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Table 2 qRT-PCR analysis of predicted target genes for selected Mg-deficiency-responsive known miRNAs in C. sinensis roots

From: MicroRNA-mediated responses to long-term magnesium-deficiency in Citrus sinensis roots revealed by Illumina sequencing

miRNA

Fold change of miRNA

Accession

Homology

Target genes

Potential roles

Relative change of target genes

miR158

9.23711361**

orange1.1g022993m

AT5G62740.1

SPFH/Band 7/PHB domain-containing membrane-associated protein family

Stress response

0.73**

miR1222

−13.23073355**

orange1.1g037429m

AT4G27220.1

NB-ARC domain-containing disease resistance protein

Disease resistance protein

ND

miR2919

6.01101607**

orange1.1g002089m

AT3G14940.1

Phosphoenolpyruvate carboxylase 3

Carbohydrate metabolism

0.53**

miR3437

3.97352136**

orange1.1g040557m

AT1G56140.1

Leucine-rich repeat transmembrane protein kinase

Transmembrane signal transduction

0.65**

miR7821

4.13197145**

orange1.1g010745m

AT1G29760.1

Putative adipose-regulatory protein (Seipin)

Triacylglycerol accumulation and LD proliferation

0.95

miR394

−5.44692358**

orange1.1g000114m

AT1G20960.1

U5 small nuclear ribonucleoprotein helicase, putative

mRNA processing

1.48

miR414

3.01957377**

orange1.1g004767m

AT1G17980.1

Poly(A) polymerase 1

mRNA processing

0.76

  

orange1.1g006232m

AT1G17980.1

Poly(A) polymerase 1

mRNA processing

0.72**

miR418

2.16768709**

orange1.1g003146m

AT1G20780.1

Senescence-associated E3 ubiquitin ligase 1

Ubl conjugation pathway

0.78

miR6150

8.95879131**

orange1.1g009434m

AT5G62810.1

Peroxin 14

Protein import into peroxisome matrix, docking

3.91**

  

orange1.1g009573m

AT5G62810.1

Peroxin 14

Protein import into peroxisome matrix, docking

2.36*

  

orange1.1g018459m

AT3G28715.1

ATPase, V0/A0 complex, subunit C/D

ATP hydrolysis coupled proton transport

0.82

miR6278

8.85634619**

orange1.1g005896m

AT3G14470.1

NB-ARC domain-containing disease resistance protein

Disease resistance protein

1.63**

  

orange1.1g030696m

AT5G17840.1

DnaJ/Hsp40 cysteine-rich domain superfamily protein

Stress response

1.56**

miR1847

−2.21361107**

orange1.1g026316m

AT5G35530.1

Ribosomal protein S3 family protein

Translation

2.76**

  

orange1.1g026835m

AT5G35530.1

Ribosomal protein S3 family protein

Translation

1.84*

  

orange1.1g029201m

AT2G31610.1

Ribosomal protein S3 family protein

Translation

1.91

miR6028

−2.29912898**

orange1.1g005923m

AT2G33580.1

LysM-containing receptor-like kinase 5

Transmembrane signal transduction

0.67**

  

orange1.1g034040m

AT5G42990.1

Ubiquitin-conjugating enzyme 18

Protein ubiquitination

ND

  

orange1.1g021729m

AT4G29100.1

Basic helix-loop-helix (bHLH) DNA-binding superfamily protein

Transcription factor

ND

  

orange1.1g026539m

AT1G79020.1

Enhancer of polycomb-like transcription factor protein

Transcription regulation

ND

  

orange1.1g045123m

AT4G35800.1

RNA polymerase II large subunit

mRNA synthesis

ND

  

orange1.1g003175m

AT4G14700.1

Origin recognition complex 1

DNA synthesis and replication

0.57**

  

orange1.1g006076m

AT3G46790.1

Tetratricopeptide repeat (TPR)-like superfamily protein

 

6.01**

  

orange1.1g029970m

AT3G49940.1

LOB domain-containing protein 38

 

6.05**

  

orange1.1g028357m

AT2G45850.2

AT-hook motif nuclear-localized protein 9 (AHL9)

Transcription factor

6.12**

miR5176

4.58746604**

orange1.1g005789m

AT4G09140.1

MUTL-homologue 1

DNA mismatch repair

3.21**

  

orange1.1g008397m

AT4G09140.1

MUTL-homologue 1

DNA mismatch repair

2.87**

  

orange1.1g010846m

AT4G09140.1

MUTL-homologue 1

DNA mismatch repair

3.13**

  

orange1.1g012406m

AT4G09140.1

MUTL-homologue 1

DNA mismatch repair

5.39*

miR7121

4.74373348**

orange1.1g005267m

AT1G71400.1

Receptor like protein 12

Hormone-mediated signaling pathway

0.66**

  

orange1.1g005542m

AT1G71400.1

Receptor like protein 12

Hormone-mediated signaling pathway

0.77**

  

orange1.1g008628m

AT1G71400.1

Receptor like protein 12

Hormone-mediated signaling pathway

1.76**

  

orange1.1g002167m

AT5G27060.1

Receptor like protein 53

Hormone-mediated signaling pathway

5.01**

  

orange1.1g012980m

AT5G53390.1

O-acyltransferase (WSD1-like) family protein

Lipid and fatty-acid metabolism

0.86

  

orange1.1g013532m

AT5G53390.1

O-acyltransferase (WSD1-like) family protein

Lipid and fatty-acid metabolism

0.72**

  

orange1.1g027358m

AT5G03080.1

Phosphatidic acid phosphatase (PAP2) family protein

Dephosphorylation

0.53**

  

orange1.1g027353m

AT5G03080.1

Phosphatidic acid phosphatase (PAP2) family protein

Dephosphorylation

0.56**

miR6190

−3.61190068**

orange1.1g029300m

AT5G64200.1

Ortholog of human splicing factor SC35

SR protein

2.65**

  

orange1.1g017284m

AT5G34850.1

Purple acid phosphatase 26

Phosphate ion homeostasis

1.82**

  

orange1.1g002842m

AT4G01810.1

Sec23/Sec24 protein transport family protein

Intracellular protein transport

1.64**

miR6446

−3.77151631**

orange1.1g016909m

AT5G09300.1

Thiamin diphosphate-binding fold (THDP-binding) superfamily protein

Lipid and fatty-acid metabolism

3.23**

  

orange1.1g023827m

AT5G09300.1

Thiamin diphosphate-binding fold (THDP-binding) superfamily protein

Lipid and fatty-acid metabolism

2.56**

  

orange1.1g001557m

AT5G20280.1

Sucrose phosphate synthase 1F

C-compound and carbohydrate metabolism

3.51**

  

orange1.1g002665m

AT5G20280.1

Sucrose phosphate synthase 1F

C-compound and carbohydrate metabolism

3.93**

miR6485

−4.69704327**

orange1.1g001969m

AT5G20730.2

Transcriptional factor B3 family protein / auxin-responsive factor AUX/IAA-related

Transcription factor

1.41*

  

orange1.1g011274m

AT3G22810.1

Plant protein of unknown function (DUF828) with plant pleckstrin homology-like region

 

1.68**

  

orange1.1g031218m

AT1G07400.1

HSP20-like chaperones superfamily protein

Stress response

0.88

  

orange1.1g009779m

AT1G08960.1

Cation exchanger 11

Transport

0.57**

  

orange1.1g029454m

AT5G51160.1

Ankyrin repeat family protein

 

0.20**

  

orange1.1g013633m

AT1G28560.1

SnRNA activating complex family protein

Auxin signaling pathway

2.27**

  

orange1.1g017698m

AT1G28560.1

SnRNA activating complex family protein

Auxin signaling pathway

1.33**

  

orange1.1g042988m

AT5G62850.1

Nodulin MtN3 family protein

Transport

0.59**

  

orange1.1g007868m

AT1G72650.2

Myb family transcription factor TRFL6

Transcription factor

4.39**

  

orange1.1g046667m

AT2G38940.1

Phosphate transporter 1;4

Phosphate transport

0.91

  

orange1.1g001289m

AT1G14610.1

Valyl-tRNA synthetase / valine-tRNA ligase (VALRS)

Protein biosynthesis

1.75**

  

orange1.1g001303m

AT1G14610.1

Valyl-tRNA synthetase / valine-tRNA ligase (VALRS)

Protein biosynthesis

1.99**

  

orange1.1g001757m

AT1G14610.1

Valyl-tRNA synthetase / valine-tRNA ligase (VALRS)

Protein biosynthesis

1.11

  

orange1.1g024117m

AT2G47920.1

Kinase interacting (KIP1-like) family protein

 

0.21**

  

orange1.1g036588m

AT4G20140.1

Leucine-rich repeat transmembrane protein kinase

Transmembrane signal transduction

4.54*

  

orange1.1g003591m

AT5G05680.1

Nuclear pore complex protein NUP88

mRNA transport, protein transport

1.59*

miR1044

−5.19771615**

orange1.1g001378m

AT1G10170.1

NF-X-like 1

Protein ubiquitination

2.00**

  

orange1.1g001376m

AT1G10170.1

NF-X-like 1

Protein ubiquitination

2.61*

  

orange1.1g047796m

AT2G38380.1

Peroxidase superfamily protein

Stress response

1.97**

  

orange1.1g042193m

AT5G03340.1

ATPase, AAA-type, CDC48 protein

Cell cycle, cell division, protein transport, transport

4.02*

  

orange1.1g019546m

AT2G40340.1

Integrase-type DNA-binding superfamily protein

Abscisic acid signaling pathway

0.60**

miR5198

−5.36879795**

orange1.1g002063m

AT1G72180.1

Leucine-rich receptor-like protein kinase family protein

Transmembrane signal transduction

1.84**

miR5029

−5.99278869**

orange1.1g012168m

AT5G53450.1

OBP3-responsive gene 1

 

0.03**

  

orange1.1g026587m

AT4G31300.3

Proteasome subunit beta type-6 (PBA1)

Protein ubiquitination

2.26**

  

orange1.1g029964m

AT4G31300.3

Proteasome subunit beta type-6 (PBA1)

Protein ubiquitination

2.21**

  

orange1.1g030788m

AT4G31300.3

Proteasome subunit beta type-6 (PBA1)

Protein ubiquitination

2.91**

  

orange1.1g014625m

AT3G23510.1

Cyclopropane-fatty-acyl-phospholipid synthase

Lipid and fatty-acid metabolism

2.44**

  

orange1.1g018123m

AT3G44160.1

Outer membrane OMP85 family protein

Transmembrane transport

1.43*

miR5261

−6.08070339**

orange1.1g018132m

AT3G56930.1

DHHC-type zinc finger family protein

 

1.94**

  

orange1.1g010695m

AT3G12640.1

RNA binding (RRM/RBD/RNP motifs) family protein

mRNA processing

2.40**

  

orange1.1g011967m

AT3G12640.1

RNA binding (RRM/RBD/RNP motifs) family protein

mRNA processing

2.80**

  

orange1.1g031636m

AT1G67620.1

Lojap-related protein

 

2.41**

  

orange1.1g033883m

AT1G67620.1

Lojap-related protein

 

2.03**

  

orange1.1g004959m

AT5G66850.1

Mitogen-activated protein kinase kinase kinase 5

Intracellular signalling

1.97*

  

orange1.1g043928m

AT2G36110.1

Polynucleotidyl transferase, ribonuclease H-like superfamily protein

3′-5′ exonuclease activity

3.32**

  

orange1.1g037980m

AT2G36110.1

Polynucleotidyl transferase, ribonuclease H-like superfamily protein

3′-5′ exonuclease activity

2.17**

  

orange1.1g004713m

AT5G54260.1

DNA repair and meiosis protein (Mre11)

DNA damage, DNA repair, meiosis

4.47**

  

orange1.1g010785m

AT3G26020.2

Protein phosphatase 2A regulatory B subunit family protein

Intracellular signalling

2.01*

  

orange1.1g000012m

AT1G55860.2

Ubiquitin-protein ligase 1 (E3 ubiquitin-protein ligase UPL1)

Protein ubiquitination

2.05**

  

orange1.1g000013m

AT1G55860.2

Ubiquitin-protein ligase 1 (E3 ubiquitin-protein ligase UPL1)

Protein ubiquitination

2.82**

  

orange1.1g029528m

AT5G01520.1

RING/U-box superfamily protein

Protein ubiquitination

4.05*

  

orange1.1g029508m

AT1G22360.1

UDP-glucosyl transferase 85A2

Flavonoid biosynthetic process

1.99**

miR3438

−9.31063262**

orange1.1g000163m

AT1G55325.2

RNA polymerase II transcription mediators

 

2.29

miR1151

−10.44661802**

orange1.1g018149m

AT5G49610.1

F-box family protein

Protein ubiquitination

1.82*

  

orange1.1g018125m

AT5G49610.1

F-box family protein

Protein ubiquitination

2.69*

  

orange1.1g023739m

AT2G41870.1

Remorin family protein

 

4.00**

  

orange1.1g027436m

AT2G41870.1

Remorin family protein

 

2.11**

  

orange1.1g023033m

AT2G36690.1

2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein

Oxidoreductase

2.03*

  

orange1.1g026453m

AT1G17020.1

Senescence-related gene 1

Oxidoreductase

2.31**

  

orange1.1g020233m

AT2G36690.1

2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein

 

3.73*

  

orange1.1g037473m

AT5G07480.1

KAR-UP oxidoreductase 1

Oxidoreductase

1.92

miR6219

−11.91465055**

orange1.1g010903m

AT5G15130.1

WRKY DNA-binding protein 72

Transcription factor

1.65**

miR7708

−8.18079862**

orange1.1g023136m

AT1G06890.1

Nodulin MtN21 /EamA-like transporter family protein

 

2.14**

miR780

−12.80878923**

orange1.1g044623m

AT5G17230.2

Phytoene synthase

Carotenoid biosynthesis

2.15*

  

orange1.1g030826m

AT2G26560.1

Phospholipase A 2A

Lipid degradation

ND

  

orange1.1g004573m

AT4G27220.1

NB-ARC domain-containing disease resistance protein

Disease resistance

1.58**

miR160

10.33203655**

orange1.1g005482m

AT4G30080.1

Auxin response factor 16

Auxin signaling pathway

4.54*

  

orange1.1g004896m

AT2G28350.1

Auxin response factor 10

Auxin signaling pathway

22.94**

  

orange1.1g005075m

AT4G30080.1

Auxin response factor 16

Auxin signaling pathway

4.01**

  

orange1.1g008078m

AT1G77850.1

Auxin response factor 17

Auxin signaling pathway

2.90*

  1. The relative changes of target genes are the ratio of Mg-deficient to -sufficient roots. The value for relative change of target gene was a mean of three biological replicates with two technical replicates; Target genes that had the expected changes in mRNA levels were marked in bold; * and ** indicate a significant difference at P < 0.05 and P < 0.01, respectively. ND, not detected
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BMC Genomics

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