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Table 2 Putative target genes of non-conserved miRNAs and miRNA candidates identified in Populus.

From: Conservation and divergence of microRNAs in Populus

miRNA Family

Populus Predicted Target

Homolog in Arabidopsis

Target Predicted Function

miRNA with target predicted in Populus with homolog in Arabidopsis

ptr-miR7000*

CX173939

At4g12800.1

Photosystem I reaction center subunit

ptr-miR7001

DT522234

At1g12230.1

Transaldolase ToTAL2

ptr-miR7002

TA2404_3696

At3g54190

Hypothetical protein

ptr-miR7006

TA2404_3696

At3g54190

Hypothetical protein

ptr-miR7007

Grail3.0035010701

At4g17980

No apical meristem (NAM)

 

EstExt_fgenesh4_pg.C_LG_II1399

At1g33060

Transcription factor (ANAC014)

ptr-miR7009-1

Eugene3.00060403

At2g41450

PAXIP1L protein

 

Fgenesh4_pg.C_LG_XII000915

At1g66350

Scarecrow transcription factor

ptr-miR7009-2

Eugene3.00060403

At2g41450

PAXIP1L protein

 

Fgenesh4_pg.C_LG_XII000915

At1g66350

Scarecrow transcription factor

ptr-miR7009-3

Eugene3.00060403

At2g41450

PAXIP1L protein

 

Fgenesh4_pg.C_LG_XII000915

At1g66350

Scarecrow transcription factor

ptr-miR7009-4

Eugene3.00060403

At2g41450

PAXIP1L protein

 

Fgenesh4_pg.C_LG_XII000915

At1g66350

Scarecrow transcription factor

ptr-miR7010

Gw1.X.2191.1

At3g12530

DNA replication protein-related

 

Gw1.41.327.1

At4g09350

DNAJ heat shock

ptr-miR7013

EstExt_Genewise1_v1.C_LG_V0549

At1g34190

No apical meristem (NAM)

 

Fgenesh4_pm.C_scaffold_29000148

At2g38250

DNA-binding protein-related

 

Eugene3.00110906

At1g53140

Dynamin family protein

 

EstExt_fgenesh4_pg.C_LG_II1399

At1g33060

Transcription factor (ANAC014)

 

EstExt_fgenesh4_pg.C_LG_XIV0205

At4g17980

Transcription factor (ANAC071)

ptr-miR7015

Fgenesh4_pg.C_LG_XVIII000967

At2g24300

Calmodulin-binding protein

 

Gw1.245.24.1

At5g36930

Toll-Interleukin-Resistance (TIR)

 

EstExt_Genewise1_v1.C_LG_XVIII0864

At5g11790

Ndr family protein

 

Eugene3.00190231

At4g27220

ATP binding

 

Gw1.245.9.1

At5g36930

TIR-NBS-LRR

 

Gw1.3272.9.1

At5g36930

TIR-NBS-LRR

 

Gw1.I.4710.1

At5g36930

TIR-NBS-LRR

 

Gw1.XI.1412.1

At5g36930

TIR-NBS-LRR

 

Gw1.XI.1580.1

At5g36930

TIR-NBS-LRR

ptr-miR7018

Grail3.0033032901

At2g45620

Nucleotidyltransferase

 

Fgenesh4_pg.C_LG_VIII001448

At5g43630

Nucleic acid binding

ptr-miR7021

Gw1.117.167.1

At5g36930

TIR-NBS-LRR class

ptr-miR7022

TA14145_3694

At5g41680.2

Putative senescence-associated

ptr-miR7023

CN519776

At5g15270.1

KH domain-containing protein

 

Eugene3.00041046

At5g15270

KH domain-containing protein

 

TA578_3690

At4g09350

Hypothetical protein

 

Fgenesh4_pg.C_scaffold_70000157

At3g06350

Dehydroquinate dehydratase

 

Gw1.41.327.1

At4g09350

DNAJ heat shock

 

Gw1.I.8684.1

At4g23740

Kinase protein

 

Gw1.X.2191.1

At3g12530

DNA replication protein Psf2

ptr-miR7024

EstExt_fgenesh4_pg.C_LG_IX0044

At1g76310

B-like cyclin

 

EstExt_fgenesh4_pg.C_LG_XVI0015

At5g47630

Acyl carrier family protein (ACP)

 

Grail3.0083002901

At5g49980

F-box

ptr-miR7025

DN496261

At3g19830

C2 domain-containing protein

ptr-miR7032

TA4511_293756

At3g05560.1

60S ribosomal protein

ptr-miR7033-1

Fgenesh4_pg.C_LG_III000186

At5g57010

Calmodulin-binding family protein

ptr-miR7033-2

Fgenesh4_pg.C_LG_III000186

At5g57010

Calmodulin-binding family protein

ptr-miR7033-3

Fgenesh4_pg.C_LG_III000186

At5g57010

Calmodulin-binding family protein

ptr-miR7033-4

Fgenesh4_pg.C_LG_III000186

At5g57010

Calmodulin-binding family protein

ptr-miR7034

Fgenesh4_pg.C_LG_XII000915

At4g08250

Scarecrow transcription factor

ptr-miR7035

Eugene3.00020435

At4g30720

Expressed protein

ptr-miR7036

Eugene3.00020435

At3g63390

Expressed protein

ptr-miR7040-1*

TA11116_113636

At4g27220.1

NBS-LRR type disease resistance

ptr-miR7040-2*

TA11116_113636

At4g27220.1

NBS-LRR type disease resistance

ptr-miR7041

CK096204

At5g53130.1

Cyclic nucleotide-gated channel C

 

TA14492_3694

At5g28450.1

Chlorophyll a-b binding 7

 

TA16704_3694

At1g80550

Hypothetical protein

 

TA20868_47664

At5g53130.1

Cyclic nucleotide-gated channel C

ptr-miR7042

CK092266

At5g27380.1

Glutathione synthetase

ptr-miR7044

TA1634_80863

At3g59480.1

Putative fructokinase 2

ptr-miR7046-1

EstExt_Genewise1_v1.C_1840054

At1g17860

Trypsin and protease inhibitor

ptr-miR7046-2

EstExt_Genewise1_v1.C_1840054

At1g17860

Trypsin and protease inhibitor

miRNA with annotated target predicted in Populus with no homolog in Arabidopsis

ptr-miR7005**

AJ777690

no

Polyphenol oxidase

 

Eugene3.00100932

no

Polyphenol oxidase

ptr-miR7012

CK110871

no

Hypothetical protein

ptr-miR7014**

AJ777690

no

Polyphenol oxidase

ptr-miR7016

AJ773830

no

Hypothetical protein

 

TA3964_3691

no

Ac1147-like protein

 

TA7847_3695

no

CDH1-D

ptr-miR7017

Gnl|PPLGI|CK106645

no

Hypothetical protein

ptr-miR7019

Gnl|PPLGI|TC19799

no

Histidine kinase like ATPase

ptr-miR7020

AJ773830

no

Hypothetical protein

 

TA3964_3691

no

Ac1147-like protein

 

TA7847_3695

no

CDH1-D [Gallus gallus (Chicken)]

ptr-miR7030

AJ777857

no

Polyphenol oxidase

 

DN483929

no

Polyphenol oxidase

 

TA14535_3695

no

Polyphenol oxidase

ptr-miR7037

TA12949_3694

no

Hypothetical protein ART3

miRNA with target predicted non-annotated in Populus with no homolog in Arabidopsis

ptr-miR7003

Gnl|PPLGI|TC35094

no

-

ptr-miR7004

BU871048

no

-

ptr-miR7014

Eugene3.89590001

no

-

ptr-miR7026

DN487711

no

-

ptr-miR7029-1

CV259704

no

-

 

CV259944

no

-

 

DT491789

no

-

ptr-miR7029-2

CV259704

no

-

 

CV259944

no

-

 

DT491789

no

-

ptr-miR7029-3

CV259704

no

-

 

CV259944

no

-

 

DT491789

no

-

ptr-miR7039

CV230379

no

-

ptr-miR7047

BU873871

no

-

  1. "-" indicates that no target was found in Populus. "no" indicates that no Arabidopsis homolog of the Populus target was found. Other target were found for some miRNAs, but they have no significant similarity either to Arabidopsis (*) or other plant (**) protein sequences.