Table 1.

Predicted citrus mRNAs annotated as transcripts and targeted by HSVd-siRNAs

HSVd-siRNA No.	sRNA 5′-enda	Alignmentb	Scorec	Citrus transcript targetd	Target predicted function
1	103	siRNA GAGAGAGGAUGCGGAGAGCGA	2.0	Orange1.1 g021690	E3 ubiquitin-protein ligase RING1-like
		∶∶∶∶∶∶∶∶∶∶∶.∶∶∶∶∶.∶∶∶
		Target CUCUCUCCGACGUCUCUUGCU
2	102	siRNA AGAGAGGAUGCGGAGAGCGAC	2.0	Cs5g11500.1	Cysteine--tRNA ligase
		∶∶ ∶∶∶∶∶∶∶ ∶∶∶∶∶∶∶∶∶
		Target UCGCUCCUACACCUCUCGCUC
3	198	siRNA UCUUCCAUUUUCUUCUUCCCU	2.0	TC24583	COP9 signalosome complex subunit 6a
		∶∶∶∶∶∶ . . ∶∶∶∶∶∶∶∶∶∶∶∶
		Target AGAAGGAGGAAGAAGAAGGGA
4	105	siRNA GGAGAGAGGAUGCGGAGAGC	2.0	Cs8g10955.1	S-adenosylmethionine synthase 3
		∶∶∶∶∶∶∶∶∶ ∶∶∶∶∶∶∶∶∶
		Target CUCUCUCCGACGUCUCUUGCU
5	199	siRNA CUUCCAUUUUCUUCUUCCCUG	2.0	EY709257	Pherophorin-C1 protein
		∶∶∶ ∶∶∶∶∶∶∶∶∶∶∶∶∶∶∶∶
		Target GAACGUAAAAGAAGAAGGGAG

^aLocation of HSVd-siRNA 5′ termini in the viroid genome

^bAlignments between HSVd-siRNAs with predicted citrus mRNAs. HSVd-siRNAs were shaded in red

^cThe score of the complementarity between small RNA and their target transcript following the scoring schema of miRU by Zhang [22]

^dThree Citrus sinensis database (transcript, cDNA, and Unigene) from the psRNATarget website were used for prediction