Table 3. Description, expression and putative target genes of known miRNAs whose expression were unchanged in Yunyan 2 (Y) but up-regulated in Guiyan 1 (G) roots, or down-regulated (−) in Yunyan 2 (Y) but unchanged in Guiyan 1 (G) roots treated with 50 μM Cd for 5 days.
| Family name | miRNA name | Sequence | Length (nt) | TPMa |
Fold changeb |
Target gene | Annotation | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| G−Cd | G + Cd | Y−Cd | Y + Cd | G | Y | ||||||
| miR156 | nta-miR156g | UGACAGAAGAUAGAGAGCAC | 20 | 317.8 | 897.3 | 955.2 | 575.1 | 1.5 | −0.7 | TC152836 | Squamosa promoter binding like protein 12 (Oryza sativa) |
| nta-miR156i | UGACAGAAGAUAGAGAGCAC | 20 | 317.8 | 952.7 | 870.9 | 580.7 | 1.6 | −0.6 | |||
| miR169 | nta-miR169t | UAGCCAAGGAUGACUUGCCUU | 21 | 925.9 | 2908.5 | 1826.0 | 4490.4 | 1.7 | 1.3 | TC128216 | CCAAT-binding transcription factor subunit B (N. tabacum) |
| TC143413 | |||||||||||
| TC167045 | |||||||||||
| NP917237 | |||||||||||
| miR482 | nta-miR482c | UUUCCAAUUCCACCCAUUCCUA | 22 | 839.5 | 2476.3 | 962.2 | 2531.9 | 1.6 | 1.4 | TC125874 | Glucose-6-phosphate isomerase (S. lycopersicum) |
| TC131822 | |||||||||||
| nta-miR482d | UUCCCGACUCCCCCCAUACCAC | 22 | 13818.7 | 53137.0 | 36640.4 | 95327.1 | 1.9 | 1.4 | TC168260 | Cyclic nucleotide-gated calmodulin-binding ion channel (N. tabacum) | |
| miR6019 | nta-miR6019a | UACAGGUGACUUGUAAAUGUUU | 22 | 715.1 | 2459.1 | 1320.4 | 1770.4 | 1.8 | 0.4 | FS424154 | Avr9/Cf-9 rapidly elicited protein 4 (N. tabacum) |
| nta-miR6019b | UACAGGUGACUUGUAAAUGUUU | 22 | 677.1 | 2155.5 | 1116.7 | 1426.0 | 1.7 | 0.4 | |||
| miR6025 | nta-miR6025a | UACCAACAAUUGAGAUAACAUC | 22 | 894.8 | 3582.3 | 1524.0 | 2315.0 | 2.0 | 0.6 | TC135300 | Ubiquitin carrier protein (Nicotiana tabacum) |
| nta-miR6025b | UGCCAACUAUUGAGAUGACAUC | 22 | 666.8 | 2147.0 | 884.9 | 1614.2 | 1.7 | 0.9 | TC124063 | NTH23 protein (N. tabacum) | |
| nta-miR6025e | UGCCAAUUAUAGAGAUGACAUC | 22 | 739.3 | 2139.2 | 1179.9 | 1384.9 | 1.5 | 0.2 | TC123463 | N-ethylmaleimide sensitive fusion protein (N.tabacum) | |
| miR6158 | nta-miR6158b | AAGUUCGAUUUGUACGAAGGGC | 22 | 1402.6 | 3871.7 | 1474.9 | 3827.0 | 1.5 | 1.4 | TC122996 | Biotin carboxylase (N. tabacum) |
| nta-miR6158c | AAGUUCGAUUUGUACGAAGGGC | 22 | 1433.7 | 3949.0 | 1503.0 | 3964.5 | 1.5 | 1.4 | FG150962 | ||
| miR6161 | nta-miR6161d | UGAACUCCAGCAUAUUAUACU | 21 | 863.7 | 2632.0 | 1812.0 | 2213.5 | 1.6 | 0.3 | TC130660 | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (N. benthamiana) |
| TC142702 | |||||||||||
| TC167586 | |||||||||||
| miR159 | nta-miR159 | UUUGGAUUGAAGGGAGCUCUA | 21 | 49940.8 | 22774.7 | 41676.0 | 9735.2 | −1.1 | −2.1 | TC148124 | TGA10 transcription factor (N. tabacum) |
| TC154362 | |||||||||||
| EB446223 | |||||||||||
| FG172155 | |||||||||||
| miR319 | nta-miR319a | UUGGACUGAAGGGAGCUCCCU | 21 | 7914.7 | 5074.6 | 17565.2 | 3011.8 | −0.6 | −2.5 | TC150601 | SlTCP3 (S. lycopersicum) |
| nta-miR319b | UUGGACUGAAGGGAGCUCCCU | 21 | 8246.3 | 4740.4 | 16919.0 | 2893.1 | −0.8 | −2.6 | |||
| miR396 | nta-miR396a | UUCCACAGCUUUCUUGAACUG | 21 | 6356.6 | 4040.3 | 11174.0 | 2444.9 | −0.7 | −2.2 | TC131399 | Growth-regulating factors (N. tabacum) |
| AM814093 | |||||||||||
| TC144468 | |||||||||||
| miR6145 | nta-miR6145e | AUUGUUACAUGUAGCACUGGC | 21 | 18468.7 | 11841.6 | 16954.2 | 5620.0 | −0.6 | −1.6 | TC125028 | Ferrochelatase (N. tabacum) |
| TC140088 | |||||||||||
| FG637935 | |||||||||||
| miR6149 | nta-miR6149b | UUGAUACGCACCUGAAUCGGC | 21 | 22994.3 | 8633.4 | 23563.0 | 5245.0 | −1.4 | −2.2 | FS390832 | TCTR2 protein (S. lycopersicum) |
aTPM value = counts of this miRNA/ total counts of this sample × 1000000.
bFold change (Cd vs control) is log2N, log2N ≥ 1.5 are up-regulated, between 0 < |log2N| < 1.5 are unchanged and log2N ≤ −1.5 are down-regulated, p < 0.01. G − Cd, G + Cd, Y − Cd and Y + Cd correspond to hydroponically grown tobacco of the cultivars Guiyan 1 and Yunyan 2 grown in basic nutrition solution (BNS) or BNS + 50 μM Cd.