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Sequence characteristics of potato virus Y recombinants

¹ Department of Plant, Soil, and Entomological Sciences, University of Idaho, Moscow, ID 83844, USA
² Bioinformatics and Computational Biology Program, University of Idaho, Moscow, ID 83844, USA
³ Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
⁴ International Institute of Tropical Agriculture, Kampala, Uganda

Correspondence
Alexander V. Karasev
akarasev{at}uidaho.edu

Potato virus Y (PVY) is one of the most economically important plant pathogens. The PVY genome has a high degree of genetic variability and is also subject to recombination. New recombinants have been reported in many countries since the 1980s, but the origin of these recombinant strains and the physical and evolutionary mechanisms driving their emergence are not clear at the moment. The replicase-mediated template-switching model is considered the most likely mechanism for forming new RNA virus recombinants. Two factors, RNA secondary structure (especially stem–loop structures) and AU-rich regions, have been reported to affect recombination in this model. In this study, we investigated the influence of these two factors on PVY recombination from two perspectives: their distribution along the whole genome and differences between regions flanking the recombination junctions (RJs). Based on their distributions, only a few identified RJs in PVY genomes were located in lower negative FORS-D, i.e. having greater secondary-structure potential and higher AU-content regions, but most RJs had more negative FORS-D values upstream and/or higher AU content downstream. Our whole-genome analyses showed that RNA secondary structures and/or AU-rich regions at some sites may have affected PVY recombination, but in general they were not the main forces driving PVY recombination.

A supplementary figure showing multiple sequence alignments of breakpoints is available with the online version of this paper.