Table S2. Sequences of miRNA or miRNA* and its variants isolated fromtwo hickory flower development stages (one or more nucleotides at 3′ends, based on the precursor sequences, were added for cca-miR159a, cca-miR164a, and cca-miR168a,and the 3' nucleotides added to these miRNAs in bold letters represent templated nucleotides; this table S1 does not include sequence variants with non-templated 3' additions)
Cca-miR156b
miRNA sequence(5'-3') / Reads / Normalized reads / RatioMF / AF / MF / AF / (AF/MF)
UUGACAGAAGAUAGAGAGCACU / 148 / 307 / 7.86 / 18.08 / 2.3
UUGACAGAAGAUAGAGAGCAC / 13,772 / 21,185 / 731.38 / 1247.6 / 1.71
UUGACAGAAGAUAGAGAGCA / 12 / 24 / 0.64 / 1.37 / 2.15
UUGACAGAAGAUAGAGAGC / 0 / 3 / 0 / 0.17 / X
UGACAGAAGAUAGAGAGCAC / 193 / 340 / 10.25 / 19.41 / 1.89
UGACAGAAGAUAGAGAGCA / 6 / 6 / 0.32 / 0.34 / 1.08
UGACAGAAGAUAGAGAGC / 0 / 1 / 0 / 0.06 / X
Cca-miR159a
miRNA sequence(5'-3') / Reads / Normalized reads / RatioMF / AF / MF / AF / (AF/MF)
UUUGGAUUGAAGGGAGCUCUAAAC / 3 / 1 / 0.16 / 0.06 / 0.36
UUUGGAUUGAAGGGAGCUCUAAA / 251 / 99 / 13.33 / 5.65 / 0.42
UUUGGAUUGAAGGGAGCUCUAA / 799 / 394 / 42.43 / 22.50 / 0.53
UUUGGAUUGAAGGGAGCUCUA / 17,950 / 13,276 / 953.25 / 781.83 / 0.82
UUUGGAUUGAAGGGAGCUCU / 675 / 531 / 35.85 / 30.32 / 0.85
UUUGGAUUGAAGGGAGCUC / 201 / 170 / 10.67 / 9.71 / 0.91
UUUGGAUUGAAGGGAGCU / 242 / 250 / 13.82 / 13.28 / 0.96
UUGGAUUGAAGGGAGCUCUA / 297 / 193 / 15.77 / 11.02 / 0.70
UUGGAUUGAAGGGAGCUCU / 11 / 7 / 0.58 / 0.40 / 0.68
UUGGAUUGAAGGGAGCUC / 6 / 2 / 0.32 / 0.11 / 0.36
UUGGAUUGAAGGGAGCU / 3 / 1 / 0.16 / 0.06 / 0.36
Cca-miR164a
miRNA sequence(5'-3') / Reads / Normalized reads / RatioMF / AF / MF / AF / (AF/MF)
UGGAGAAGCAGGGCACGUGCAAA / 4 / 4 / 0.21 / 0.23 / 1.08
UGGAGAAGCAGGGCACGUGCAA / 8 / 11 / 0.42 / 0.63 / 1.48
UGGAGAAGCAGGGCACGUGCA / 8,115 / 12,961 / 430.96 / 763.28 / 1.77
UGGAGAAGCAGGGCACGUGC / 25 / 54 / 1.33 / 3.08 / 2.32
UGGAGAAGCAGGGCACGUG / 2 / 14 / 0.11 / 0.80 / 7.53
UGGAGAAGCAGGGCACGU / 1 / 4 / 0.05 / 0.23 / 4.30
GGAGAAGCAGGGCACGUGCAA / 0 / 1 / 0.00 / 0.06 / X
GGAGAAGCAGGGCACGUGCA / 15 / 24 / 0.80 / 1.37 / 1.72
GGAGAAGCAGGGCACGUGC / 1 / 1 / 0.05 / 0.06 / 1.08
Cca-miR166a
miRNA sequence(5'-3') / Reads / Normalized reads / RatioMF / AF / MF / AF / (AF/MF)
UCGGACCAGGCUUCAUUCCCCC / 190 / 280 / 10.09 / 16.49 / 1.63
UCGGACCAGGCUUCAUUCCCC / 390,069 / 679,687 / 20715 / 40027.17 / 1.93
UCGGACCAGGCUUCAUUCCC / 1,713 / 4,361 / 90.97 / 249 / 2.74
UCGGACCAGGCUUCAUUCC / 1,341 / 1,814 / 71.22 / 103.57 / 1.45
UCGGACCAGGCUUCAUUC / 205 / 826 / 10.89 / 47.16 / 4.33
CGGACCAGGCUUCAUUCCCCC / 4 / 12 / 0.21 / 0.69 / 3.23
CGGACCAGGCUUCAUUCCCC / 533 / 910 / 28.31 / 51.96 / 1.84
CGGACCAGGCUUCAUUCCC / 4 / 21 / 0.21 / 1.2 / 5.64
Cca-miR166a*
miRNA sequence(5'-3') / Reads / Normalized reads / RatioMF / AF / MF / AF / (AF/MF)
GGAAUGUUGUCUGGCUCGAGG / 14,128 / 29,582 / 750.28 / 1,689.01 / 2.25
GGAAUGUUGUCUGGCUCGAG / 95 / 122 / 5.05 / 6.97 / 1.38
GGAAUGUUGUCUGGCUCGA / 7 / 11 / 0.37 / 0.63 / 1.69
GAAUGUUGUCUGGCUCGAGG / 35 / 52 / 1.86 / 2.97 / 1.60
GAAUGUUGUCUGGCUCGAG / 9 / 12 / 0.48 / 0.69 / 1.43
GAAUGUUGUCUGGCUCGA / 7 / 2 / 0.37 / 0.11 / 0.31
Cca-miR167a
miRNA sequence(5'-3') / Reads / Normalized reads / RatioMF / AF / MF / AF / (AF/MF)
UGAAGCUGCCAGCAUGAUCUAA / 25 / 42 / 1.33 / 2.47 / 1.86
UGAAGCUGCCAGCAUGAUCUA / 22,652 / 27,884 / 1202.96 / 1642.11 / 1.37
UGAAGCUGCCAGCAUGAUCU / 162 / 229 / 8.6 / 13.07 / 1.52
UGAAGCUGCCAGCAUGAUC / 26 / 33 / 1.38 / 1.88 / 1.36
UGAAGCUGCCAGCAUGAU / 3 / 7 / 0.16 / 0.4 / 2.51
GAAGCUGCCAGCAUGAUCUA / 9 / 16 / 0.48 / 0.91 / 1.91
GAAGCUGCCAGCAUGAUCU / 0 / 1 / 0 / 0.06 / X
Cca-miR168a
miRNA sequence(5'-3') / Reads / Normalized reads / RatioMF / AF / MF / AF / (AF/MF)
UCGCUUGGUGCAGGUCGGGAACUGA / 2 / 0 / 0.11 / 0.00 / 0.00
UCGCUUGGUGCAGGUCGGGAACUG / 45 / 32 / 2.39 / 1.83 / 0.76
UCGCUUGGUGCAGGUCGGGAACU / 6 / 12 / 0.32 / 0.69 / 2.15
UCGCUUGGUGCAGGUCGGGAAC / 63 / 72 / 3.35 / 4.11 / 1.23
UCGCUUGGUGCAGGUCGGGAA / 21,945 / 21,241 / 1165.411 / 1250.895 / 1.07
UCGCUUGGUGCAGGUCGGGA / 64 / 65 / 3.40 / 3.71 / 1.09
UCGCUUGGUGCAGGUCGGG / 1 / 1 / 0.06 / 0.16 / 2.67
CGCUUGGUGCAGGUCGGGAA / 16 / 19 / 0.85 / 1.08 / 1.28
CGCUUGGUGCAGGUCGGGA / 231 / 151 / 12.27 / 8.62 / 0.70
CGCUUGGUGCAGGUCGGG / 1 / 0 / 0.05 / 0.00 / 0.00
CGCUUGGUGCAGGUCGG / 2 / 3 / 0.11 / 0.17 / 1.61
Cca-miR171a
miRNA sequence(5'-3') / Reads / Normalized reads / RatioMF / AF / MF / AF / (AF/MF)
UGAUUGAGCCGUGCCAAUAUC / 3,718 / 7,761 / 197.45 / 457.05 / 2.31
UGAUUGAGCCGUGCCAAUAU / 7 / 11 / 0.37 / 0.63 / 1.69
UGAUUGAGCCGUGCCAAUA / 31 / 34 / 1.65 / 1.94 / 1.18
UGAUUGAGCCGUGCCAAU / 4 / 1 / 0.21 / 0.06 / 0.27
GAUUGAGCCGUGCCAAUAUC / 4 / 6 / 0.21 / 0.34 / 1.61
GAUUGAGCCGUGCCAAUAU / 2 / 0 / 0.11 / 0.00 / 0.00
GAUUGAGCCGUGCCAAUA / 1 / 0 / 0.05 / 0.00 / 0.00
Cca-miR171i
miRNA sequence(5'-3') / Reads / Normalized reads / RatioMF / AF / MF / AF / (AF/MF)
UGAUUGAGCCGUGCCAAUAUC / 3,671 / 7,644 / 194.95 / 450.16 / 2.31
UGAUUGAGCCGUGCCAAUAU / 7 / 11 / 0.37 / 0.63 / 1.69
UGAUUGAGCCGUGCCAAUA / 31 / 34 / 1.65 / 1.94 / 1.18
UGAUUGAGCCGUGCCAAU / 1 / 4 / 0.06 / 0.21 / 3.50
UGAUUGAGCCGUGCCAA / 1 / 3 / 0.05 / 0.17 / 3.23
GAUUGAGCCGUGCCAAUAUC / 3 / 1 / 0.16 / 0.06 / 0.36
GAUUGAGCCGUGCCAAUAU / 4 / 6 / 0.21 / 0.34 / 1.61
GAUUGAGCCGUGCCAAUA / 2 / 0 / 0.11 / 0.00 / 0.00
Cca-miR172c
miRNA sequence(5'-3') / Reads / Normalized reads / RatioMF / AF / MF / AF / (AF/MF)
AGAAUCUUGAUGAUGCUGCAU / 15,449 / 32,286 / 820.43 / 1901.34 / 2.32
AGAAUCUUGAUGAUGCUGCA / 20 / 43 / 1.06 / 2.46 / 2.31
AGAAUCUUGAUGAUGCUGC / 1 / 4 / 0.05 / 0.23 / 4.30
AGAAUCUUGAUGAUGCUG / 1 / 4 / 0.05 / 0.23 / 4.30
AGAAUCUUGAUGAUGCU / 1 / 1 / 0.05 / 0.06 / 1.08
GAAUCUUGAUGAUGCUGCAU / 5 / 10 / 0.27 / 0.57 / 2.15
GAAUCUUGAUGAUGCUGCA / 25 / 39 / 1.33 / 2.23 / 1.68
GAAUCUUGAUGAUGCUGC / 1 / 0 / 0.05 / 0.00 / 0.00
Cca-miR319a
miRNA sequence(5'-3') / Reads / Normalized reads / RatioMF / AF / MF / AF / (AF/MF)
UUGGACUGAAGGGAGCUCCC / 882 / 1,413 / 46.84 / 83.21 / 1.78
UUGGACUGAAGGGAGCUCC / 11 / 22 / 0.58 / 1.26 / 2.15
UUGGACUGAAGGGAGCUC / 13 / 19 / 0.74 / 1.01 / 1.36
UUGGACUGAAGGGAGCU / 10 / 10 / 0.53 / 0.57 / 1.08
UGGACUGAAGGGAGCUCCC / 0 / 35 / 0.00 / 2.00 / X
UGGACUGAAGGGAGCUCC / 0 / 1 / 0.00 / 0.06 / X
UGGACUGAAGGGAGCUC / 0 / 2 / 0.00 / 0.11 / X
Cca-miR319d
miRNA sequence(5'-3') / Reads / Normalized reads / RatioMF / AF / MF / AF / (AF/MF)
AUUGGACUGAAGGGAGCUCC / 116 / 82 / 6.160 / 4.829 / 0.78
AUUGGACUGAAGGGAGCUC / 17 / 13 / 0.90 / 0.74 / 0.82
AUUGGACUGAAGGGAGCU / 5 / 5 / 0.27 / 0.29 / 1.08
UUGGACUGAAGGGAGCUCC / 22 / 11 / 1.26 / 0.58 / 0.47
UUGGACUGAAGGGAGCUC / 19 / 13 / 1.01 / 0.74 / 0.74
UUGGACUGAAGGGAGCU / 1 / 1 / 0.05 / 0.06 / 1.08
Cca-miR393a
miRNA sequence(5'-3') / Reads / Normalized reads / RatioMF / AF / MF / AF / (AF/MF)
AUCAUGCUAUCCCUUUGGAUU / 145 / 232 / 7.70 / 13.66 / 1.77
AUCAUGCUAUCCCUUUGGAU / 2 / 3 / 0.11 / 0.17 / 1.61
AUCAUGCUAUCCCUUUGGA / 1 / 2 / 0.06 / 0.11 / 1.83
AUCAUGCUAUCCCUUUGG / 1 / 1 / 0.05 / 0.06 / 1.08
UCAUGCUAUCCCUUUGGAUU / 4 / 10 / 0.21 / 0.57 / 2.69
UCAUGCUAUCCCUUUGGAU / 0 / 14 / 0.00 / 0.80 / X
Cca-miR396c
miRNA sequence(5'-3') / Reads / Normalized reads / RatioMF / AF / MF / AF / (AF/MF)
GUUCAAUAAAGCUGUGGGAAG / 132 / 950 / 7.01 / 55.95 / 7.98
GUUCAAUAAAGCUGUGGGAA / 1 / 3 / 0.05 / 0.17 / 3.23
UUCAAUAAAGCUGUGGGAAGA / 17 / 151 / 0.90 / 8.62 / 9.55
UUCAAUAAAGCUGUGGGAAG / 9 / 113 / 0.48 / 6.45 / 13.50
UUCAAUAAAGCUGUGGGAA / 3 / 6 / 0.16 / 0.34 / 2.15
Cca-miRn1
miRNA sequence(5'-3') / Reads / Normalized reads / RatioMF / AF / MF / AF / (AF/MF)
UGUGAAUGAUGCGGGAGAUAAU / 5 / 11 / 0.27 / 0.65 / 2.44
UGUGAAUGAUGCGGGAGAUAA / 450 / 745 / 23.9 / 42.54 / 1.78
UGUGAAUGAUGCGGGAGAUA / 50 / 81 / 2.66 / 4.62 / 1.74
UGUGAAUGAUGCGGGAGAU / 13 / 18 / 0.69 / 1.03 / 1.49
UGUGAAUGAUGCGGGAGA / 1 / 2 / 0.05 / 0.11 / 2.15
GUGAAUGAUGCGGGAGAUAA / 0 / 2 / 0 / 0.11 / X
GUGAAUGAUGCGGGAGAUA / 1 / 0 / 0.05 / 0 / 0
Cca-miR160a
miRNA sequence(5'-3') / Reads / Normalized reads / RatioMF / AF / MF / AF / (AF/MF)
UGCCUGGCUCCCUGUAUGCCA / 621 / 6,046 / 32.980 / 356.05 / 10.80
UGCCUGGCUCCCUGUAUGCC / 5 / 19 / 0.27 / 1.08 / 4.09
UGCCUGGCUCCCUGUAUGC / 2 / 6 / 0.11 / 0.34 / 3.23
UGCCUGGCUCCCUGUAUG / 0 / 4 / 0.00 / 0.23 / X
UGCCUGGCUCCCUGUAU / 0 / 1 / 0.00 / 0.06 / 0.00
Cca-miR396e*
miRNA sequence(5'-3') / Reads / Normalized reads / RatioMF / AF / MF / AF / (AF/MF)
UUCCACAGCUUUCUUGAACUU / 166 / 1,584 / 8.82 / 90.44 / 10.26
UUCCACAGCUUUCUUGAACU / 1 / 13 / 0.05 / 0.74 / 13.98
UUCCACAGCUUUCUUGAAC / 1 / 10 / 0.05 / 0.57 / 10.75
UUCCACAGCUUUCUUGAA / 1 / 4 / 0.05 / 0.23 / 4.30
UUCCACAGCUUUCUUGA / 0 / 4 / 0.00 / 0.23 / X
Cca-miR172g
miRNA sequence(5'-3') / Reads / Normalized reads / RatioMF / AF / MF / AF / (AF/MF)
GGAAUCUUGAUGAUGCUGCAG / 72 / 159 / 3.82 / 9.36 / 2.45
GAAUCUUGAUGAUGCUGCAG / 1 / 1 / 0.05 / 0.06 / 1.08
AAUCUUGAUGAUGCUGCAG / 1 / 0 / 0.05 / 0.00 / 0.00
AUCUUGAUGAUGCUGCAG / 1 / 1 / 0.05 / 0.06 / 1.08
UCUUGAUGAUGCUGCAG / 0 / 1 / 0.00 / 0.06 / X