Fig. 2.

Generation sites of vsiRNAs are associated with the putative secondary structures in the virus genomes RNA of HLFPV-Ch. (A) Genome organization of HLFPV-Ch. Boxes represent ORFs of replicase (128.5 kDa), polymerase (186.5 kDa), MP (31.1 kDa), and CP (17.6 kDa). The nucleotide numbers show the start and stop locations of ORFs. Dotted vertical line in the box indicates amber stop codon. Untranslated regions at the 5′-and 3′-terminals are represented by horizontal lines. Internal poly(A) is represented by black solid box. The data shown was the representative results of three replicates of sRNA-seq. (B) Distribution and hotspots for vsiRNAs along HLFPV-Ch genome. Green and red colors denoted vsiRNAs derived from positive and negative strands of HLFPV-Ch genome, respectively. (C) Secondary structures of HLFPV-Ch genome predicted with RNAfold server (http://rna.tbi.univie.ac.at/). Color bar with No. 0-1 denotes the possibilities of bases paring. (D) This is enlarged images of the boxed areas of the HLFPV sequence in panel C to show the 5′-and 3′-terminal regions. vsiRNA, virus-derived siRNA; HLFPV, Hibiscus latent Fort Pierce virus; ORF, open reading frame; MP, movement protein; CP, coat protein; UTR, untranslated region.