Table 1.

Selected miRNAs (including some as PHAS trigger) with differentially expression changes in response to co-infection of TYLCCNV and TYLCCNB in N. benthamiana

miRNA family	Expression change (fold)*	Predicted target	References for virus response	As PHAS trigger#	References for PHAS
Conserved
miR160	↑7.6	Auxin response factor	[3,8,9]	ND
miR164	↑2.2	NAC domain protein	[3,7,9]	ND
miR169	↓2.0	CCAAT-binding transcription factor (CBF)	[3,8]	ND
miR319	↓2.0	TCP/MYB	[8]	Yes
miR391	↓3.5	Putative TAS	[8]	Yes
miR396	↑2.4	LRR receptor-like serine/threonine-protein kinase, RLP/Pentatricopeptide repeat protein	[8]	Yes
miR397	↑3.5	Laccase	[8]	Yes
miR398	↑18.4	CSD; Zinc finger, LIM-type/Rhodanese-like	[8,10]	Yes
miR482 /miR2118	↑11.0	NBS-LRR	[21]	Yes	[15,18,21]
miR827	↓3.1	AP2 domain-containing transcription factor/RCC1-like protein		Yes
miR4376	↓3.7	ACA		Yes	[22]
miR6020	↓2.0	Pentatricopeptide repeat/Glycosyl transferase	[20]	Yes	[20]
Novel
Nbe-miR2	↓5.9	RCC domain-containing protein		ND
Nbe-miR3	↓6.7	Not known		ND
Nbe-miR4	↓3.8	Not known		ND
Nbe-miR6	↑2.8	GH3 family protein		ND
Nbe-miR8	↑2.3	Heat shock protein binding protein		ND
Nbe-miR64	↑2.1	C2 membrane targeting protein		Yes
Nbe-miR70	↑2.1	Basic helix-loop-helix dimerisation region bHLH		ND
Nbe-miR84	↑3.4	Cyclic nucleotide gated channel		ND
Nbe-miR99	↑3.5	F-box family protein		Yes
Nbe-miR107	↑9.1	DNA repair protein radA		ND
Nbe-miR124	↑2.9	Lactoylglutathione lyase		ND
Nbe-miR129	↑2.1	Harpin-induced protein-like		ND
Nbe-miR134	↑2.8	CHP-rich zinc finger protein/F-box family protein		Yes
Nbe-miR142	↓2.0	Receptor like kinase, RLK		ND

References for virus response and PHAS by previous studies were listed. A detailed list was shown as Additional file 5: Table S5.

*Fold of P2/P1; #ND: not determined.