Table 3.
Identified targets of known miRNAs in soybean
| miRNA | Target gene | Target annotation | Class | Abundance(TP10M) | cleavage site(nt) | target site location |
|---|---|---|---|---|---|---|
| gma-miR156 | Glyma04g37390# | SBP domain protein | I | 39 | 938 | 5'UTR |
| Glyma06g17700# | SBP domain protein | I | 39 | 1185 | CDS | |
| Glyma05g00200* | SBP domain protein | I | 42 | 1202 | CDS | |
| Glyma04g32070* | SBP domain protein | II | 42 | 130 | 3'UTR | |
| Glyma17g08840* | SBP domain protein | I | 42 | 1011 | CDS | |
| Glyma05g38180# | SBP domain protein | I | 33 | 1356 | CDS | |
| Glyma08g01450# | SBP domain protein | I | 33 | 1154 | CDS | |
| Glyma18g00890 | SBP domain protein | II | 75 | 249 | CDS | |
| Glyma12g27330 | SBP domain protein | II | 17 | 621 | 5'UTR | |
| Glyma11g36980 | SBP domain protein | II | 47 | 1223 | CDS | |
| Glyma02g30670 | SBP domain protein | I | 109 | 688/689 | CDS | |
| Glyma18g36960 | SBP domain protein | I | 14 | 723 | CDS | |
| Glyma02g13370 | SBP domain protein | I | 173 | 1219/1220 | CDS | |
| gma-miR159 | Glyma15g35860# | MYB family transcription factor | II | 27 | 937 | CDS |
| Glyma13g25720# | MYB family transcription factor | II | 27 | 838 | CDS | |
| Glyma20g11040 | MYB family transcription factor | I | 17 | 918 | CDS | |
| gma-miR160 | Glyma11g20490# | Auxin response factor | II | 134 | 1510 | CDS |
| Glyma10g35480# | Auxin response factor | I | 134 | 740 | CDS | |
| Glyma12g08110# | Auxin response factor | II | 134 | 1501 | CDS | |
| Glyma13g20370* | Auxin response factor | I | 177 | 1670 | CDS | |
| Glyma10g06080* | Auxin response factor | I | 177 | 1355 | CDS | |
| Glyma13g02410 | Auxin response factor | I | 74 | 1280 | CDS | |
| Glyma14g33730 | Auxin response factor | I | 29 | 1184 | CDS | |
| Glyma19g36570 | Auxin response factor | II | 807 | 652 | CDS | |
| Glyma04g43350 | Auxin response factor | II | 43 | 1337 | 5'UTR | |
| Glyma13g40030 | Auxin response factor | II | 67 | 1277 | CDS | |
| Glyma20g32040 | Auxin response factor | I | 19 | 1313 | CDS | |
| Glyma12g29720 | Auxin response factor | I | 25 | 1626 | CDS | |
| gma-miR162 | Glyma12g35400* | embryo-related protein | IV | 13 | 995 | CDS |
| Glyma13g35110* | embryo-related protein | IV | 13 | 963 | CDS | |
| gma-miR164 | Glyma17g10970# | NAC family transcription factor | I | 750 | 795 | CDS |
| Glyma05g00930# | NAC family transcription factor | II | 750 | 751 | CDS | |
| Glyma06g21020# | NAC family transcription factor | I | 750 | 741 | CDS | |
| Glyma04g33270# | NAC family transcription factor | I | 750 | 634 | CDS | |
| Glyma13g34950* | NAC family transcription factor | I | 153 | 747 | CDS | |
| Glyma12g35530* | NAC family transcription factor | II | 153 | 712 | CDS | |
| Glyma15g40510# | NAC family transcription factor | II | 34 | 730 | CDS | |
| Glyma08g18470# | NAC family transcription factor | II | 34 | 731 | CDS | |
| Glyma12g26190 | NAC family transcription factor | I | 87 | 778 | CDS | |
| miRNA | Target gene | Target annotation | Class | Abundance(TP10M) | cleavage site(nt) | target site location |
| gma-miR164 | Glyma06g35660 | NAC family transcription factor | I | 24 | 811 | CDS |
| gma-miR166 | Glyma15g13640#b | HD-ZIP transcription factor | II | 273 | 568/570 | CDS |
| Glyma08g21610#b | HD-ZIP transcription factor | II | 235 | 898 | CDS | |
| Glyma04g09000# | HD-ZIP transcription factor | II | 273 | 93-95 | CDS | |
| Glyma07g01950# | HD-ZIP transcription factor | II | 273 | 618/620 | CDS | |
| Glyma08g21620# | HD-ZIP transcription factor | II | 273 | 789/791 | CDS | |
| Glyma07g01940# | HD-ZIP transcription factor | II | 273 | 919/921 | CDS | |
| Glyma06g09100#b | HD-ZIP transcription factor | II | 273 | 567/569 | CDS | |
| Glyma05g30000* | HD-ZIP transcription factor | II | 59 | 1041 | CDS | |
| Glyma08g13110* | HD-ZIP transcription factor | II | 59 | 571 | CDS | |
| Glyma09g02750* | HD-ZIP transcription factor | II | 59 | 568 | CDS | |
| Glyma12g08080# | HD-ZIP transcription factor | II | 160 | 1239 | CDS | |
| Glyma11g20520# | HD-ZIP transcription factor | II | 160 | 605/607 | CDS | |
| gma-miR167 | Glyma15g09750* | Auxin response factor | II | 159 | 2444 | CDS |
| Glyma13g29320* | Auxin response factor | II | 159 | 3359 | CDS | |
| Glyma05g27580# | Auxin response factor | II | 86 | 2288 | CDS | |
| Glyma08g10550# | Auxin response factor | II | 86 | 2477 | CDS | |
| Glyma18g05330 | Auxin response factor | II | 54 | 2880 | CDS | |
| Glyma15g00770 | zinc finger family protein | I | 112 | 1815 | 5'UTR | |
| Glyma02g40650 | Auxin response factor | II | 76 | 2924 | CDS | |
| gma-miR168 | Glyma16g34300# | AGO protein | II | 74 | 534 | CDS |
| Glyma09g29720# | AGO protein | II | 74 | 409 | CDS | |
| gma-miR169 | Glyma08g45030* | NUCLEAR FACTORY | II | 31 | 1294 | 5'UTR |
| Glyma18g07890* | NUCLEAR FACTORY | I | 31 | 957 | CDS | |
| Glyma17g05920# | NUCLEAR FACTORY | I | 64 | 1262 | 5'UTR | |
| Glyma13g16770# | NUCLEAR FACTORY | II | 64 | 1022 | CDS | |
| Glyma09g07960* | NUCLEAR FACTORY | II | 33 | 931 | 5'UTR | |
| Glyma15g18970* | NUCLEAR FACTORY | II | 33 | 981 | 5'UTR | |
| Glyma19g38800 | NUCLEAR FACTORY | I | 23 | 1385 | 5'UTR | |
| gma-miR171 | Glyma08g08590# | polyubiquitin protein | IV | 13 | 195 | CDS |
| Glyma05g25610# | polyubiquitin protein | IV | 13 | 187 | CDS | |
| Glyma09g04950 | TCP family transcription factor | IV | 19 | 39 | 3'UTR | |
| gma-miR172 | Glyma19g35560* | heat shock cognate protein | IV | 47 | 282 | CDS |
| Glyma03g32850* | heat shock cognate protein | IV | 47 | 480 | CDS | |
| Glyma15g04930# | AP2 transcription factor | II | 425 | 1279 | CDS | |
| Glyma13g40470# | AP2 transcription factor | II | 348 | 1798 | CDS | |
| Glyma11g15650# | AP2 transcription factor | II | 425 | 1811 | 5'UTR | |
| Glyma12g07800# | AP2 transcription factor | II | 425 | 1763 | CDS | |
| Glyma01g39520* | AP2 transcription factor | II | 44 | 1709 | CDS | |
| Glyma11g05720* | AP2 transcription factor | II | 44 | 1777 | CDS | |
| Glyma19g36200# | AP2 transcription factor | II | 111 | 1447 | CDS | |
| Glyma03g33470# | AP2 transcription factor | II | 111 | 1243 | CDS | |
| miRNA | Target gene | Target annotation | Class | Abundance(TP10M) | cleavage site(nt) | target site location |
| gma-miR172 | Glyma17g18640 | AP2 transcription factor | III | 26 | 1973 | CDS |
| Glyma02g09600 | AP2 transcription factor | II | 78 | 1469 | CDS | |
| Glyma05g27370# | TCP family transcription factor | II | 109 | 922 | 5'UTR | |
| gma-miR319 | Glyma13g29160# | TCP family transcription factor | II | 112 | 2078 | CDS |
| Glyma08g10350# | TCP family transcription factor | II | 109 | 1172 | CDS | |
| Glyma15g09910# | TCP family transcription factor | II | 112 | 959 | CDS | |
| Glyma13g34690* | TCP family transcription factor | II | 195 | 656 | CDS | |
| Glyma12g35720* | TCP family transcription factor | II | 195 | 1223 | CDS | |
| Glyma14g06680# | Plasma membrane intrinsic protein | III | 49 | 935 | CDS | |
| Glyma02g42220# | Plasma membrane intrinsic protein | III | 49 | 1029 | 5'UTR | |
| Glyma13g36840* | TCP family transcription factor | II | 73 | 1220 | CDS | |
| Glyma12g33640* | TCP family transcription factor | II | 73 | 740 | CDS | |
| gma-miR390 | Glyma15g14670 | expressed protein | IV | 14 | 569 | CDS |
| gma-miR393 | Glyma03g36770# | Auxin signaling F-BOX protein | II | 65 | 1750 | CDS |
| Glyma19g39420# | Auxin signaling F-BOX protein | II | 65 | 1751 | CDS | |
| Glyma16g05500* | Auxin signaling F-BOX protein | II | 46 | 2279 | CDS | |
| Glyma19g27280* | Auxin signaling F-BOX protein | II | 46 | 2207 | CDS | |
| Glyma10g02630# | Auxin signaling F-BOX protein | IV | 14 | 2166 | CDS | |
| Glyma02g17170# | Auxin signaling F-BOX protein | IV | 14 | 1741 | CDS | |
| gma-miR394 | Glyma01g06230* | NADP+ | IV | 24 | 42 | CDS |
| Glyma06g01850* | NADP+ | IV | 24 | 588 | CDS | |
| gma-miR396 | Glyma03g02500# | Growth regulating factor | I | 57 | 550 | CDS |
| Glyma01g34650# | Growth regulating factor | I | 57 | 128 | CDS | |
| Glyma09g34560* | Growth regulating factor | I | 361 | 323 | CDS | |
| Glyma01g35140* | Growth regulating factor | II | 361 | 290 | CDS | |
| Glyma07g04290# | Growth regulating factor | II | 117 | 473 | CDS | |
| Glyma16g00970# | Growth regulating factor | I | 117 | 353 | CDS | |
| Glyma13g16920* | Growth regulating factor | I | 77 | 742 | CDS | |
| Glyma17g05800* | Growth regulating factor | I | 77 | 422 | CDS | |
| Glyma09g07990* | Growth regulating factor | II | 77 | 380 | CDS | |
| Glyma11g11820# | Growth regulating factor | I | 279 | 386 | CDS | |
| Glyma11g01060# | Growth regulating factor | II | 279 | 349 | CDS | |
| Glyma12g01730# | Growth regulating factor | II | 279 | 504 | CDS | |
| Glyma01g44470# | Growth regulating factor | I | 279 | 428 | CDS | |
| Glyma17g35090* | Growth regulating factor | II | 1007 | 913 | CDS | |
| Glyma17g35100* | Growth regulating factor | II | 1007 | 724 | CDS | |
| Glyma14g10090* | Growth regulating factor | II | 1007 | 704 | CDS | |
| Glyma04g40880 | Growth regulating factor | I | 46 | 233 | CDS | |
| Glyma06g13960 | Growth regulating factor | II | 46 | 831 | CDS | |
| Glyma13g22840 | Growth regulating factor | IV | 13 | 282 | 3'UTR | |
| Glyma14g10100 | Growth regulating factor | II | 373 | 711 | CDS | |
| Glyma15g19460 | Growth regulating factor | II | 69 | 347 | CDS | |
| miRNA | Target gene | Target annotation | Class | Abundance(TP10M) | cleavage site(nt) | target site location |
| gma-miR398 | Glyma15g13870 | MtN19-like protein | I | 15 | 172 | CDS |
| Glyma14g39910 | Serine-type endopeptidase | II | 87 | 1370 | CDS | |
| Glyma19g42890 | Copper/zinc superoxide dismutase | III | 30 | 174 | CDS | |
| gma-miR1509a | Glyma05g24110 | elongation factor | IV | 15 | 436 | CDS |
| gma-miR1511a | Glyma10g05580* | 60S ribosomal protein | II | 28 | 1220 | CDS |
| Glyma13g19930* | 60S ribosomal protein | III | 28 | 1318 | CDS | |
| gma-miR1514a | Glyma11g35820# | NSF attachment protein | IV | 13 | 651 | CDS |
| Glyma18g02590# | NSF attachment protein | IV | 13 | 615 | CDS | |
| Glyma07g05370 | NAC family transcription factor | II | 19 | 832 | CDS | |
| Glyma16g01940 | NAC family transcription factor | II | 25 | 844 | CDS | |
| Glyma16g01930 | NAC family transcription factor | I | 47 | 742 | CDS | |
| gma-miR1515a | Glyma12g00830 | Autophagy protein | III | 17 | 889 | CDS |
| gma-miR1516a | Glyma04g42690 | Disulfide isomerase | III | 33 | 1016 | CDS |
| gma-miR1522a | Glyma03g36390 | FAD linked oxidase family protein | III | 45 | 1826 | 5'UTR |
| gma-miR1523a | Glyma20g27950 | polyubiquitinated protein | IV | 114 | 864 | CDS |
| gma-miR1530a | Glyma10g32330# | Auxin inducible transcription factor | III | 24 | 79 | 3'UTR |
| Glyma20g35280# | Auxin inducible transcription factor | III | 24 | 445 | CDS | |
| Glyma09g41100 | expressed protein | II | 20 | 1324 | 5'UTR | |
| Glyma02g28890 | transketolase | III | 104 | 67 | CDS | |
| gma-miR1536a | Glyma19g06340# | ribulose-1,5-bisphosphate carboxylase | III | 108 | 795 | 5'UTR |
| Glyma19g06370# | ribulose-1,5-bisphosphate carboxylase | III | 108 | 668 | 5'UTR | |
| Glyma13g07610 | ribulose-1,5-bisphosphate carboxylase | III | 115 | 661 | 5'UTR | |
CDS: coding sequence; UTR: untranslated region; TP10M: transcripts per 10 million; Cleavage site: nucleotide number from 5' end of cDNA; Adjacent target genes with same # or * were matched by identical reads; alegume or soybean specific miRNAs; bMiRNA targets validated by RLM-5' RACE.