Phylogenetic study of recombinant strains of Potato virus Y

Kelsie J Green; Celeste J Brown; Stewart M Gray; Alexander V Karasev

doi:10.1016/j.virol.2017.03.018

Phylogenetic study of recombinant strains of Potato virus Y

Virology. 2017 Jul:507:40-52. doi: 10.1016/j.virol.2017.03.018. Epub 2017 Apr 8.

Authors

Kelsie J Green¹, Celeste J Brown², Stewart M Gray³, Alexander V Karasev⁴

Affiliations

¹ Department of PSES, University of Idaho, Moscow, ID, USA; Bioinformatics and Computational Biology Program, University of Idaho, Moscow, ID, USA.
² Department of Biological Sciences, University of Idaho, Moscow, ID, USA; Bioinformatics and Computational Biology Program, University of Idaho, Moscow, ID, USA.
³ USDA-ARS and Section of Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science, Cornell University, Ithaca, NY 14853, USA.
⁴ Department of PSES, University of Idaho, Moscow, ID, USA; Bioinformatics and Computational Biology Program, University of Idaho, Moscow, ID, USA. Electronic address: akarasev@uidaho.edu.

PMID: 28399436
DOI: 10.1016/j.virol.2017.03.018

Abstract

Potato virus Y (PVY) exists as a complex of strains, including a growing number of recombinants. Evolution of PVY proceeds through accumulation of mutations and more rapidly through recombination. Here, the role of recombination in PVY evolution and the origin of common PVY recombinants were studied through whole genome analysis of 119 newly sequenced PVY isolates largely from U.S. potato, and subsequent combined phylogenetic and recombination analyses with an additional 166 whole PVY genomes from the GenBank database. Two novel PVY^C recombinants were sequenced and identified, along with one novel PVY^N:O recombinant. Sequence diversity in the parental sequences made it possible to trace the origins of all recombinant types of PVY, which also showed remarkable sequence diversity in most cases. The results suggested that the common recombinant PVY strains originated more than once, from different parental sequences.

Keywords: Evolution of recombinants; Potato virus Y; Recombination.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Capsid Proteins / genetics
Genome, Viral
Phylogeny
Plant Diseases / virology*
Potyvirus / classification
Potyvirus / genetics*
Potyvirus / isolation & purification
RNA, Viral / genetics
Recombination, Genetic*
Sequence Analysis, DNA
Solanum tuberosum / virology*

Substances

Capsid Proteins
RNA, Viral