Molecular diversity of RNA-2 genome segments in pecluviruses causing peanut clump disease in West Africa and India.

Abstract

The complete nucleotide sequence of RNA-2 genome segments of four isolates of Peanut clump virus (PCV) and two isolates of Indian peanut clump virus (IPCV) were determined. Comparisons among the complete RNA-2 sequences of six isolates from this study and two published earlier, revealed a high degree of variability in size (between 4290 and 4652 nucleotides) and nucleotide sequence identities (between 58 % and 79 %). Amino acid sequence alignments of the five open reading frames (ORF) showed that ORF 4, which encodes the second of the triple gene block proteins, is highly conserved (90 to 98 % identical) whereas the protein encoded by ORF 2, whose function is unknown, is less conserved (25 to 60 % identical). The coat protein of the eight isolates showed amino acid identities between 37 % and 89 % and contained several conserved residues. Phylogenetic comparisons, based on complete RNA-2 sequences, revealed that the eight isolates grouped into two distinct clusters with no geographical distinction between PCV and IPCV isolates. Phylogenetic tree topologies for individual ORFs showed an overall similarity with that obtained from entire RNA-2 sequences, although the relative positions of individual isolates vary within each cluster. The results indicate that there is substantial divergence among the RNA-2 genomes of pecluviruses and suggest that different proteins have evolved differently, possibly due to different selection pressures.