Table 2.
The abundance of conserved bdi-miRNAs and their targets before and after cold treatment.
| miRNA | Target gene | Function | Ca | miRNAC/W | mRNA C/W |
De C/W |
|---|---|---|---|---|---|---|
| bdi-miR156 | Bradi4g34667.1 | Squamosa promoter binding protein |
0 | - | - | - |
| Bradi3g03510.1 | Squamosa promoter binding protein |
3 | - | ↓ | - | |
| Bradi1g26720.1 | Squamosa promoter binding protein |
3 | - | - | - | |
| Bradi2g59110.1 | Squamosa promoter binding protein |
0 | - | - | ↓ | |
| bdi-miR160 | Bradi3g06487.1 | Glucosyltransferase-like protein | 0 | - | ↑ | ↓ |
| Bradi1g33160.1 | Auxin response factor | 0 | - | - | ↑ | |
| Bradi5g15904.1 | Auxin response factor | 0 | - | - | - | |
| Bradi3g28950.1 | Auxin response factor | 0 | - | - | ↑ | |
| Bradi3g49320.1 | Auxin response factor | 0 | - | - | - | |
| bdi-miR164 | Bradi1g32660.1 | NAC domain-containing protein | 3 | - | - | - |
| Bradi3g46900.1 | NAC domain-containing protein | 2 | - | ↓ | ↑ | |
| Bradi4g02060.1 | NAC domain-containing protein | 0 | - | - | - | |
| bdi-miR166 | Bradi3g28970.1 | HD-ZIPIII transcription factor | 0 | - | - | - |
| bdi-miR167 | Bradi1g32547.1 | Auxin response factor | 0 | - | - | - |
| bdi-miR168 | Bradi1g29577.1 | Argonaute 1-like protein | 0 | - | ↓ | ↓ |
| Bradi3g05060.1 | Hydroxyphenylpyruvatedioxygenase | 0 | - | - | ↑ | |
| bdi-miR169 | Bradi4g01380.1 | Nuclear transcription factor | 0 | - | ↓ | - |
| Bradi3g57320.1 | Nuclear transcription factor | 0 | - | - | - | |
| Bradi1g11800.1 | Uncharacterized protein | 0 | - | - | - | |
| Bradi1g72960.1 | Nuclear transcription factor | 0 | - | ↓ | - | |
| bdi-miR171 | Bradi1g52240.1 | Scarecrow-like protein | 0 | - | ↓ | - |
| bdi-miR172 | Bradi5g24100.1 | APETALA-like protein | 0 | ↑ | - | - |
| Bradi2g37800.1 | APETALA-like protein | 0 | ↑ | ↓ | - | |
| Bradi1g03880.1 | APETALA-like protein | 0 | ↑ | ↓ | - | |
| Bradi1g30337.1 | APETALA-like protein | 0 | ↑ | ↓ | - | |
| bdi-miR393 | Bradi5g08680.1 | TIR1-like protein | 2 | ↑ | ↓ | ↑ |
| Bradi2g35720.1 | TIR1-like protein | 0 | ↑ | - | ↓ | |
| bdi-miR394 | Bradi2g59200.1 | F-Box protein | 0 | - | - | - |
| bdi-miR395 | Bradi1g09030.1 | ATP-sulfurylase-like protein | 0 | - | - | - |
| bdi-miR396 | Bradi3g44250.1 | Serine/threonine-protein kinase | 0 | ↑ | - | - |
| Bradi2g11230.1 | PTI1-like protein | 0 | ↑ | ↓ | - | |
| Bradi4g16450.1 | Uncharacterized protein | 0 | ↑ | ↓ | ↑ | |
| Bradi3g52547.1 | Uncharacterized protein | 0 | ↑ | ↑ | - | |
| Bradi3g57267.1 | Uncharacterized protein | 0 | ↑ | ↓ | ↑ | |
| Bradi1g12650.1 | Uncharacterized protein | 0 | ↑ | ↓ | ↑ | |
| Bradi3g51685.1 | Uncharacterized protein | 0 | ↑ | ↓ | ↑ | |
| Bradi1g50597.1 | Uncharacterized protein | 0 | ↑ | N | ↑ | |
| Bradi1g09900.1 | Uncharacterized protein | 0 | ↑ | ↓ | - | |
| bdi-miR528 | Bradi1g24125.1 | Uncharacterized protein | 0 | - | - | ↑ |
N: not detected. Ca: category of miRNA target identification. 0: >1 raw read at the position, abundance at position is equal to the maximum on the transcript, and there is only one maximum on the transcript; 1: >1 raw read at the position, abundance at position is equal to the maximum on the transcript, and there is more than one maximum position on the transcript; 2: >1 raw read at the position, abundance at position is less than the maximum but higher than the median for the transcript; 3: >1 raw read at the position, abundance at position is equal to or less than the median for the transcript; De: PARE reads for miRNA target degradation products. W: sequencing data for non-cold-treated samples. C: sequencing data for cold-treated samples.: no significant changes (log2 fold of change was between ±1.5) was identified after cold treatment;: obvious upregulation (log2 fold of change >1.5) was identified after cold treatment;: obvious downregulation (log2 fold of change < -1.5) was identified after cold treatment. Only conserved miRNAs identified in [57] were involved in the target identification analysis. The miRNA target identification was performed with DW and DC library. The results were confirmed by DW replicate and DC replicate library. To avoid repetition, targets were shown for different members of one miRNA family only when these members exhibited different tend of change in cold stress response. Otherwise, the targets were only shown for the whole miRNA family. No target was detected for miR169e. To reduce the possibility of including false targets in our analysis, miRNA targets not identified in the biological replicate libraries were excluded. The miRNA targets with <5 raw reads at the potential cleavage position were also excluded.