease resistance protein (TIR-NBS-LRR class) |
| NCES-141 | miR5238 | Medtr3g077740.2 | 2.5 | 1 | 151 | 0.7 | pantothenate kinase |
| NCES-141 | miR5561-3p | Medtr2g045295.1 | 3 | 1 | 9 | 11.1 | hypothetical protein |
| NCES-141 | miR5752b | Medtr8g066820.1 | 4 | 8 | 765 | 1.1 | PLATZ transcription factor family protein |
| NCES-141 | miR7696a-5p | Medtr1g072130.1 | 3 | 2 | 135 | 1.5 | PHD finger protein, putative |
| NCES-141 | miR7696c-5p | Medtr7g076830.1 | 3 | 5 | 78 | 6.4 | DEAD-box ATP-dependent RNA helicase-like protein |
| NCES-141 | miR7696d-5p | Medtr3g112250.1 | 3.5 | 9 | 44 | 20.5 | hypothetical protein |
| NCES-141 | miR7696c-3p | Medtr4g011600.2 | 3.5 | 1 | 124 | 0.8 | sulfate transporter-like protein |
| NCES-141 | miR7696c-3p | Medtr7g085650.4 | 3.5 | 1 | 10 | 10 | sulfate adenylyltransferase subunit 1/adenylylsulfate kinase |
| NCES-141 | miR7701-3p | Medtr3g108910.1 | 2.5 | 2 | 444 | 0.5 | hypothetical protein |