Table 2.

Enrichment of Pfam domains based on the preliminary functional characterization of most abundant differentially expressed gene families, which could be regulated by highly differentially expressed miRNAs.

Pfam ID	Pfam Description	Number of targeted genes models	Number of miRNAs
PF00560	Leucine Rich Repeat (LRR)	163	274
PF00069	Protein kinase domain	97	139
PF00931	NB-ARC (nucleotide-binding adaptor R-gene shared) domain	90	169
PF01535	Pentatricopeptide (PPR) repeat	84	105
PF01582	Toll-Interleukin receptor (TIR) domain	52	138
PF00004	ATPase family associated with various cellular activities (AAA)	52	85
PF00515	Tetratricopeptide (TPR) repeat	44	57
PF00637	Clathrin heavy chain/VPS (vacuolar protein sorting-associated)	30	40
PF00394	Multicopper oxidase	15	44
PF02536	mTERF (Mitochondrial transcription termination factor)	11	15
PF00646	F-box domain	11	11
PF00249	Myb-like DNA-binding domain	10	12
PF00847	AP2 domain	8	8
PF01397	Terpene synthase, N-terminal domain	8	8
PF00418	Microtubule-associated protein (MAP) Tau, tubulin-binding repeat	5	7
PF06345	DRF (Diaphanous-related formins) autoregulatory domain	4	11
PF00566	Rab-GTPase-TBC domain	4	5
PF01715	tRNA Delta(2)- isopentenylpyrophosphate transferase (IPP transferase)	3	15
PF00046	Homeobox domain	3	11
PF00201	UDP-glucoronosyl and UDP-glucosyl transferase	3	5
PF08263	Leucine rich repeat N-terminal domain	3	4
PF11721	Di-glucose binding within endoplasmic reticulum	3	4
PF04937	Protein of unknown function (DUF 659)	3	3
PF08744	Plant transcription factor NOZZLE	3	3
PF03110	SBP (SQUAMOSA promoter binding protein-like) domain	2	40
PF00106	short chain dehydrogenase	2	7
PF00514	Armadillo/beta-catenin-like repeat	2	5
PF00227	Proteasome subunit	2	4
PF01764	Lipase (class 3)	2	4
-	Pfam domains families with less than 3 genes, total	211
-	Not annotated gene models	209
	Total number of target gene models	1,139