Tomato yellow leaf curl virus intergenic siRNAs target a host long noncoding RNA to modulate disease symptoms
Fig 2
Identification of a 25-nt segment and a vsRNA that induce stunt and curled leaves in tomato.
(A) VsRNAs generated by the IR and sequence alignment of vsRNAs and SlLNR1. Location and frequency of TYCLV-derived siRNAs (vsRNAs) were mapped to the IR in sense- (above the x-axis) or antisense- (below the x-axis) orientation. Genome organization of the IR was shown at the top in which the inverted repeat was symbolized as a stem loop. Numbers indicate the first (2616) and last (147) nucleotides of the IR sequence. The histogram of location, frequency and size distribution of vsRNAs corresponding to the 25-nt-fragment (2730–2754) were shown at the medium panel. The fragment was highly complemented with SlLNR1(-). The scissor means the cleavage site determined by 5’-RACE analysis. (B) Phenotypes of tomato inoculated with pTRV2:4TR. TYLCV-susceptible tomato plants were inoculated with pTRV2 containing 4×25-nt-fragment (2730–2754). The photos were taken at 15 dpi. (C) Validation of siRNA(-2752-21) in the tomato plants by siRNA Northern blot. The leaves of susceptible tomato plants inoculated by TYLCV infectious clone, natural infection by viruliferous whiteflies, agroinfiltrated with pTRV2:4TR and pTRV2:IR were used for total RNA extraction and analyzed at 24 dpi. U6 gene was set as the internal control. (D) Validation of siRNA(-2752-21) presence and downregulation of SlLNR1 in the overexpressed plants. Two individual transgenic lines (pCAMBIA2301:siRNA-1/2) with overexpression of siRNA(-2752-21) were used for total RNA extraction and analyzed. EV indicates the transgenic plant with the EV. The lower panel shows the relative expression of SlLNR1 that was measured by qRT-PCR and calculated in relation to the transgenic plants according to the ΔΔCt method using tomato actin gene as the reference. Error bars represented SE of three biological replicates and significant differences by Student’s t test (*, p<0.05) (E) Phenotypes of siRNA(-2752-21) overexpressed plants. The typical photos were taken at 60 days after seed germination.