Skip to main content

Table 5 Potential miRNA target genes regulated during barley seed development

From: miRNA regulation in the early development of barley seed

EST smRNAs with perfect offset Degradome
ID Closest homolog Sp. E-score Cat. Family nb RPM-A RPM-B RPM-C RPM-A RPM-B RPM-C
  Transcription factors            
U21_18652 APETALA2-like protein tae 0.E + 00 I miR172 3 14.78 58.87 58.84 1.64 0.63 0.36
U21_19162 CBF (NF-YA2 homolog) osa 8.E-80 I miR169 2 4.10 1.49 0.78 1.02 0.30 1.60
U21_13817 CBF (NF-YA5 homolog) osa 4.E-29 I miR169 4 7.66 5.54 5.68 3.84 1.16 0.71
U21_8533 CBF (NF-YA9 homolog) tae 5.E-40 II miR169 2 4.10 1.49 0.78 7.38 2.41 3.48
U21_9757 NAC osa 1.E-126 I miR164 20 324.78 560.70 314.03 0.72 0.83 0.82
U21_3667 GAMyb protein hvu 0.E + 00 I miR159 5 6.44 4.46 3.35 6.07 6.84 2.28
U21_18637 SPL16 osa 6.E-83 I miR156 77 4418.37 8965.97 7953.70 1.48 0.03 0.21
U21_19856 SPL18 osa 2.E-52 I miR156 77 4418.37 8965.97 7953.70 2.00 1.06 0.14
U21_13717 DOF1 tae 1.E-154 II pot-miRNA 3 25.59 29.03 35.61 0.39 0.00 0.00
  Chloroplast functions            
U21_4432 RNP-A, chloroplastic osa 1.E-112 II pot-miRNA 1 1.37 1.08 0.77 1.18 0.17 0.00
U21_495 Carbonic anhydrase, chloro. osa 1.E-115 III pot-miRNA 1 1.64 1.08 1.16 0.26 0.40 1.56
U21_40749 Chlorophyll a-b binding prot. tae 3.E-40 II pot-miRNA 3 3.28 1.22 1.55 0.00 0.40 0.00
U21_1307 Ferredoxin, chloroplastic tae 1.E-54 III pot-miRNA 2 2.33 1.08 1.03 91.01 112.87 75.62
U21_6135 PGlcT ath 9.E-40 I pot-miRNA 1 0.41 0.68 0.10 0.53 8.32 8.46
  Phytohormone signalling            
U21_11104 VP1/ABI3 osa 4E-90 III miR516 2 2.05 6.08 6.19 0.00 0.00 0.78
U21_48909 ABI8 tae 1E-71 III pot-miRNA 5 15.06 15.53 22.71 0.00 0.20 0.00
U21_9888 GA 3-oxidase 1 hvu 0.E + 00 I pot-miRNA 7 145.90 168.22 129.92 0.00 0.23 0.14
U21_9040 GID1 hvu 1E-133 II pot-miRNA 8 3.83 37.94 114.57 0.49 0.07 0.00
U21_7409 TIR1 osa 9.E-231 III miR393 1 0.14 0.81 0.90 3.64 4.26 2.52
U21_12845 ARF1 (AtARF6-like) osa 1.E-119 I miR167 37 1424.78 2234.51 2583.93 3.91 1.82 2.63
U21_8147 ARF2 (AtARF6-like) osa 8.E-176 I miR167 37 1424.78 2234.51 2583.93 3.91 1.82 2.63
U21_19718 ARF3 (AtARF6-like) osa 1.E-116 I miR167 37 1424.78 2234.51 2583.93 3.91 1.82 2.63
U21_1664 ARF4 (AtARF2-like) osa 5.E-302 II tasiR-ARFs 8 299.60 129.61 36.00 0.82 0.13 0.00
U21_19004 ARF5 (AtARF3-like) osa 1E-56 II tasiR-ARFs 8 299.60 129.61 36.00 0.26 0.20 0.00
U21_24760 ARF6 (AtARF3-like) tae 1E-119 II tasiR-ARFs 8 299.60 129.61 36.00 1.12 0.50 0.00
U21_26602 ARF7 (AtARF3-like) tae 1E-124 III tasiR-ARFs 3 49.68 14.18 4.39 3.25 0.43 0.64
U21_22467 ACC oxidase osa 1E-24 II pot-miRNA 1 2.05 2.16 0.90 0.00 0.17 0.00
  Defence response            
U21_18842 OsMLA10-like osa 1E-47 I miR5071 23 651.63 537.46 257.39 0.98 0.40 0.00
U21_23305 OsMLA1-like osa 1E-72 III pot-miRNA 4 35.31 28.76 22.19 3.97 0.86 1.17
  1. List of 29 of the 96 potential miRNA targets identified in this study. The left part of the table shows ESTs predicted to be regulated through miRNA-mediated cleavage, their category of confidence (cat.), and their associated function according to homology with the closest annotated gene from one of the following species (sp.): Hordeum vulgare (hvu), Triticum aestivum (tae), Oriza sativa (osa) or Arabidopsis thaliana (ath). Genes are arranged by functional group indicated by the headings in the closest homolog column. The middle part of the table shows the number (nb) of smRNAs matching the target with a perfect offset, the sum of their reads (in RPM) in each library and to which family they belong (pot-miRNA indicates when no match was found to a known or new miRNA identified in this study). The right part shows the number of degradome sequences (in RPM) resulting from the cleavage. The grey boxes indicate when the number of reads was significantly higher than the threshold.