Table 2.
Identified miRNA families and their frequencies (reads per ten million [RPTM]) in whole plants, roots and shoots of three alfalfa genotypes (miRNA-stars were marked in bold)
| Whole plants | Roots | Shoots | ||||||
|---|---|---|---|---|---|---|---|---|
| Altet-4 | NECS-141 | NF08ALF06 | Altet-4 | NECS-141 | NF08ALF06 | Altet-4 | NECS-141 | |
| miR156-5p | 4712 | 7243 | 6436 | 1001 | 3466 | 3145 | 19,808 | 47,306 |
| miR156-3p | 3262 | 4012 | 2992 | 545 | 755 | 548 | 4634 | 6420 |
| miR159-3p | 6315 | 11,050 | 8484 | 3910 | 23,465 | 10,549 | 61,929 | 103,370 |
| miR160-5p | 225 | 417 | 351 | 20 | 277 | 113 | 3505 | 8706 |
| miR162-3p | 140 | 229 | 292 | 194 | 454 | 361 | 533 | 517 |
| miR164-5p | 108 | 275 | 306 | 6 | 77 | 57 | 48 | 431 |
| miR166-3p | 336,905 | 552,267 | 534,054 | 34,634 | 111,596 | 134,679 | 101,118 | 131,196 |
| miR166-5p | 544 | 960 | 614 | 228 | 508 | 438 | 800 | 1216 |
| miR167-5p | 218 | 470 | 722 | 107 | 240 | 357 | 699 | 1389 |
| miR167-3p | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| miR168-5p | 1121 | 1980 | 1691 | 735 | 2960 | 1317 | 3460 | 5049 |
| miR168-3p | 672 | 691 | 768 | 182 | 443 | 194 | 5550 | 5638 |
| miR169-5p | 19 | 34 | 35 | 47 | 55 | 35 | 46 | 59 |
| miR169-3p | 7 | 12 | 5 | 6 | 18 | 7 | 2 | 2 |
| miR171-3p | 51 | 120 | 232 | 44 | 238 | 316 | 60 | 85 |
| miR171e-5p | 26 | 39 | 44 | 22 | 37 | 42 | 7 | 6 |
| miR172-3p | 62 | 138 | 240 | 0 | 1 | 1 | 2 | 3 |
| miR172-5p | 3 | 8 | 20 | 1 | 1 | 2 | 2 | 2 |
| miR319-3p | 1631 | 3689 | 2101 | 1607 | 6281 | 3323 | 4330 | 10,864 |
| miR319-5p | 46 | 72 | 74 | 3 | 20 | 14 | 129 | 559 |
| miR390-5p | 95 | 410 | 318 | 86 | 656 | 234 | 121 | 382 |
| miR393-5p | 11 | 24 | 34 | 4 | 8 | 10 | 22 | 45 |
| miR395-3p | 3 | 8 | 7 | 12 | 13 | 7 | 2 | 0 |
| miR396-5p | 12,185 | 21,926 | 22,411 | 2835 | 14,549 | 8121 | 39,236 | 58,336 |
| miR396-3p | 250 | 437 | 437 | 76 | 312 | 188 | 323 | 356 |
| miR397-5p | 57 | 28 | 15 | 37 | 16 | 11 | 94 | 61 |
| miR398a-5p | 19 | 16 | 25 | 0 | 2 | 1 | 4 | 3 |
| miR398-3p | 3814 | 3223 | 2272 | 2101 | 4086 | 3176 | 35,538 | 26,478 |
| miR399-3p | 17 | 11 | 11 | 25 | 26 | 13 | 62 | 43 |
| miR408-3p | 2656 | 1301 | 1096 | 977 | 737 | 570 | 6380 | 2866 |
| miR408-5p | 17 | 7 | 12 | 12 | 14 | 8 | 55 | 35 |
| miR482-3p | 28 | 27 | 49 | 18 | 19 | 45 | 41 | 105 |
| miR482-5p | 7 | 10 | 10 | 11 | 19 | 13 | 9 | 12 |
| miR530-5p | 2 | 7 | 8 | 0 | 1 | 1 | 2 | 4 |
| miR1507–3 | 963 | 1789 | 1701 | 881 | 1596 | 1230 | 1778 | 3349 |
| miR1510-5p | 1959 | 4278 | 3520 | 523 | 3505 | 1429 | 12,496 | 34,705 |
| miR1510-3p | 96 | 151 | 167 | 52 | 118 | 63 | 256 | 617 |
| miR2111 | 47 | 20 | 10 | 44 | 15 | 42 | 278 | 22 |
| miR2118 | 5607 | 11,948 | 16,134 | 106 | 610 | 307 | 79,977 | 165,310 |
| miR2199 | 95 | 15 | 42 | 21 | 18 | 30 | 156 | 13 |
| miR2585 | 57 | 7 | 74 | 28 | 1 | 22 | 239 | 10 |
| miR2587 | 0 | 6 | 9 | 0 | 10 | 10 | 13 | 28 |
| miR2590 | 15 | 41 | 42 | 23 | 55 | 25 | 109 | 177 |
| miR2592 | 393 | 1350 | 395 | 119 | 1612 | 268 | 1224 | 1742 |
| miR2601-5p | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 |
| miR2603-5p | 0 | 8 | 1 | 1 | 1 | 1 | 5 | 24 |
| miR2629-5p | 2 | 5 | 4 | 1 | 3 | 7 | 2 | 5 |
| miR2632-5p | 0 | 1 | 0 | 0 | 0 | 0 | 1 | 18 |
| miR2634-3p | 5 | 3 | 7 | 6 | 4 | 15 | 9 | 6 |
| miR2643-3p | 1502 | 2689 | 2106 | 382 | 1462 | 948 | 9682 | 24,971 |
| miR2651-3p | 27 | 52 | 22 | 4 | 21 | 7 | 40 | 49 |
| miR2661-5p | 3 | 4 | 5 | 2 | 4 | 5 | 13 | 9 |
| miR2666-3p | 0 | 21 | 0 | 0 | 14 | 0 | 0 | 29 |
| miR2674-3p | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
| miR2678-3p | 2 | 6 | 4 | 0 | 4 | 4 | 4 | 12 |
| miR4414-3p | 2 | 4 | 4 | 0 | 1 | 1 | 3 | 7 |
| miR4414-5p | 1 | 3 | 4 | 1 | 1 | 0 | 5 | 7 |
| miR5037-5p | 4 | 3 | 13 | 3 | 8 | 24 | 2 | 4 |
| miR5204-3p | 4 | 10 | 6 | 3 | 28 | 17 | 6 | 10 |
| miR5205-5p | 7 | 22 | 14 | 0 | 6 | 6 | 15 | 6 |
| miR5207-5p | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 1 |
| miR5208-3p | 2 | 1 | 1 | 0 | 0 | 0 | 1 | 1 |
| miR5208d-5p | 0 | 0 | 1 | 0 | 1 | 0 | 1 | 1 |
| miR5211-5p | 432 | 85 | 23 | 559 | 71 | 41 | 292 | 59 |
| miR5213-5p | 801 | 836 | 887 | 181 | 891 | 829 | 1397 | 1379 |
| miR5214-3p | 63 | 155 | 153 | 97 | 414 | 452 | 153 | 201 |
| miR5225-5p | 4 | 2 | 8 | 3 | 1 | 8 | 1 | 1 |
| miR5230-5p | 1 | 2 | 1 | 0 | 1 | 0 | 6 | 1 |
| miR5231-5p | 10 | 7 | 7 | 3 | 11 | 1 | 43 | 69 |
| miR5232-5p | 67 | 253 | 419 | 56 | 503 | 417 | 602 | 3964 |
| miR5237-3p | 2 | 2 | 0 | 0 | 2 | 1 | 6 | 4 |
| miR5238-5p | 2 | 0 | 2 | 1 | 2 | 1 | 0 | 0 |
| miR5239-5p | 347 | 269 | 430 | 16 | 52 | 72 | 622 | 773 |
| miR5241-3p | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
| miR5243-3p | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
| miR5244-3p | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 1 |
| miR5248-5p | 0 | 2 | 1 | 0 | 2 | 1 | 0 | 3 |
| miR5255-3p | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 1 |
| miR5257-5p | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| miR5261-3p | 76 | 89 | 93 | 22 | 302 | 127 | 283 | 227 |
| miR5266-5p | 0 | 0 | 0 | 4 | 2 | 3 | 0 | 1 |
| miR5267-5p | 1 | 3 | 1 | 0 | 1 | 1 | 0 | 2 |
| miR5269-3p | 0 | 1 | 1 | 1 | 0 | 0 | 0 | 0 |
| miR5271-5p | 1 | 1 | 1 | 1 | 2 | 2 | 1 | 1 |
| miR5272-5p | 17 | 22 | 12 | 12 | 34 | 21 | 18 | 18 |
| miR5273-3p | 1 | 3 | 1 | 1 | 3 | 1 | 4 | 2 |
| miR5277-3p | 60 | 108 | 62 | 75 | 99 | 48 | 16 | 20 |
| miR5279-5p | 3 | 19 | 13 | 1 | 16 | 8 | 8 | 7 |
| miR5281-3p | 29 | 47 | 29 | 35 | 69 | 18 | 141 | 150 |
| miR5282-3p | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| miR5284-3p | 20 | 52 | 50 | 4 | 14 | 17 | 10 | 23 |
| miR5285-5p | 0 | 0 | 1 | 1 | 1 | 0 | 2 | 3 |
| miR5286-3p | 2 | 0 | 2 | 1 | 3 | 2 | 3 | 2 |
| miR5287-3p | 6 | 10 | 14 | 8 | 9 | 4 | 17 | 19 |
| miR5289-3p | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 |
| miR5290-3p | 0 | 5 | 1 | 1 | 2 | 1 | 2 | 6 |
| miR5291-3p | 0 | 1 | 1 | 0 | 3 | 1 | 0 | 1 |
| miR5292-3p | 16 | 35 | 21 | 6 | 34 | 21 | 53 | 82 |
| miR5294-3p | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
| miR5295-3p | 9 | 29 | 13 | 3 | 15 | 9 | 7 | 6 |
| miR5296-3p | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| miR5297-3p | 0 | 1 | 2 | 1 | 0 | 1 | 1 | 1 |
| miR5298-3p | 4 | 4 | 1 | 4 | 0 | 1 | 3 | 15 |
| miR5299-3p | 0 | 1 | 0 | 0 | 1 | 1 | 0 | 0 |
| miR5558-5p | 539 | 1938 | 1820 | 220 | 415 | 412 | 1103 | 1276 |
| miR5559-5p | 7 | 3 | 0 | 0 | 0 | 0 | 8 | 5 |
| miR5561-3p | 5 | 14 | 18 | 0 | 5 | 5 | 4 | 5 |
| miR5561-5p | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 |
| miR5743-5p | 19 | 113 | 6 | 0 | 1 | 1 | 70 | 398 |
| miR5744-5p | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 |
| miR5745-3p | 28 | 39 | 41 | 69 | 144 | 171 | 126 | 113 |
| miR5752-3p | 0 | 4 | 0 | 0 | 1 | 0 | 8 | 11 |
| miR5754-5p | 0 | 6 | 19 | 0 | 1 | 3 | 2 | 41 |
| miR7696-5p | 0 | 1 | 1 | 0 | 1 | 0 | 0 | 1 |
| miR7696-3p | 174 | 95 | 253 | 40 | 138 | 184 | 1173 | 255 |
| miR7701-3p | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |