Distinct recombination patterns in genomes of potyviruses

Abstract

The rapid evolution and emergence of RNA viruses are consequences of their mutation and recombination-prone nature. The evolutionary mechanism of recombination refers to the exchange of genome segments between distinct viruses during mixed infections. Recombination is often involved in the emergence of viruses with evolutionary novelties, such as the ability to infect new hosts or overcome the genetic resistance of plants. Potyviruses are single-stranded (ss)RNA plant viruses that cause considerable losses in agriculture worldwide. Studies indicate that intra- and interspecific recombination may be involved in the emergence of novel potyvirus species and strains. However, whether there is or not an evolutionary conserved recombination pattern among potyviruses remains to be elucidated. In this study, we evaluated the existence of recombination hotspots across genomes of potyviruses. Nine species data sets comprised of about 1,500 complete genomes of potyvirus isolates collected from around the world were retrieved from Genbank. Breakpoint distribution analyses were conducted in order to determine if specific genomic regions are targeted by recombination events more frequently than expected by chance. The sequence context at recombination hotspots was further characterized by nucleotide composition analyses, prediction of RNA secondary structures and intrinsically disordered regions of their protein products. Recombination hotspots were detected into three out of nine potyvirus species data sets. The hotspots were located at P3, CI and HC-Pro encoding sequences in genomes of isolates belonging to the species Potato virus Y (PVY), Sugarcane mosaic virus (SCMV) and Turnip mosaic virus (TuMV), respectively. The RNA sequences surrounding the hotspot positions showed similar profiles of nucleotide composition and were highly structured in all potyvirus genomes analyzed in this study. The even distribution of recombination breakpoints in most species data sets and the detection of hotspots at distinct positions in the SCMV, TuMV and PVY genomes indicate that the recombination patterns are not conserved amongst the evaluated potyviruses. In addition, neither sequence composition, RNA secondary nor intrinsically disordered protein regions seem to explain the breakpoints clustering in genomes of potyviruses.