Skip to main content

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