Complete genome structure and phylogenetic analysis of little cherry virus, a mealybug-transmissible closterovirus

The 5'-terminal genomic region (8597 nt) of little cherry virus (LChV), a mealybug-borne clostero-virus, was cloned from double-stranded RNA, and its sequence determined to complete the 16934 nt sequence of the monopartite LChV RNA genome. In the 5' to 3' direction, the sequence encompasses ORF la, encoding the conserved replicative domains of methyltransferase and helicase, and ORF 1b, encoding RNA polymerase. ORFs 1a and Ib partially overlap (in 0/+1 configuration), and the LChV replicase is probably expressed by ribosomal frameshifting as a fusion product with a molecular mass of 318 kDa, The N-terminal part of the ORF fa product contains a papain-like cysteine proteinase (PCP) domain with a predicted cleavage site between Gly-619 and Ser-620. The PCP and the upstream protein domains can be aligned with the equivalent parts of the leader proteins encoded by the whitefly-transmitted lettuce infectious yellows and sweet potato sunken vein clostero-viruses. Phylogenetic reconstruction based on the aligned RNA polymerase sequences clearly suggests that the aphid-transmissible and whitefly-transmissible closteroviruses represent two distinct evolutionary lineages, with the mealybug-transmissible LChV being the most remote member of the 'whitefly' lineage.