Table 3.

Identified target transcripts of differentially expressed known miRNAs by degradome analysis of IFC and CFC ovaries.

Target mRNA	Annotationb	TF familyc	Cleavage position	Peak category		TPB
				IFC	CFC	IFC	CFC
CLASS Ia
miR159
GRMZM2G089361_T01	TCP family transcription factor	TCP	10	0	0	473	1199
3030GRMZM2G020805_T01	TCP family transcription factor	TCP	10	0	0	2542	2458
GRMZM2G028054_T01, T02, T03	myb domain protein	MYB	10	0	0	709	580
GRMZM2G015037_T01, T02	TCP family transcription factor	TCP	10	0	0	473	929
AC217264.3_FGT005	myb domain protein	MYB	10	0	0	650	240
miR160
GRMZM2G159399_T01	auxin response factor	ARF	10	0	0	52379	66723
GRMZM2G005284_T01	auxin response factor	ARF	10	1	0	177	120
miR164
GRMZM2G063522_T01	NAC domain containing protein	NAC	10	0	0	9932	12170
miR166
GRMZM2G038198_T01	Homeobox-leucine zipper protein		10	0	0	5819	7554
AC187157.4_FGT005	Homeobox-leucine zipper protein		10	0	0	709	899
miR169
GRMZM2G040349_T01, T02	nuclear factor Y	NF-YA	10	0	0	207	150
GRMZM2G000686_T01, T02, T03, T04, T05, T06, T08	nuclear factor Y	NF-YA	10	0	0	177	187
miR172
GRMZM2G076602_T01	DNA-binding protein	AP2	10	0	0	1064	480
miR393
GRMZM2G137451_T01,T02	auxin signaling F-box / AFB		10	0	0	276	520
miR396
GRMZM2G033612_T02	growth-regulating factor	GRF	11	0	0	10819	17865
GRMZM2G018414_T01, T02	growth-regulating factor	GRF	11	0	0	532	1529
GRMZM2G099862_T01, T02, T03, T04	growth-regulating factor	GRF	11	0	0	665	689
GRMZM2G041223_T01	growth-regulating factor	GRF	11	0	0	335	560
GRMZM2G034876_T01, T02, T03	growth-regulating factor	GRF	11	0	0	355	380
GRMZM2G129147_T01, T02	growth-regulating factor	GRF	11	0	0	2256	2987
CLASS II
miR159
GRMZM2G004090_T01	myb domain protein	MYB	10	2	0	118	210
GRMZM2G028054_T01, T02, T03	myb domain protein	MYB	10	2	2	117	240
miR160
GRMZM2G159399_T01	auxin response factor	ARF	10	2	2	946	1079
miR166
GRMZM2G552083_T01	Homeobox-leucine zipper protein		10	2	0	25	188
GRMZM2G123644_T01	agenet-containing protein		10	2	2	25	188
GRMZM2G336718_T01	agenet-containing protein		10	2	2	25	188
miR171
GRMZM2G051785_T01	GRAS transcription factor	GRAS	10	0	2	0	180
GRMZM2G110579_T01	GRAS transcription factor	GRAS	10	2	2	635	555
GRMZM2G037792_T01	GRAS transcription factor	GRAS	10	2	2	315	360
GRMZM5G825321_T01, T02	GRAS transcription factor	GRAS	10	2	2	296	360
miR393
GRMZM5G848945_T02	auxin signaling F-box / AFB		10	2	2	276	520
miR396
GRMZM2G067743_T01, T03	growth-regulating factor	GRF	11	2	0	39	160
GRMZM2G067743_T02	growth-regulating factor	GRF	11	1	0	39	160
Class III
miR159
GRMZM2G113073_T01	P21-Rho-binding domain		10	2	4	177	60
GRMZM2G127720_T01	—		10	4	0	59	0
AC217264.3_FGT005	myb domain protein	MYB	10	0	4	0	60
GRMZM2G070523_T01, T02, T03	myb domain protein	MYB	10	4	0	20	0
miR166
GRMZM2G003509_T01, T02	Homeobox-leucine zipper protein	HD-ZIP	10	3	2	25	231
miR169
GRMZM2G037630_T01	nuclear factor Y, subunit A6	NF-YA	10	4	0	59	120
miR171
GRMZM2G000039_T01	SIT4 phosphatase-associated protein		10	3	4	20	40
miR172
GRMZM5G856084_T01	DNAJ heat shock family protein		10	4	0	59	0
miR390
GRMZM2G121820_T01	Leucine-rich repeat family protein		10	0	4	0	20
GRMZM5G815009_T01, T02	Leucine-rich repeat family protein		10	0	4	0	20
miR396
GRMZM2G024293_T01, T03	P-loop nucleoside triphosphate hydrolases		10	3	3	59	90

A comprehensive list could be found in Supplementary Table S5.

^aClassification of the three different classes was made according to Karlova et al. (2013).

^bPutative functions were derived from Ensembl Plants (plants.ensembl.org, release 28).

^cTF family members were classified according to the Plant Transcription Factor Database v3.0 (Jin et al., 2013).

IFC, incompletely fused carpels; CFC, completely fused carpels; TPB, tags per billion.