Table 3. Seventeen selected hop transcripts as potential targets of vd-sRNA actions analysed by RT-qPCR.

No	Contig	Seq length	Viroid/vd-sRNA orientation	Prediction Tools	Transcript annotation	Group
1	30192	2042	HLVd / -	psRNATarget	phospholipase A1 (PLA1)	Metabolism of plant hormones
2	316	2396	HLVd / +	Both	linoleate 13S-lipoxygenase (LOX)
3	51543	1395	CBCVd / -	psRNATarget	gibberellin 2-oxidase (GA2ox)
4	24780	2290	CBCVd / +	psRNATarget	jasmonic acid-amino acid synthetase (JAR1)
5	4643	5027	CBCVd / +	psRNATarget	endoribonuclease dicer homolog 3a (DCL3a)	Small RNA biogenesis
6	2112	9228	CBCVd /-,+	Both	endoribonuclease dicer homolog 1 (DCL1)
7	29806	1124	CBCVd / +	psRNATarget	cold-regulated 413-plasma membrane protein 2 (COR413PM2)	CBCVd targets of vd-sRNAs with high cellular presence
8	44350	820	CBCVd / +	Both	GATA transcription factor (GATA)
9	7166	2536	CBCVd / -	psRNATarget	acyl-CoA-binding domain-containing protein 5 (ACBD5)
10	8499	1990	CBCVd / -	psRNATarget	uncharacterized protein 1 (UP1)
11	11357	813	CBCVd / -	Both	multiprotein-bridging factor 1c (MBF1c)
12	20309	4464	CBCVd / -, +	Both	putative polyprotein (Ppol)
13	71362	215	CBCVd / -	Both	uncharacterized protein 2 (UP2)
14	18517	7611	CBCVd / +	Both	uncharacterized protein 3 (UP3)	Genes with high complementarity with vd-sRNAs
15	21090	537	CBCVd / +	Both	AP-3 complex subunit sigma (AP3)
16	24148	1065	CBCVd / +	Both	splicing factor 3B subunit 4 (SF3B)
17	10708	1747	HLVd / +	Both	protein trichome birefringence-like 24 (TBL24)