Table 3. Predicted targets of novel miRNAs identified by small RNA deep sequencing in maize
miRNA
Predicted targets
Putative function of targets
miRC1
miRC4
GRMZM2G029833_T01
GRMZM2G171796_T01; GRMZM2G355906_T03;
GRMZM2G355906_T04
GRMZM2G053298_T01; GRMZM2G053298_T02;
GRMZM2G466549_T02; GRMZM2G140085_T01;
GRMZM2G140085_T02
GRMZM2G000039_T01 ; GRMZM2G304956_T01
DNA binding / DNA-directed RNA polymerase
Phosphofructokinase, putative; glutamate decarboxylase, putative
miRC5
miR171o,
miR171p
miRC9
GRMZM2G084248_T01; GRMZM2G318689_T01
miRC12
miRC13
AC215605.2_FGT007
GRMZM2G177110_T01; GRMZM2G467356_T01
miRC14
miRC16
GRMZM2G334899_T01
GRMZM2G000686_T01; GRMZM2G000686_T02
GRMZM2G000686_T03; GRMZM2G000686_T04
GRMZM2G000686_T05; GRMZM2G000686_T06
GRMZM2G000686_T07; GRMZM2G000686_T08
GRMZM2G000686_T09; GRMZM2G000686_T10
GRMZM2G165488_T01; GRMZM2G165488_T02
GRMZM2G165488_T03; GRMZM2G165488_T04
GRMZM2G091964_T01; GRMZM2G091964_T02
GRMZM2G091964_T03; GRMZM2G078124_T01
GRMZM2G418749_T01
GRMZM2G042347_T01; GRMZM2G056335_T01;
GRMZM2G071304_T01; GRMZM2G084942_T01;
GRMZM2G084942_T02; GRMZM2G088753_T01;
GRMZM2G405022_T01
AC194259.3_FGT001; GRMZM2G068519_T01;
GRMZM2G068519_T02; GRMZM2G162233_T01;
GRMZM2G162233_T02; GRMZM2G455075_T01
AC194587.2_FGT001
GRMZM2G307567_T02
miRC23
miR398c
miRC26
miRC30
miR171q
miRC32
miRC35
miRC36
AC234201.1_FGT003; GRMZM2G011947_T01;
GRMZM2G037792_T01; GRMZM2G051785_T01;
GRMZM2G060265_T01; GRMZM2G079470_T01;
GRMZM2G079980_T01; GRMZM2G098800_T01;
GRMZM2G098800_T02; GRMZM2G106748_T01;
GRMZM2G111191_T01; GRMZM2G111191_T02;
GRMZM2G418899_T01
GRMZM2G167253_T01
AC204517.3_FGT002; GRMZM2G137037_T01;
GRMZM2G137037_T02; GRMZM2G175995_T01;
GRMZM2G360081_T01
AC216801.3_FGT003; GRMZM2G031326_T01
RWP-RK domain-containing protein; GRAS family transcription
factor containing protein
SIT4 phosphatase-associated family protein; regulatory protein,
putative
Leucine-rich repeat transmembrane protein kinase, putative;
ethylene receptor, putative
Expressed protein
DUF260 domain containing protein, putative; ferredoxin 1-like
isoform 1, putative
Tubulin/FtsZ domain containing protein, putative
Nuclear transcription factor Y subunit; pentatricopeptide (PPR)
repeat-containing protein
Peroxidase, putative; cytokinin-O-glucosyltransferase 1, putative;
LIG1-putative DNA ligase I; arogenate dehydrogenase 1; 1,4alpha-glucan-branching enzyme; GDU1, putative
Expressed protein; UDP-glucoronosyl and UDP-glucosyl
transferase domain containing protein
Cycloartenol synthase, putative
CCR4-Not complex component, Not1domain containing protein
Prenylcysteine oxidase 1 precursor, putative; scarecrow, putative;
lipoxygenase, putative; zinc finger family protein, putative
Receptor-like protein kinase HAIKU2 precursor, putative
FAD dependent oxidoreductase, putative; expressed protein;
transcription factor binding / ubiquitin-protein ligase
DNA binding / transcription coactivator; nucleolar complex
protein, putative
Table 3. continued
miRNA
Predicted targets
Putative function of targets
miRC37
GRMZM2G030823_T01; GRMZM2G030823_T02 ;
GRMZM2G030823_T03; GRMZM2G090152_T02;
GRMZM2G390678_T01
GRMZM2G045421_T01; GRMZM2G102174_T01;
GRMZM2G102174_T02; GRMZM2G115390_T01;
GRMZM2G115390_T02; GRMZM2G115390_T03;
GRMZM2G115390_T04; GRMZM2G115390_T05;
GRMZM2G149175_T01; GRMZM2G149175_T03;
GRMZM2G149175_T06 ; GRMZM2G369939_T01
GRMZM2G030823_T01; GRMZM2G030823_T02;
GRMZM2G030823_T03; GRMZM2G061339_T01;
GRMZM2G399048_T01
GRMZM2G123805_T01
F-box, LRR and FBD domain containing protein; unknown
protein; GDSL-like lipase/acylhydrolase, putative
miRC40
miRC42
miRC46
PWWP domain containing protein; PWWP domain containing
protein, expressed; unknown protein; eIF-5, putative
F-box, LRR and FBD domain containing protein, expressed;
glycosyltransferase sugar-binding region containing DXD motif,
putative
Lipase/ nutrient reservoir