Table 1.
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