Table 2. Conserved miRNAs and their expression levels among different tissues.
| miRNAfamily | ReferencemiRNA | Sequence (5′–3′) | Length (nt) | Reads | ||||
| leaf | root | seed1 | seed2 | endosperm | ||||
| 156 | rco-miR156a | TGACAGAAGAGAGTGAGCAC | 20 | 115967 | 554938 | 20415 | 397950 | 259577 |
| rco-miR156b | TGACAGAAGAGAGTGAGCAC | 20 | 116382 | 555423 | 20532 | 398971 | 261537 | |
| rco-miR156c | TGACAGAAGAGAGTGAGCAC | 20 | 115967 | 554938 | 20414 | 397950 | 259577 | |
| rco-miR156d | TGACAGAAGAGAGTGAGCAC | 20 | 117010 | 555518 | 20426 | 398098 | 259709 | |
| rco-miR156e | TTGACAGAAGAGAGAGAGCAC | 21 | 1734 | 2320 | 819809 | 928064 | 912186 | |
| rco-miR156f | TTGACAGAAGATAGAGAGCAC | 21 | 4581548 | 2141241 | 170320 | 254303 | 517291 | |
| rco-miR156g | TTGACAGAAGATAGAGAGCAC | 21 | 4574207 | 2143679 | 169362 | 253236 | 517521 | |
| rco-miR156h | TTGACAGAAGATAGAGAGCAC | 21 | 4581205 | 2140983 | 170329 | 254302 | 517216 | |
| 159 | rco-miR159 | TTTGGATTGAAGGGAGCTCTA | 21 | 11246 | 8102 | 8950 | 4359 | 1711 |
| 160 | rco-miR160a | TGCCTGGCTCCCTGTATGCCA | 21 | 100 | 38 | 9 | 28 | 71 |
| rco-miR160b | TGCCTGGCTCCCTGTATGCCA | 21 | 93 | 80 | 8 | 28 | 71 | |
| rco-miR160c | TGCCTGGCTCCCTGAATGCCA | 21 | 63 | 0 | 4 | 22 | 37 | |
| 162 | rco-miR162 | TCGATAAACCTCTGCATCCAG | 21 | 1125 | 925 | 1682 | 866 | 713 |
| 164 | rco-miR164a | TGGAGAAGCAGGGCACGTGCA | 21 | 1792 | 5372 | 30683 | 448 | 2143 |
| rco-miR164b | TGGAGAAGCAGGGCACGTGCA | 21 | 1788 | 5256 | 30613 | 447 | 2141 | |
| rco-miR164c | TGGAGAAGCAGGGCACGTGCA | 21 | 1812 | 5269 | 30783 | 447 | 2150 | |
| rco-miR164d | TGGAGAAGCAGGGCACATGCT | 21 | 2 | 51 | 147 | 3 | 5 | |
| 166 | rco-miR166a | TCGGACCAGGCTTCATTCCCC | 21 | 1041527 | 630125 | 521438 | 192914 | 200808 |
| rco-miR166b | TCGGACCAGGCTTCATTCCCC | 21 | 1040582 | 629444 | 521029 | 192753 | 200683 | |
| rco-miR166c | TCGGACCAGGCTTCATTCCCC | 21 | 1044631 | 634097 | 533841 | 193804 | 201735 | |
| rco-miR166d | TCGGACCAGGCTTCATTCCCC | 21 | 1077411 | 712533 | 540960 | 199357 | 206911 | |
| rco-miR166e | TCGGACCAGGCTTCATTCCCC | 21 | 1040582 | 629429 | 521021 | 192738 | 200671 | |
| 167 | rco-miR167a | TGAAGCTGCCAGCATGATCTA | 21 | 25258 | 17649 | 72490 | 21432 | 32506 |
| rco-miR167b | TGAAGCTGCCAGCATGATCTAA | 22 | 199726 | 26315 | 657226 | 165097 | 258009 | |
| rco-miR167c | TGAAGCTGCCAGCATGATCTG | 21 | 15711 | 2542 | 10441 | 6967 | 7664 | |
| rco-miR167d* | TAAAGCTGCCAGCATGATCTA | 21 | 808 | 456 | 604 | 292 | 148 | |
| 168 | rco-miR168 | TCGCTTGGTGCAGGTCGGGAA | 21 | 64409 | 112339 | 19109 | 78883 | 52530 |
| 169 | rco-miR169a | CAGCCAAGGATGACTTGCCGG | 21 | 24 | 417 | 8 | 79 | 456 |
| rco-miR169b | CAGCCAAGGATGACTTGCCGG | 21 | 24 | 406 | 7 | 64 | 414 | |
| rco-miR169c | TGAGCCAAGGATGACTTGCCG | 21 | 22 | 200 | 6 | 3 | 31 | |
| rco-miR169d | CAGCCAAGGATGACTTGCCGA | 21 | 0 | 152 | 0 | 0 | 5 | |
| rco-miR169e | CAGCCAAGGATGACTTGCCGA | 21 | 0 | 152 | 0 | 0 | 0 | |
| rco-miR169f | CAGCCAAGGATGACTTGCCGA | 21 | 0 | 154 | 0 | 1 | 0 | |
| rco-miR169g | TAGCCAAGGATGACTTGCCTG | 21 | 0 | 0 | 0 | 0 | 9 | |
| rco-miR169h | TAGCCAAGGATGACTTGCCTG | 21 | 0 | 0 | 0 | 0 | 8 | |
| rco-miR169i | TAGCCAAGGATGACTTGCCCA | 21 | 0 | 0 | 0 | 0 | 5 | |
| rco-miR169j | TAGCCAAGGATGACTTGCCCG | 21 | 0 | 27 | 0 | 10 | 30 | |
| rco-miR169k | TAGCCAAGGATGACTTGCCCG | 21 | 0 | 19 | 0 | 8 | 20 | |
| rco-miR169l | TAGCCAAGGATGACTTGCCCA | 21 | 0 | 0 | 0 | 0 | 10 | |
| 171 | rco-miR171a | TGATTGAGCCGTGCCAATATC | 21 | 539 | 260 | 195 | 364 | 1274 |
| rco-miR171b | TGATTGAGCCGTGCCAATATC | 21 | 539 | 260 | 195 | 364 | 1274 | |
| rco-miR171c | TGATTGAGCCGTGCCAATATC | 21 | 511 | 268 | 193 | 374 | 1294 | |
| rco-miR171d | TGATTGAGCCGTGCCAATATC | 21 | 510 | 257 | 191 | 364 | 1261 | |
| rco-miR171e | TGATTGAGCCGTGCCAATATC | 21 | 516 | 435 | 241 | 432 | 1487 | |
| rco-miR171f | TGATTGAGCCGTGCCAATATC | 21 | 510 | 257 | 191 | 364 | 1261 | |
| rco-miR171g | TTGAGCCGCGCCAATATCACT | 21 | 4 | 107 | 6 | 5 | 0 | |
| rco-miR171h | TTGAGCCGCGTCAATATCTCC | 21 | 27 | 143 | 0 | 24 | 60 | |
| rco-miR171i | CGAGCCGAATCAATATCACTC | 21 | 2448 | 78 | 45 | 626 | 635 | |
| 172 | rco-miR172a | GGAATCTTGATGATGCTGCAG | 21 | 0 | 1 | 702 | 24 | 82 |
| rco-miR172b | AGAATCTTGATGATGCTGCAT | 21 | 16659 | 964 | 1160 | 2865 | 3119 | |
| rco-miR172c | AGAATCTTGATGATGCTGCAT | 21 | 16659 | 964 | 1160 | 2865 | 3119 | |
| rco-miR172d | AGAATCTTGATGATGCTGCAT | 21 | 16659 | 964 | 1160 | 2865 | 3119 | |
| 319 | rco-miR319a | TTGGACTGAAGGGAGCTCCC | 20 | 21 | 10 | 7 | 9 | 2 |
| rco-miR319b | TTGGACTGAAGGGAGCTCCC | 20 | 21 | 9 | 7 | 9 | 2 | |
| rco-miR319c | TTGGACTGAAGGGAGCTCCC | 20 | 22 | 21 | 8 | 9 | 2 | |
| rco-miR319d | TTGGACTGAAGGGAGCTCCTT | 21 | 0 | 10 | 1 | 4 | 1 | |
| 390 | rco-miR390a | AAGCTCAGGAGGGATAGCGCC | 21 | 308 | 6671 | 6698 | 246 | 554 |
| rco-miR390b | AAGCTCAGGAGGGATAGCGCC | 21 | 326 | 6759 | 6844 | 254 | 562 | |
| 393 | rco-miR393a | TCCAAAGGGATCGCATTGATCT | 22 | 31 | 8 | 76 | 101 | 135 |
| rco-miR393b | TCCAAAGGGATCGCATTGATCC | 22 | 24 | 7 | 35 | 8 | 21 | |
| 394 | rco-miR394a* | TTGGCATTCTGTCCACCTCC | 20 | 9 | 0 | 10 | 25 | 108 |
| rco-miR394b* | TTGGCATTCTGTCCACCTCC | 20 | 14 | 0 | 13 | 25 | 110 | |
| 395 | rco-miR395a | CTGAAGTGTTTGGGGGAACTC | 21 | 341 | 58 | 10 | 14 | 30 |
| rco-miR395b | CTGAAGTGTTTGGGGGAACTC | 21 | 341 | 58 | 10 | 14 | 30 | |
| rco-miR395c | CTGAAGTGTTTGGGGGAACTC | 21 | 337 | 58 | 10 | 13 | 30 | |
| rco-miR395d | CTGAAGTGTTTGGGGGAACTC | 21 | 336 | 58 | 10 | 13 | 30 | |
| rco-miR395e | CTGAAGTGTTTGGGGGAACTC | 21 | 341 | 58 | 10 | 14 | 30 | |
| 396 | rco-miR396a | TTCCACAGCTTTCTTGAACTT | 21 | 171 | 36 | 951 | 94 | 96 |
| rco-miR396b | TTCCACAGCTTTCTTGAACTG | 21 | 1859 | 1001 | 1088 | 579 | 1032 | |
| rco-miR396c | TTCCACAGCTTTCTTGAACTG | 21 | 1854 | 1005 | 1092 | 580 | 1035 | |
| 397 | rco-miR397 | TCATTGAGTGCAGCGTTGATG | 21 | 368 | 3350 | 509 | 582 | 237 |
| 398 | rco-miR398a | TTCTCAGGTCACCCCTTTGGG | 21 | 1 | 0 | 2 | 1 | 3 |
| rco-miR398b | TGTGTTCTCAGGTCGCCCCTG | 21 | 47 | 60 | 13 | 1 | 3 | |
| 399 | rco-miR399a | TGCCAAAGGAGAGTTGCCCTG | 21 | 177 | 16 | 34 | 70 | 95 |
| rco-miR399b | TGCCAAAGGAGATTTGCCCGG | 21 | 1 | 284 | 2 | 7 | 15 | |
| rco-miR399c | TGCCAAAGGAGATTTGCCCGG | 21 | 1 | 280 | 2 | 7 | 15 | |
| rco-miR399d | TGCCAAAGGAGAGCTGCCCTG | 21 | 0 | 1 | 1 | 1 | 0 | |
| rco-miR399e | TGCCAAAGGAGATTTGCC | 18 | 0 | 5 | 1 | 4 | 7 | |
| 403 | rco-miR403a | TTAGATTCACGCACAAACTCG | 21 | 761 | 309 | 368 | 2293 | 1061 |
| rco-miR403b | TTAGATTCACGCACAAACTCG | 21 | 761 | 309 | 368 | 2293 | 1061 | |
| 408 | rco-miR408 | CTGCACTGCCTCTTCCCTGGC | 21 | 77 | 250 | 243 | 94 | 69 |
| 482 | rco-miR482* | GGAATGGGCGGTTTGGGAAAG | 21 | 3467 | 178492 | 5481 | 2955 | 34179 |
| 535 | rco-miR535 | TGACAACGAGAGAGAGCACGC | 21 | 44477 | 37580 | 56970 | 27692 | 21852 |
| 827 | rco-miR827* | TTAGATGACCATCAACAAACA | 21 | 2338 | 132 | 86 | 15 | 201 |
| 2111 | rco-miR2111* | TAATCTGCATCCTGAGGTTTA | 21 | 180 | 0 | 132 | 109 | 153 |
| 4414 | rco-miR4414* | TATGAATGATGCGGGAGATAA | 21 | 3033 | 22022 | 60 | 1905 | 51 |
Note: *: New conserved miRNA in known miRBase in other species. The loci on genome were identified for six miRNAs newly identified in this study. rco-miR167d, 29883∶144402:144497:+; homologue: Arabidopsis thaliana miR167a; rco-miR394a,b, 30170∶3866594:3866721:+; 30116∶128336:128443:+; homologue: Arabidopsis thaliana miR394a,b; rco-miR482, 29586∶144986:145094:-; homologue: Malus domestica miR482a; rco-miR827, 28266∶68399:68502:+; homologue: Gossypium hirsutum miR827a; rco-miR2111, 29973∶58727:58830:+; homologue: Arabidopsis thaliana miR2111a; rco-miR4414, 29729∶702439:702549:+; homologue: Medicago truncatula miR4414b.