Fig. 2

Genome organization and mapping coverage of Aphid lethal paralysis virus (ALPV) RNA sequences from samples P7 and P9. The positive-sense single-stranded RNA genome of ALPV has a length of approximately 9800 nucleotides (nt). A protein molecule (VPg: virus-protein-genome linked) is covalently attached to the 5′-end of the genomic RNA, which has a 3′-poly(A) tail indicated by A_n. The 5′-untranslated region (5′-UTR) and the intergenic region (IGR) are 338 and 197 nt, respectively, and each function as an internal ribosome entry site (IRES) for translation of the two open reading frames (ORFs: gray boxes). ORF1 is 6111 nt long and is predicted to encode a 2037 amino acid precursor for the viral non-structural proteins. The ORF1 product contains the conserved motif for the 3C–like protease domain between residues 1395–1443 of the ORF1 product. Only putative functional domains in the virus-encoded proteins that can be predicted with a high degree of certainty are shown in the genome map (upper panel). Predicted helicase and RNA dependent RNA polymerase (RdRp) domains (indicated by blue boxes) were determined by searching for sequence homology in the NCBI conserved domain database. ORF2 is 2403 nt long and is translated into an 801 amino acid polyprotein that self-processes into four mature structural proteins VP2, VP4, VP3 and VP1 (indicated by blue boxes). The cleavage sites for the ALPV structural proteins have not yet been experimentally determined. However, their deduced positions based on amino acids alignments have been proposed [36]. By searching for the conserved motifs the cleavage position was determined for VP2/VP4 (I₂₂₈ AATAQ/VGTEAI₂₃₈) to be between residues 228–238 and VP3/VP1(I₅₅₃ to RGVAQ/VNVAES₅₆₃) to be between residues 553–563 of the amino acid sequence of ORF2 of ALPV. Sequence reads from samples P7 and P9 were mapped against an ALPV sequence from GenBank (reference NC004365) in CLC workbench version 5.1. The pink traces represent the depths of coverage at each nucleotide position which was × 1997 and × 1983 for samples P7 and P9, respectively