Table 2.
Degradome sequencing results from 7 day N-starved rice roots
| Roots sRNA-Seq reads (RP40M) | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| miRNA | -N_0d | -N_1d | -N_7d | Target transcript ID (Category) | PenaltyScore (≤5.0) | Description | Cleavage site (nt) | Cleaved reads (RPM) | Reads on cleavage site (%) | p-Value |
| Osa-miR156(a-j)-5p | 908,961.7 | 1,151,055 | 968,459.5 | Os02t0174100–01 (III) | 1 | SPL4 | 2231 | 0.41 | 2.28 | 1.1.E-02 |
| Os06t0663500–00 (0) | 1 | SPL11 | 759 | 15.52 | 34.32 | 1.4.E-03 | ||||
| Os06t0703500–03 (II) | 1 | SPL12 | 1095 | 3.55 | 26.71 | 3.1.E-03 | ||||
| Osa-miR156k-5p | 1099.9 | 2027.7 | 1218.8 | Os01t0922600–01 (0) | 0 | SPL2 | 630 | 85.88 | 76.18 | 1.4.E-03 |
| Os02t0139400–01 (II) | 1 | SPL3 | 1879 | 9.24 | 16.69 | 1.5.E-02 | ||||
| Os09t0507100–00 (0) | 0 | SPL18 | 1044 | 63.53 | 59.46 | 3.4.E-03 | ||||
| Osa-miR159(a-3p.2, b)-3p a | 21,468.9 | 12,155.8 | 8436 | Os06t0605600–01 (0) | 3.5 | GAMYBL1 | 414 | 18.57 | 68.28 | 5.6.E-04 |
| Os11t0569600–01 (0) | 5 | Receptor kinase-like protein, leucine-rich repeat-containing | 656 | 10.38 | 61.79 | 4.2.E-03 | ||||
| Osa-miR159(c, d)-3p a | 314.6 | 469.5 | 652.3 | Os03t0785800–01 (IV) | 3.5 | OsPCF6 | 1193 | 0.02 | 0.36 | 3.4.E-03 |
| Osa-miR159f-3p | 8930.5 | 6188 | 7552.9 | Os01t0812000–03 (0) | 2.5 | OsGAMYB | 1268 | 15.23 | 32.03 | 2.8.E-04 |
| Osa-miR160(a-d)-5p a | 7484.8 | 2521.3 | 2763.7 | Os02t0628600–01 (0) | 1 | ARF8 | 1411 | 515.20 | 84.3 | 2.8.E-04 |
| Osa-miR160e-5p | 7351.4 | 4602.3 | 5552.2 | Os04t0519700–01 (0) | 1 | ARF10 | 1496 | 110.12 | 90.26 | 2.8.E-04 |
| Os06t0685700–01 (0) | 1 | ARF18 | 2006 | 105.70 | 56.83 | 8.4.E-04 | ||||
| Os10t0479900–01 (0) | 1 | ARF22 | 1649 | 105.68 | 82.54 | 5.6.E-04 | ||||
| Osa-miR164(a, b, f)-5p | 24,702 | 21,252.1 | 15,538.9 | Os02t0579000–01 (0) | 2 | NAC1 | 752 | 11.70 | 20.54 | 1.7.E-03 |
| Os04t0460600–01 (II) | 2 | NAC2 | 923 | 10.74 | 20.03 | 4.1.E-03 | ||||
| Os06t0675600–01 (III) | 2 | NAC11 | 965 | 0.20 | 100 | 3.1.E-03 | ||||
| Osa-miR164d-5p a | 41,779.7 | 16,096 | 10,610.4 | Os04t0460600–02 (II) | 2 | NAC2 | 801 | 11.63 | 21.05 | 5.1.E-03 |
| Os12t0610600–01 (0) | 1 | NAC60 | 922 | 65.67 | 54.15 | 8.4.E-04 | ||||
| Osa-miR168(a-5p.1)-5p a | 183,169.3 | 64,155.2 | 26,233.1 | Os02t0672200–01 (0) | 5 | AGO1a | 616 | 17.94 | 17.62 | 4.7.E-03 |
| Os03t0687000–01 (III) | 5 | NPF2.4/OsPTR29 c | 1682 | 2.50 | 2.14 | 2.2.E-01 | ||||
| Os04t0566500–02 (0) | 5 | AGO1b | 708 | 3.71 | 9.88 | 3.4.E-03 | ||||
| Osa-miR169f-5p a | 3214.3 | 1219.4 | 761 | Os03t0411100–02 (II) | 3 | NF-YA2 | 1252 | 3.94 | 18.19 | 1.1.E-02 |
| Osa-miR169(n, o)-5p a | 2129 | 503.9 | 307.1 | Os03t0696300–02 (II) | 3 | NF-YA4 | 469 | 5.24 | 35.11 | 8.2.E-03 |
| Os12t0618600–01 (0) | 1.5 | NF-YA10 | 1188 | 45.75 | 58.28 | 1.4.E-03 | ||||
| Osa-miR169r-5p a | 2816.4 | 1375.9 | 556.9 | Os03t0174900–01 (III) | 4 | NF-YA1 | 1004 | 5.35 | 11.08 | 4.6.E-03 |
| Os03t0647600–01 (III) | 3.5 | NF-YA3 | 1729 | 4.12 | 10.12 | 6.1.E-03 | ||||
| Osa-miR171a-3p a | 10,020 | 3781.9 | 3301.6 | Os02t0663100–01 (0) | 1 | GRAS transcription factor | 1531 | 31.30 | 34.69 | 1.7.E-03 |
| Os06t0105350–00 (II) | 0.5 | Similar to Scarecrow-like 6 | 476 | 10.95 | 26.16 | 1.0.E-03 | ||||
| Osa-miR171i-3p a | 1172.8 | 705.1 | 396.7 | Os04t0555000–01 (II) | 1 | GRAS transcription factor | 1332 | 22.01 | 26.92 | 3.1.E-03 |
| Osa-miR172(a, d)-3p a | 520.8 | 227 | 568.4 | Os05t0121600–01 (III) | 2 | AP2/EREBP family transcription factor | 1423 | 5.10 | 1.95 | 3.1.E-03 |
| Osa-miR319(a-3p.2,b)-3p | 6489 | 3137 | 2180.1 | Os03t0785800–01 (0) | 1.5 | OsPCF6 | 1192 | 6.28 | 99.64 | 2.8.E-04 |
| Os07t0152000–00 (0) | 1.5 | TCP21 | 1265 | 24.95 | 45.95 | 5.6.E-04 | ||||
| Osa-miR393(a, b)-5p | 20,525.3 | 30,023.2 | 37,524.4 | Os04t0395600–02 (0) | 1 | Auxin signaling F-box 2 | 1789 | 8.38 | 62.37 | 1.1.E-03 |
| Os05t0150500–00 (0) | 1 | OsTIR1 | 1566 | 50.80 | 40.65 | 2.8.E-04 | ||||
| Osa-miR396(a, b)-5p a | 1622.8 | 866.8 | 803 | Os12t0484900–01 (0) | 4 | OsGRF7 | 743 | 15.18 | 86.51 | 8.4.E-04 |
| Osa-miR444(b.1,c.1)-3p | 110,596.5 | 92,299 | 126,685.4 | Os04t0461300–01 (II) | 0 | MADS27b | 1204 | 4.85 | 21.96 | 4.1.E-03 |
| Osa-miR444(b.2,c.2)-3p | 152,234.5 | 199,621.8 | 95,687.8 | Os02t0579600–00 (0) | 0 | MADS27a | 575 | 19.64 | 67.16 | 2.8.E-04 |
| Os04t0461300–01 (0) | 0 | MADS27b | 1210 | 10.77 | 48.76 | 1.1.E-03 | ||||
| Osa-miR444a.4-3p a | 242,647.4 | 197,955.4 | 91,760.7 | Os04t0304400–01 (0) | 5 | MADS25 c | 483 | 14.09 | 98.72 | 3.3.E-02 |
| Osa-miR1425-5p b | 120,499.8 | 100,180.7 | 90,360.7 | Os10t0167600–01 (II) | 5 | Similar to CPD photolyase | 870 | 5.05 | 30.41 | 1.8.E-02 |
| Os10t0495200–02 (III) | 4.5 | RF1 (PPR domain containing protein) | 1307 | 3.73 | 100 | 1.1.E-02 | ||||
| Os10t0495400–01 (III) | 4.5 | PPR domain containing protein | 118 | 4.14 | 29.45 | 1.2.E-02 | ||||
| Os10t0497300–01 (0) | 3.5 | PPR domain containing protein | 1319 | 5.87 | 55.36 | 2.8.E-04 | ||||
| Osa-miR3979-3p b | 131,109.3 | 216,357.6 | 110,742.2 | Os07t0513200–01 (0) | 5 | PPR domain containing protein | 768 | 4.26 | 95.89 | 2.8.E-02 |
aN-responsive miRNAs detected in small RNA-Seq
bmiRNAs whose primary transcripts are N-responsive in RNA-Seq
cPreviously non-annotated target genes