Sugarcane yellow leaf virus: An emerging virus that has evolved by recombination between luteoviral and poleroviral ancestors

We have derived the genomic nucleotide sequence of an emerging virus, the S ugarcane yellow leaf virus (ScYLV), and shown that it produces one to two s ubgenomic RNAs. The family Luteoviridae currently includes the Luteovirus, Polerovirus, and Enamovirus genera. With the new ScYLV nucleotide sequence and existing Luteoviridae sequence information, we have utilized new phylog enetic and evolutionary methodologies to identify homologous regions of Lut eoviridae genomes, which have statistically significant altered nucleotide substitution ratios and have produced a reconstructed phylogeny of the Lute oviridae. The data indicate that Pea enation mosaic virus-1 (PEMV-1), Soybe an dwarf virus (SbDV), and ScYLV exhibit spatial phylogenetic variation (SP V) consistent with recombination events that have occurred between polerovi ral and luteoviral ancestors, after the divergence of these two progenitor groups. The reconstructed phylogeny confirms a contention that a continuum in the derived sequence evolution of the Luteoviridae has been established by intrafamilial as well as extrafamilial RNA recombination and expands the database of recombinant Luteoviridae genomes that are currently needed to resolve better defined means for generic discrimination in the Luteoviridae (D'Arcy, C. J. and Mayo, M. 1997. Arch. Virol. 142, 1285-1287). The analys es of the nucleotide substitution ratios from a nucleotide alignment of Lut eoviridae genomes substantiates the hypothesis that hot spats for RNA recom bination in this virus family are associated with the known sites for the t ranscription of subgenomic RNAs (Miller et al. 1995. Crit Rev. Plant Sci. 1 4, 179-211), and provides new information that might be utilized to better design more effective means to generate transgene-mediated host resistance. (C) 2000 Academic Press.