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Table 6 Target genes of P-responsive miRNAs in soybean

From: Genome-wide identification of soybean microRNAs and their targets reveals their organ-specificity and responses to phosphate starvation

miRNA

Target gene

Target description

Cleavage site (nt)

Abundance

Target site location

    

(TP10M)

 

UP-regulated miRNAs by -Pi

m

Glyma20g37690.1

No annotationc

2526

 

CDS

miR166u

Glyma05g06070.1

Mybb

1806

 

CDS

miR169o

Glyma06g03940.1

Peptidase S24-likea

584

38.429

CDS

miR169q

Glyma18g07890.1

NF-YAb

949

 

CDS

miR396j

Glyma02g45340.1

LRR/NB-ARC domain/TIR domainb

710

 

CDS

 

Glyma10g00320.1

Protease family S9Bb

1252

 

CDS

 

Glyma12g28570.1

Core-2/I-Branching enzymeb

753

 

CDS

 

Glyma16g00260.1

Core-2/I-Branching enzymeb

711

 

CDS

 

Glyma17g35500.1

Syntaxin 6, N-terminalb

988

 

CDS

miR396k

Glyma12g01390.1

Cytokinin dehydrogenasec

730

 

CDS

miR397a

Glyma11g19150.1

Male sterility proteina

1484

34.8634

CDS

 

Glyma12g09270.1

Male sterility proteina

1475

34.8634

CDS

miR399a/b/c/d

Glyma10g04230.1

Phosphate transporterb

407

 

CDS

 

Glyma01g13410.1

AP2b

27

 

CDS

 

Glyma14g36650.1

Phosphate transporterb

240

 

CDS

 

Glyma13g31290.1

PHO2b

1050

 

5’UTR

miR399e

Glyma10g04230.1

Phosphate transporterc

407

 

CDS

 

Glyma13g31290.1

PHO2c

1050

 

5’UTR

miR408c

Glyma06g12680.1

Plastocyanin-like domaina

207

55.8606

CDS

 

Glyma08g13510.1

Plastocyanin-like domaina

198

18.224

CDS

miR1510b-5p

Glyma10g16090.1

PCI domain/eIF3 subunit 6 N terminal domainc

1451

 

3’UTR

miR1510d

Glyma11g04630.1

Domain of unknown function (DUF296)c

1152

 

3’UTR

miR482f

Glyma05g01650.1

PPRc

521

 

CDS

miR482g

Glyma05g01650.1

PPRc

521

 

CDS

miR482j

Glyma05g06070.1

Mybb

282

 

CDS

miR482k

Glyma05g06070.1

Mybb

282

 

CDS

miR482b-3p

Glyma09g39410.1

LRR/NB-ARC domain/leucine-rich repeat-containing proteinc

513

 

CDS

miR1512b

Glyma08g17790.1

D-mannose binding lectin/Domain of unknown function (DUF3403)b

1209

 

CDS

miR3508

Glyma06g42170.1

Protein of unknown function (DUF_B2219)/Polyphenol oxidase middle domainb

1048

 

CDS

 

Glyma07g31290.1

Protein of unknown function (DUF_B2220)/Polyphenol oxidase middle domainb

2569

 

CDS

 

Glyma07g31310.1

Protein of unknown function (DUF_B2221)/Polyphenol oxidase middle domainb

1117

 

CDS

 

Glyma13g25150.1

Polyphenol oxidase middle domain/Common central domain of tyrosinaseb

1096

 

CDS

 

Glyma13g25180.1

Protein of unknown function (DUF_B2219)/Polyphenol oxidase middle domainb

1025

 

CDS

 

Glyma13g25260.1

Protein of unknown function (DUF_B2220)/Polyphenol oxidase middle domainb

1199

 

CDS

 

Glyma15g07710.1

Protein of unknown function (DUF_B2221)/Polyphenol oxidase middle domainb

1077

 

CDS

miR4416a

Glyma10g06650.1

Uncharacterized nodulin-like proteinb

1544

 

CDS

miRnov_2

Glyma08g21620.1

START domaina

2712

19.0164

CDS

 

Glyma08g21620.2

START domaina

1892

13.8661

CDS

 

Glyma18g51750.1

LRR/NB-ARC domaina

1840

46.3525

CDS

miRnov_7

Glyma19g37520.1

Enolasea

755

904.8633

CDS

Down-regulated miRNAs by -Pi

miR159e-3p

Glyma13g25716.1

Myba

1340

97.459

CDS

 

Glyma15g35860.1

Myba

937

198.4836

CDS

miR169c

Glyma10g10240.1

NF-YAc,d

1174

 

3’UTR

miR169r

Glyma18g07890.1

NF-YAb

949

 

CDS

miR2109

Glyma16g29650.1

Heavy-metal-associated domaina

297

56.653

CDS

 

Glyma16g33950.1

Leucine-rich repeat-containing proteina

86

25.3552

CDS

 

Glyma16g33980.1

Plant basic secretory proteina

833

51.8989

CDS

 

Glyma16g34060.1

transmembrane receptor activitya

185

28.9208

CDS

 

Glyma16g34060.2

transmembrane receptor activitya

185

28.9208

CDS

miR3522

Glyma07g31270.1

Protein of unknown function (DUF_B2219)/Polyphenol oxidase middle domainc

418

 

CDS

miR4376a

Glyma09g36420.1

F-box/LRRc

1297

  

miRnov_5a

Glyma06g08730.1

No annotationa

681

60.2186

CDS

 

Glyma06g08730.2

No annotationa

926

60.2186

CDS

 

Glyma06g08730.4

No annotationa

968

318.9207

CDS

miRnov_5b

Glyma06g08730.1

No annotationa

681

60.2186

CDS

 

Glyma06g08730.2

No annotationa

926

60.2186

CDS

 

Glyma06g08730.4

No annotationa

968

318.9207

CDS

miRnov_6a

Glyma05g07780.1

DEAD/DEAH box helicasea

1019

19.8087

CDS

 

Glyma06g23290.1

DEAD/DEAH box helicasea

1036

19.8087

CDS

 

Glyma14g40680.1

EamA-like transporter familya

818

72.1038

CDS

 

Glyma17g13230.1

DEAD/DEAH box helicasea

268

47.9372

CDS

 

Glyma18g22940.1

DEAD/DEAH box helicasea

1005

19.8087

CDS

miRnov_9

Glyma05g00880.1

Sensor histidine kinase-relatedb

1165

 

CDS

 

Glyma04g39860.1

Peroxidaseb

260

 

CDS

 

Glyma06g15030.1

Peroxidaseb

256

 

CDS

miRnov_10

Glyma08g20840.1

Dof domain, zinc fingerb

1001

 

CDS

 

Glyma20g26290.1

Cyclinb

895

 

CDS

 

Glyma10g40990.1

Cyclinb

626

 

CDS

 

Glyma13g17410.1

CAAX amino terminal protease family alpha/beta hydrolase domain containingb

3678

 

CDS

  1. The potential targets of soybean P-responsive miRNAs in leaves and roots were predicted by degradome sequencing and computationally using Pairfinder and psRNAtarget. The Glycine max transcriptome is available in Phytozome (http://www.phytozome.org). For conserved miRNAs, homology of which can be found in other plant species apart from legume; for less-conserved miRNAs, homology of which can be found in legume (legume-specific); for novel miRNAs, which were not previously in miRBase and not assigned into any family were denoted by miRnov (soybean-specific).
  2. a: predicted from degradome;
  3. b: predicted with Pairfinder developed by BGI (http://www.bgi.cn);
  4. c: predicted from psRNAtarget (http://plantgrn.noble.org/psRNATarget/?function=3);
  5. d: experimentally confirmed target[20, 27, 28].
  6. AP2, AP2 domain protein; CDS: coding sequence; Cleavage site: nucleotide position in cDNA cleaved by miRNA from 5’ to 3’; Myb, Myb family of transcription factors; NF-Y, NUCLEAR FACTOR Y (also CCAAT, CCAAT-binding transcription factor); TP10M: transcripts per 10 million reads; UTR: untranslated region.