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Table 1 Predicted citrus mRNAs annotated as transcripts and targeted by HSVd-siRNAs

From: Identification of Hop stunt viroid infecting Citrus limon in China using small RNAs deep sequencing approach

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

   
  1. aLocation of HSVd-siRNA 5′ termini in the viroid genome
  2. bAlignments between HSVd-siRNAs with predicted citrus mRNAs. HSVd-siRNAs were shaded in red
  3. cThe score of the complementarity between small RNA and their target transcript following the scoring schema of miRU by Zhang [22]
  4. dThree Citrus sinensis database (transcript, cDNA, and Unigene) from the psRNATarget website were used for prediction