Table 3

Targets of P. trichocarpa miRNAs verified by degradome sequencing
miRNA Target transcript Category Cleavage Reads at Position Target annotation
Site Cleavage Penalty
Site Score
Ptc-miR156k POPTR_0013s06910.1 III 799 224 4 Glucose-6-phosphate/phosphate
Ptc-miR159a-c POPTR_0011s11490.1 III 428 153 4 Methionine sulfoxide reductase B 1
Ptc-miR159e POPTR_0006s16050.1 III 1014 134 4 Catalytic
Ptc-miR159f POPTR_0002s05060.1 III 372 99 4 Protein kinase
Ptc-miR164f POPTR_0007s12070.1 III 623 337 4 PS II oxygen-evolving complex 1
Ptc-miR164f POPTR_0005s13860.1 III 623 337 4 PS II oxygen-evolving complex 1
Ptc-miR166a-q POPTR_0009s01990.1/2 I 574 469 3 Transcription factor
Ptc-miR166a-q POPTR_0004s22090.1 I 563 766 2.5 Transcription factor
Ptc-miR167a-e POPTR_0012s09730.1 I 946 694 3.5 NOP56 (Arabidopsis homolog of
nucleolar protein)
Ptc-miR167f/g POPTR_0013s01580.1 II 285 239 4 Function unknown
Ptc-miR169z POPTR_0018s11310.1 III 2204 118 4 Eukaryotic translation initiation factor 4F
Ptc-miR171l-n POPTR_0003s06200.1 III 1615 89 3 Function unknown
Ptc-miR172a-c/f POPTR_0014s06330.1 III 799 110 4 Glycoprotease M22 family
Ptc-miR172d/e POPTR_0016s02570.1 III 103/172 1222 4 Function unknown
Ptc-miR172d/e POPTR_0001s44680.1 III 186 111 4 Apolipoprotein D-related
Ptc-miR172g/h POPTR_0001s44680.1 III 186 111 3.5 Apolipoprotein D-related
Ptc-miR172i POPTR_0015s13920.1 III 446 174 3.5 Chlororespiration reduction 1
Ptc-miR390a-d POPTR_0017s07350.1 II 2472 689 3.5 LOX2 (lipoxygenase 2)
Ptc-miR390a-d POPTR_0001s05330.1 II 2622 689 3.5 LOX2 (lipoxygenase 2)
Ptc-miR390a-d POPTR_0005s11640.1 III 9458 108 4 FAT domain-containing protein
Ptc-miR390a-d POPTR_0328s00200.1 II 2622 1180 3.5 LOX2 (lipoxygenase 2)
Ptc-miR396a/b POPTR_0004s18020.1/2 III 547 140 3.5 MYB4
Ptc-miR396f POPTR_0004s18020.1/2 III 547 140 3.5 MYB4
Ptc-miR397c POPTR_0002s01740.1 III 135 163 3.5 PETE1 (plastocyanin 1)
Ptc-miR397c POPTR_0009s05960.1 III 1660 104 4 Hydrolase
Ptc-miR398a POPTR_0010s06990.1/2 III 1428 346 4 DC1 domain-containing
Ptc-miR473a POPTR_0602s00210.1 I 850 327 4 VEP1 (vein patterning 1)
Ptc-miR475d POPTR_0003s20310.1/3 I 1898 544 4 Zinc finger (CCCH-type) family protein
Ptc-miR476a POPTR_0001s21140.1 III 145 137 3.5 Post-illumination chlorophyll
Fluorescence increase protein
Ptc-miR403a-c POPTR_0016s03150.1 III 637 156 4 Cytochrome p450
Ptc-miR403a-c POPTR_0016s03160.1 III 634 156 4 Cytochrome p450
Ptc-miR482.1 POPTR_0017s06100.1 I 1247 1312 3.5 UDP-glucosyl transferase
Ptc-miR482.1 POPTR_0009s13280.1 III 1036 94 4 Translation initiation factor
Ptc-miR482.1 POPTR_0010s13860.1 III 152 101 4 ATP-dependent Clp protease
Adaptor protein
Ptc-miR482.1 POPTR_0017s06080.1 I 914 1312 3.5 UDP-glucosyl transferase
Ptc-miR482.1 POPTR_0322s00200.1 I 1247 1312 3.5 UDP-glucosyl transferase
Ptc-miR482.1 POPTR_0017s06120.1 I 1010 1312 3.5 UDP-glucosyl transferase
Ptc-miR482.1 POPTR_0001s27260.1 III 1033 144 3.5 Carotenoid cleavage dioxygenase 1
Ptc-miR482.1 POPTR_0009s06530.1 III 1051 144 4 Carotenoid cleavage dioxygenase 1
Ptc-miR482.1 POPTR_0007s00550.1 III 337 228 4 NADP-dependent
Ptc-miR530b POPTR_0002s24070.1 III 424 104 4 Photosystem I subunit L
Ptc-miR1444a POPTR_0014s10790.1 III 2569 159 3.5 Preprotein translocase secA
Ptc-miR1444a POPTR_0014s11380.1 III 2368 135 3.5 Pentatricopeptide (PPR)
Ptc-miR1446a-e POPTR_0014s06190.1/2 II 677 511 4 Unfertilized embryo sac 10
Ptc-miR1446a-e POPTR_0001s34380.1/2 III 295 178 4 16S rRNA processing
Ptc-miR1446a-e POPTR_0011s13770.2 III 55 204 3.5 UBQ10 (Polyubiquitin 10)
Ptc-miRn6 POPTR_0001s11990.1/2/3 III 259 98 1 Function unknown
Ptc-miRn7 POPTR_0001s11990.1/2/3 III 259 98 0.5 Function unknown
Ptc-miRn7 POPTR_0014s01740.1/2 II 723 366 3.5 APT1 (Adenine phosphoribosyl
transferase 1)
Ptc-miRn8 POPTR_0001s40480.1 III 656 1443 4 Glycolate oxidase
Ptc-miRn13 POPTR_0018s08940.1 III 1605 116 4 Abnormal inflorescence meristem
Ptc-miRn26 POPTR_0016s00510.1 III 1233 265 4 Heat shock protein 81-4
Ptc-miRn30 POPTR_0002s07540.1 III 528 75 3.5 SKP2A (F-box protein)
Ptc-miRn32 POPTR_0014s16800.1 III 504 93 4 Beta-catenin repeat family protein
Ptc-miRn33 POPTR_0019s08960.1 III 3244 134 4 Function unknown
Ptc-miRn37 POPTR_0003s08800.1 III 585 108 4 Pentatricopeptide (PPR)
Ptc-miRn38 POPTR_0011s17280.1 III 584 170 4 PEX5 (Peroxin 5)
Signal-1 binding
Ptc-miRn40 POPTR_0001s07220.1 III 305 79 2 mTERF(mitochondrial transcription
termination factor family protein)
Ptc-miRn40 POPTR_0005s20140.1 III 1030 119 4 Thylakoidal ascorbate peroxidase
Ptc-miRn49 POPTR_0011s01280.1 III 791 90 4 Copper/zinc-superoxide
dismutase 2

‘Cleavage site’, the cleavage site location at the area of coding sequence; ‘Position penalty score’, the same penalty score as the prediction of new miRNA targets; ‘MFE’, minimum free energy of the stem loop structure. The bold font of transcripts indicates that they were identified by prediction.

Shuai et al.

Shuai et al. BMC Genomics 2013 14:233   doi:10.1186/1471-2164-14-233

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