Table 2.
Predicted conserved miRNAs with identified precursors from A. membranaceus.
| miRNA Family | miRNA Name | miRNA Sequence (5′-3′) | Length (nt) | Representative Homologous miRNA | Total Reads | Conservation in Other Plant Specie | |||
|---|---|---|---|---|---|---|---|---|---|
| gma | ath | ptc | osa | ||||||
| MIR156 | ame-miR156-1 | ugacagaagagagugagcac | 20 | gma-miR156u | 13,342 | ++ | + | + | + |
| ame-miR156-2 | ugacagaagagagagagcac | 20 | gma-miR156b | 10 | ++ | + | + | + | |
| ame-miR156-3 | uugacagaagauagagagcac | 21 | gma-miR156d | 45,036 | ++ | ++ | ++ | + | |
| ame-miR156-4 | ugacagaagauagagagcac | 20 | gma-miR156d | 603 | + | + | + | + | |
| MIR159 | ame-miR159-1 | uuuggauugaagggagcucua | 21 | gma-miR159a-3p | 40,206 | ++ | ++ | ++ | + |
| ame-miR159-2 | uuuggauugaagggagcu | 18 | gma-miR159a-3p | 135 | ++ | ++ | ++ | ++ | |
| ame-miR159-3 | uuuggacugaagggagcuccu | 21 | csi-miR159d | 88 | + | + | + | + | |
| ame-miR159-4 | uuggacugaaggggccucuu | 20 | gma-miR319f | 48 | ++ | + | + | + | |
| ame-miR159-5 | uuggacugaagggagcuccc | 20 | ath-miR319a | 1459 | ++ | ++ | ++ | + | |
| ame-miR159-6 | uggacugaagggagcuccuuc | 21 | gma-miR319q | 437 | ++ | + | + | + | |
| MIR160 | ame-miR160-1 | ugccuggcucccugaaugcca | 21 | mtr-miR160c | 261 | + | + | ++ | ++ |
| ame-miR160-2 | ugccuggcucccuguaugcca | 21 | gma-miR160a-5p | 2374 | ++ | ++ | ++ | ++ | |
| ame-miR160-3 | gcguaugaggagccaagcaua | 21 | gma-miR160a-3p | 127 | ++ | + | + | + | |
| MIR162 | ame-miR162-1 | ucgauaaaccucugcauccag | 21 | ath-miR162a-3p | 961 | ++ | ++ | ++ | ++ |
| ame-miR162-2 | ggaggcagcgguucaucgauc | 21 | csi-miR162-5p | 60 | + | + | + | + | |
| MIR164 | ame-miR164-1 | uggagaagcagggcacgugca | 21 | ath-miR164a | 1584 | ++ | ++ | ++ | ++ |
| ame-miR164-2 | caugugccccucuuccccauc | 21 | zma-miR164c-3p | 41 | + | + | |||
| MIR166 | ame-miR166-1 | ucggaccaggcuucauucccc | 21 | gma-miR166d | 71,955 | ++ | + | + | + |
| ame-miR166-2 | ucggaccaggcuucauucccg | 21 | gma-miR166j-3p | 8165 | ++ | ||||
| ame-miR166-3 | ucucggaccaggcuucauucc | 21 | gma-miR166k | 7665 | ++ | + | + | + | |
| ame-miR166-4 | ggaauguugucuggcucgagg | 21 | gma-miR166a-5p | 276 | ++ | + | + | ||
| ame-miR166-5 | ggaauguuguuuggcucgagg | 21 | gma-miR166h-5p | 162 | ++ | + | + | ||
| MIR167_1 | ame-miR167-1 | ugaagcugccagcaugaucuga | 22 | gma-miR167g | 6608 | ++ | + | + | + |
| ame-miR167-2 | ugaagcugccagcaugaucug | 21 | gma-miR167c | 3720 | ++ | ++ | ++ | ++ | |
| ame-miR167-3 | ugaagcugccagcaugaucua | 21 | gma-miR167a | 2600 | ++ | ++ | ++ | ++ | |
| ame-miR167-4 | gucaugcugugacagccucacu | 22 | cas-miR167b | 210 | + | ||||
| ame-miR167-5 | agaucauguggcaguuucacc | 21 | ahy-miR167-3p | 68 | ++ | + | |||
| MIR168 | ame-miR168-1 | cccgccuugcaucaacugaau | 21 | aly-miR168a-3p | 478 | ++ | ++ | + | |
| ame-miR168-2 | ucgcuuggugcaggucggga | 20 | gma-miR168a | 30 | ++ | ++ | ++ | + | |
| MIR169_2 | ame-miR169-1 | cagccaaggaugacuugccgg | 21 | gma-miR169a | 105 | ++ | ++ | ++ | ++ |
| ame-miR169-2 | ugagccagggaugacuugccgg | 22 | gma-miR169d | 12 | + | + | + | + | |
| ame-miR169-3 | ugagccaaggaugacuugccgg | 22 | gma-miR169d | 47 | ++ | + | + | + | |
| ame-miR169-4 | ugcagccaaggaugacuugcc | 21 | gma-miR169b | 39 | + | + | + | + | |
| ame-miR169-5 | ggcaaguuggccuuggcuau | 20 | zma-miR169r-3p | 4 | + | + | + | ||
| MIR171 | ame-miR171-1 | ugauugagccgugccaauauc | 21 | gma-miR171e | 1419 | ++ | + | ++ | ++ |
| ame-miR171-2 | uugagccgcgccaauaucacu | 21 | gma-miR171k-3p | 439 | ++ | + | + | + | |
| ame-miR171-3 | uugagccgugccaauaucac | 20 | gma-miR171i-3p | 87 | + | + | + | + | |
| ame-miR171-4 | uugagccgcgucaauaucuca | 21 | gma-miR171m | 1713 | ++ | + | + | + | |
| ame-miR171-5 | agguauuggcgcgccucaauu | 21 | osa-miR171i-5p | 5 | + | + | + | + | |
| ame-miR171-6 | cgauguuggugagguucaauc | 21 | gma-miR171k-5p | 40 | ++ | + | + | + | |
| MIR172 | ame-miR172-1 | agaaucuugaugaugcugcau | 21 | gma-miR172a | 1122 | ++ | ++ | ++ | ++ |
| ame-miR172-2 | ggagcaucaucaagauucaca | 21 | aly-miR172c-5p | 5 | + | + | ++ | + | |
| ame-miR172-3 | agaaucuugaugaugcugcag | 21 | ath-miR172c | 133 | + | ++ | + | + | |
| ame-miR172-4 | gcagcaucaucaagauucaca | 21 | csi-miR172b-5p | 6 | ++ | + | + | + | |
| MIR390 | ame-miR390-1 | aagcucaggagggauagcgcc | 21 | gma-miR390a-5p | 350 | ++ | ++ | ++ | ++ |
| ame-miR390-2 | cgcuauccauccugaguuuca | 21 | gma-miR390a-3p | 11 | ++ | ++ | + | + | |
| MIR394 | ame-miR394-1 | uuggcauucuguccaccucc | 20 | gma-miR394c-5p | 546 | ++ | ++ | ++ | ++ |
| MIR396 | ame-miR396-1 | uuccacagcuuucuugaacuu | 21 | gma-miR396b-5p | 6105 | ++ | ++ | ++ | ++ |
| ame-miR396-2 | guucaauaaagcugugggaag | 21 | gma-miR396i-3p | 1717 | ++ | ++ | + | ++ | |
| ame-miR396-3 | cucaagaaagcugugggaga | 20 | gma-miR396b-3p | 1313 | + | + | + | + | |
| ame-miR396-4 | cuuccacagcuuucuugaacug | 22 | gma-miR396a-5p | 523 | + | + | + | + | |
| MIR397 | ame-miR397-1 | ucauugagugcagcguugaug | 21 | gma-miR397a | 579 | ++ | ++ | ++ | ++ |
| MIR398 | ame-miR398-1 | uguguucucaggucaccccuu | 21 | gma-miR398a | 3826 | ++ | ++ | ++ | ++ |
| ame-miR398-2 | gggucguccugagaccacaug | 21 | bra-miR398-5p | 13 | + | + | + | ||
| ame-miR398-3 | uguguucucaggucgccccug | 21 | gma-miR398c | 666 | ++ | + | ++ | ++ | |
| ame-miR398-4 | ggagugaaucugagaacacaag | 22 | gma-miR398b-5p | 440 | + | + | |||
| MIR408 | ame-miR408-1 | augcacugccucuucccuggc | 21 | gma-miR408a-3p | 3496 | ++ | ++ | ++ | + |
| MIR477 | ame-miR477-1 | ucccucaaaggcuuccaguau | 21 | ppt-miR477c | 31 | + | + | ||
| MIR530 | ame-miR530-1 | ucugcauuugcaccugcacuu | 21 | stu-miR530 | 49 | + | + | + | |
| MIR858 | ame-miR858-1 | cucguugucuguucgaccuug | 21 | csi-miR858-3p | 15 | + | |||
| MIR1514 | ame-miR1514-1 | uuuucauuuuuaaaauaggca | 21 | gma-miR408a-3p | 10 | + | |||
| MIR2111 | ame-miR2111-1 | uaaucugcauccugagguuu | 20 | gma-miR2111b | 197 | ++ | + | + | |
| ame-miR2111-2 | uaaucugcauccugagguu | 19 | gma-miR2111b | 14 | + | + | + | ||
| ame-miR2111-3 | uaaucugcauccugaggugu | 20 | gma-miR2111b | 95 | + | + | + | ||
| ame-miR2111-4 | guccuugggaugcagauuacc | 21 | gma-miR2111a | 82 | + | + | + | ||
| MIR2118 | ame-miR2118-1 | uuaccgauuccacccaugccuc | 21 | mtr-miR2118 | 850 | + | + | + | |
| MIR4415 | ame-miR4415-1 | uugauucucaucacaacuugg | 21 | gma-miR4415a-3p | 1879 | + | |||
| ame-miR4415-2 | auguugugaugggaaucaaug | 21 | gma-miR4415b-5p | 50 | + | ||||
| MIR5083 | ame-miR5083-1 | agacuacaauuaucugaucaau | 22 | osa-miR5083 | 15 | + | |||
The abbreviations represent: gma, Glycine max; ath, Arabidopsis thaliana; ptc, Populus trichocarpa; osa, Oryza sativa; csi, Citrus sinensis; mtr, Medicago truncatula; zma, Zea mays; csa, Camelina sativa; ahy, Arachis hypogaea; aly, Arabidopsis lyrate; bra, Brassica rapa; ppt, Physcomitrella patens; stu, Solanum tuberosum. The plus symbols indicate: ++, miRNA sequences of A. membranaceus were exactly identical to those in other species; +, miRNA sequences of A. membranaceus were conserved in other species but have variations in some nucleotide positions.