accumulating variation at conserved sites in potyvirus genomes is driven by species discovery and affects degenerate primer design积累变化保存地点potyvirus基因组是由物种的发现和影响简并引物设计.pdfVIP

Accumulating Variation at Conserved Sites in Potyvirus Genomes Is Driven by Species Discovery and Affects Degenerate Primer Design 1. 1 2 3 4 1. Linda Zheng *, Paul J. Wayper , Adrian J. Gibbs , Mathieu Fourment , Brendan C. Rodoni , Mark J. Gibbs 1 School of Botany and Zoology, Australian National University, Canberra, Australian Capital Territory, Australia, 2 Yarralumla, Australian Capital Territory, Australia, 3 Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia, 4 Department of Primary Industries, Knoxfield, Victoria, Australia Abstract Unknown and foreign viruses can be detected using degenerate primers targeted at conserved sites in the known viral gene sequences. Conserved sites are found by comparing sequences and so the usefulness of a set of primers depends crucially on how well the known sequences represent the target group including unknown sequences. Methodology/Principal Findings: We developed a method for assessing the apparent stability of consensus sequences at sites over time using deposition dates from Genbank. We tested the method using 17 conserved sites in potyvirus genomes. The accumulation of knowledge of sequence variants over 20 years caused ‘consensus decay’ of the sites. Rates of decay were rapid at all sites but varied widely and as a result, the ranking of the most conserved sites changed. The discovery and reporting of sequences from previously unknown and distinct species, rather than from strains of known species, dominated the decay, indicating it was largely a sampling effect related to the progressive discovery of species, and recent virus mutation was probably only a minor contributing factor. Conclusion/Significanc