TreeBASE Search-Matrices for study 571

@ARTICLE{TreeBASE2Ref16730, author = {Francis Moonan and Jose Molina and T. E. Mirkov}, title = {Sugarcane yellowleaf virus: an emerging virus that has evolved by recombination between Polerovirus and Luteovirus ancestors.}, year = {2000}, keywords = {}, doi = {10.1006/viro.1999.0162}, url = {}, pmid = {}, journal = {Virology}, volume = {269}, number = {1}, pages = {156--171}, abstract = {We have derived the genomic nucleotide sequence of a new virus, the sugarcane yellow leaf virus (ScYLV), and shown that it produces two subgenomic RNAs. The current genera of the Luteoviridae include the monopartite Luteovirus and Polerovirus genera, and the bipartite Enamovirus genus, that is represented in present by pea enation mosaic virus (PeMV). Utilizing the new ScYLV nucleotide sequence with existing Luteoviridae sequence information, we have utilized new analyses to identify homologous regions of the Luteoviridae genomes which have statistically significant altered nucleotide substitution ratios, and produce a reconstructed phylogeny of the Luteoviridae that indicates that the RNA1 of PeMV, and the genomes of ScYLV and SbDV, exhibit spatial phylogenetic variation (SPV) consistent with recombination events between Polerovirus and Luteovirus ancestors, that occurred after the evolutionary divergence of these 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 and Mayo (1997) Arch. Virol. 142, 1285-7 ). The analyses of the nucleotide substitution ratios from a nucleotide alignment of Luteoviride genomes substantiates the hypothesis that hotspots for RNA recombination in this virus family are associated with the known sites for the transcriptions of subgenomic RNAs (Miller et al. (1995) Crit. Rev. Plant Sci. 14, 179 211), re-enforces the emphasis that specifically refined strategies should be required for safe use of Luteoviridae sequences in the production of transgene-mediated viral disease resistance, and provides new information that might be utilized to better design safer and more effective means to generate transgene-mediated host resistance.} }