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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.
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BMC Genomics

ISSN: 1471-2164

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