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European Journal of Plant Pathology

, Volume 142, Issue 2, pp 411–417 | Cite as

Low genetic diversity of a natural population of Garlic virus D from Poland

  • Maria Bereda
  • Elżbieta Kalinowska
  • Elżbieta Paduch-Cichal
  • Marek Stefan Szyndel
Article

Abstract

Thirty Garlic virus D isolates collected on a local scale over a 2-year period were analysed and compared to others available in GenBank. In total, 1139 nt were sequenced for each isolate, representing about 13 % of the complete virus genome. Bioinformatic analysis revealed that despite the wide geographic distribution and different growing conditions of hosts, GarV-D maintains an amino acid similarity between 95 to 100 % and 88 to 100 %, indicating high spatial and temporal genetic stability of the coat protein (CP) and nucleic acid binding protein (NABP) genes. The sequence alignments of all isolates of GarV-D were also searched for evidence of recombination and diversifying selection. The ratio of non-synonymous to synonymous polymorphic sites indicated that mostly purifying selection has acted within the analysed genes. However, three codons (two in CP and one in NABP sequences) showed to be under positive selection, including codon located inside conserved zinc-motif finger.

Keywords

GarV-D Selection CP NABP Recombination 

Notes

Acknowledgment

Research supported by grant 2012/07/N/NZ9/00037 from National Science Center, Poland.

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Copyright information

© Koninklijke Nederlandse Planteziektenkundige Vereniging 2015

Authors and Affiliations

  • Maria Bereda
    • 1
  • Elżbieta Kalinowska
    • 1
  • Elżbieta Paduch-Cichal
    • 1
  • Marek Stefan Szyndel
    • 1
  1. 1.Department of Plant PathologyWarsaw University of Life Sciences-SGGWWarsawPoland

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