Genetic variability among coat protein of Prune dwarf virus variants from different countries and different Prunus species

Elżbieta Kalinowska,Karolina Mroczkowska,Maria Chodorska,Elżbieta Paduch-Cichal

doi:10.1007/s10658-014-0502-x

Elżbieta Kalinowska, Karolina Mroczkowska + Show 2 more

Open Access

https://doi.org/10.1007/s10658-014-0502-x

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Abstract

Prune dwarf virus (PDV) isolates have been investigated for genetic diversity. Full-length nucleotide and amino acid sequences of viral coat protein from 23 isolates collected from different stone fruit trees (sour and sweet cherry trees, wild cherry tree, plum tree, almond tree, peach tree) and different countries (Poland, Italy, Germany, USA, Israel) were analysed and compared to 57 others available in GenBank. Comparison of all sequenced virus isolates revealed diversity of 86–100 % at nucleotide level and 79–100 % at amino acid level. The ratio of non-synonymous to synonymous polymorphic sites indicated that purifying selection dominated in case of PDV. However, six codons showed to be under strong positive selection, including the codon located inside the structure involved in RNA-binding activity.

Highlights

Prune dwarf virus (PDV) isolates have been investigated for genetic diversity
RNA 3 encodes movement protein (MP) and coat protein (CP), which is expressed via sub-genomic RNA 4 (Bachman et al, 1994)
Despite of differences in serological and biological properties of PDV isolates a molecular characterization of viral coat protein sequences did not reveal a correlation between amino acid composition and host species and/or origin of the viral isolate (Vaškova et al, 2000)

Summary

Introduction

Prune dwarf virus (PDV) isolates have been investigated for genetic diversity. Full-length nucleotide and amino acid sequences of viral coat protein from 23 isolates collected from different stone fruit trees (sour and sweet cherry trees, wild cherry tree, plum tree, almond tree, peach tree) and different countries (Poland, Italy, Germany, USA, Israel) were analysed and compared to 57 others available in GenBank. Despite of differences in serological and biological properties of PDV isolates a molecular characterization of viral coat protein sequences did not reveal a correlation between amino acid composition and host species and/or origin of the viral isolate (Vaškova et al, 2000). Subsequent studies of PDV CP nucleotide sequences revealed higher divergence in almond isolates of PDV than in isolates obtained from other hosts (Fonseca et al, 2005) and indicated presence of four phylogroups: 1.

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