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Table 2 The abundance of conserved bdi-miRNAs and their targets before and after cold treatment.

From: A global profiling of uncapped mRNAs under cold stress reveals specific decay patterns and endonucleolytic cleavages in Brachypodium distachyon

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

-

-

↑

  1. 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.
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Genome Biology

ISSN: 1474-760X

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