Table 4. Description, expression and putative target genes of novel miRNAs from the roots of Guiyan 1 (G) and Yunyan 2 (Y) treated with 50 μM Cd for 5 days.
| miRNA name | Sequence | Length (nt) | TPMa |
Fold changeb |
Target gene | Annotation | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| G − Cd | G + Cd | Y − Cd | Y + Cd | G | Y | |||||
| novel-miR1 | ATCATGCTATCCCTTTGGACT | 21 | 122.8 | 123.2 | 129.5 | 130.5 | 1.0 | 1.0 | TC156152 | CC-NBS-LRR protein (S. tuberosum) |
| TC156159 | ||||||||||
| AM844322 | ||||||||||
| TC166323 | ||||||||||
| FS375002 | ||||||||||
| novel-miR2 | GGAATGTTGTCTGGCTCGAGG | 21 | 37.5 | 37.5 | 41.4 | 39.6 | 1.0 | 0.0 | TC141351 | Guanine nucleotide-binding protein subunit beta-2 (N. tabacum) |
| TC144685 | ||||||||||
| TC147733 | ||||||||||
| novel-miR3 | CTAGAACTCCAGCATAATATACT | 23 | 9.8 | 10.1 | 10.4 | 9.8 | 1.0 | −0.1 | TC126710 | EBP6 (N. tabacum) |
| novel-miR4 | TCCACATCCTTGTTGATAACTG | 22 | 9.1 | 8.8 | 9.7 | 9.1 | 0.0 | −0.1 | TC123427 | EIL5 (N. tabacum) |
| FG137480 | ||||||||||
| TC126725 | ||||||||||
| FG163120 | ||||||||||
| novel-miR5 | TTGTGAGACAAAAAGAAGCCT | 21 | 6.2 | 6.4 | 6.6 | 6.5 | 1.0 | 0.0 | TC127378 | G6PD (N. tabacum) |
| novel-miR6 | TCCAAAGGGATCGCATTGATC | 21 | 5.5 | 5.8 | 5.5 | 5.7 | 0.9 | 1.0 | TC133182 | Transport inhibitor response 1 (G. hirsutum) |
| TC148720 | ||||||||||
| novel-miR7 | ATTTGGTCTAGTGGTATGATTCT | 23 | 4.3 | 4.4 | 4.7 | 4.6 | 1.0 | 0.0 | TC122895 | CYP (N. tabacum) |
| TC125350 | ||||||||||
| FG640560 | ||||||||||
| novel-miR8 | TTGGTGATATTTCTTCGGATT | 21 | 4.0 | 5.2 | 4.1 | 5.4 | 0.8 | 0.8 | TC123057 | Villin 2 (N. tabacum) |
| TC131622 | ||||||||||
| novel-miR9 | TTCTTTTGGACAAGTAGCACC | 21 | 3.0 | 3.1 | 3.1 | 3.1 | 1.0 | 1.0 | AM810590 | DEAD-box ATP-dependent RNA helicase 37 (O. sativa) |
| novel-miR10 | CATAGCCAATCTTTGGAGCCT | 21 | 2.3 | 2.3 | 2.4 | 2.4 | 1.0 | 0.0 | TC124312 | ASR4 (S. lycopersicum) |
| TC146505 | ||||||||||
| EB428262 | ||||||||||
| TC127090 | DS2 protein (S. tuberosum) | |||||||||
| FS433531 | ||||||||||
| TC125178 | Abscisic stress ripening protein (S. chacoense) | |||||||||
| novel-miR11 | TATCGGTTTAGCTCTTATCGGGC | 23 | 1.5 | 1.5 | 1.6 | 1.7 | 1.0 | 0.9 | FG185054 | Expansin-like protein precursor (S. lycopersicum) |
| novel-miR12 | CTGGGTGGTGTAGTCGGTTATC | 22 | 1.4 | 1.4 | 1.6 | 1.6 | 1.0 | 1.0 | TC134073 | Extensin (N. tabacum) |
| TC145834 | ||||||||||
| TC169113 | ||||||||||
| DW002761 | ||||||||||
| novel-miR13 | TTAACTTTTGAACTTGGAACTCA | 23 | 1.2 | 1.3 | 1.4 | 1.2 | 0.9 | −0.1 | TC124856 | SGT1 (N. benthamiana) |
| TC161731 | ||||||||||
| FG142982 | ||||||||||
| novel-miR14 | GATACATGTGTCGCAGAAGACTT | 23 | 1.2 | 1.3 | 1.4 | 1.3 | 0.9 | −0.1 | TC130797 | CDC5-like protein (S. lycopersicum) |
| TC130688 | ||||||||||
| novel-miR15 | TGAAGAAGAATGAACTAGCACC | 22 | 1.1 | 1.1 | 1.2 | 1.2 | 1.0 | 1.0 | HS085450 | F28C11.9 (A. thaliana) |
| novel-miR16 | AATCCGAGCCCCACATTCATC | 21 | 0.9 | 1.0 | 0.9 | 0.9 | 0.9 | 1.0 | TC127696 | Phi-1 protein (N. tabacum) |
| novel-miR17 | CGTCTCCTTGATTGTGGTAGGC | 22 | 3.2 | 3.4 | 0.0 | 3.3 | — | ↑ | TC141992 | Actin-related protein 3 (N. tabacum) |
| FS430341 | ||||||||||
| novel-miR18 | AAGGATTCAAGGTAGAGCTGCTT | 23 | 1.8 | 1.9 | 0.0 | 1.1 | — | ↑ | TC126568 | IAA9 protein (N. tabacum) |
| TC151478 | ||||||||||
| novel-miR19 | TATTTGTAGGAAAAGGTTACCT | 22 | 1.5 | 0.0 | 1.7 | 0.0 | ↓ | ↓ | TC126513 | S-adenosyl-methionine-sterol-C-methyltransferase homolog (N. tabacum) |
| TC134252 | ||||||||||
| novel-miR20 | CAGGATAAGTATGTTGGAACTCC | 23 | 1.5 | 0.7 | 0.0 | 0.0 | — | — | FG155555 | Serine/threonine protein phosphatase (S. lycopersicum) |
| FG195049 | ||||||||||
| novel-miR21 | ACGAGGTTCGGACAAGTTGCA | 21 | 0.8 | 0.8 | 0.0 | 0.4 | — | ↑ | FG191056 | PttA (Petunia x hybrida) |
| novel-miR22 | CAACATGTGGAAGATCTTAGCA | 22 | 0.8 | 0.8 | 0.0 | 0.9 | — | ↑ | AM815929 | WRKY transcription factor (N. tabacum) |
| FG193928 | ||||||||||
| novel-miR23 | AACCAAGGATATGTAGGCAGCT | 22 | 0.8 | 0.0 | 0.0 | 0.0 | ↓ | — | TC123450 | Elongation factor 1-alpha (N. tabacum) |
| TC123811 | ||||||||||
| TC124472 | ||||||||||
| FG141704 | ||||||||||
| novel-miR24 | TCCAGCGGCTGGAAGAGCAC | 20 | 0.0 | 0.0 | 18.3 | 8.7 | — | — | TC128664 | Ethylene receptor ERS homolog (N. tabacum) |
| TC147271 | ||||||||||
| TC148676 | ||||||||||
| FS427700 | ||||||||||
| FS406072 | ||||||||||
| novel-miR25 | TATTATGCTGGACCGGTATACT | 22 | 0.0 | 0.0 | 3.6 | 0.0 | — | ↓ | FG162393 | EIL1 (Petunia x hybrida) |
| FG170485 | ||||||||||
| novel-miR26 | TGAGTGTGAGGCGTTGGATTGA | 22 | 0.0 | 2.8 | 3.1 | 3.0 | ↑ | — | TC131218 | Glucose-1-phosphate adenylyltransferase (N. tabacum) |
| TC140583 | ||||||||||
| TC123361 | ||||||||||
| TC129146 | ||||||||||
| novel-miR27 | CCGTCTCCTTGATTGTGGTAGG | 22 | 0.0 | 0.0 | 3.1 | 0.0 | — | ↓ | TC124278 | Cytochromes P450 (N. tabacum) |
| TC122897 | ||||||||||
| FG165245 | ||||||||||
| TC122880 | ||||||||||
| TC130596 | ||||||||||
| TC160946 | ||||||||||
| novel-miR28 | ATAATATACTGGAGATTGGAGCC | 23 | 0.0 | 0.0 | 0.9 | 0.4 | — | — | TC147905 | Extensin 1 (N. tabacum) |
| novel-miR29 | AGAGAGACTGTTTCCGATAGACC | 23 | 0.0 | 0.0 | 0.0 | 7.0 | — | ↑ | TC123392 | Eukaryotic initiation factor (N. tabacum) |
| TC124140 | ||||||||||
| EB440487 | ||||||||||
| FG190354 | ||||||||||
| TC122931 | ||||||||||
| novel-miR30 | GTGAGCATACCTGTCGGGACCC | 22 | 0.0 | 0.0 | 0.0 | 12.7 | — | ↑ | TC159027 | Vacuolar ATP synthase 16 kDa proteolipid subunit (N. tabacum) |
| TC124894 | ||||||||||
| TC127633 | ||||||||||
| TC123167 | ||||||||||
| TC127603 | ||||||||||
| TC138401 | ||||||||||
| TC167606 | ||||||||||
| FG633653 | ||||||||||
| FS406852 | ||||||||||
aTPM value indicates the expression level of miRNA; TPM 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. “↑” indicates only expressed in Cd-treated, “↓” only expressed in control, “—” not expressed in both conditions or unchanged. 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.