Molecular characterization of domestic and exotic potato virus S isolates and a global analysis of genomic sequences

Molecular characterization of domestic and exotic potato virus S isolates and a global analysis... Five potato virus S (PVS) isolates from the USA and three isolates from Chile were characterized based on biological and molecular properties to delineate these PVS isolates into either ordinary (PVS O ) or Andean (PVS A ) strains. Five isolates – 41956, Cosimar, Galaxy, ND2492-2R, and Q1 – were considered ordinary strains, as they induced local lesions on the inoculated leaves of Chenopodium quinoa , whereas the remaining three (FL206-1D, Q3, and Q5) failed to induce symptoms. Considerable variability of symptom expression and severity was observed among these isolates when tested on additional indicator plants and potato cv. Defender. Additionally, all eight isolates were characterized by determining the nucleotide sequences of their coat protein (CP) genes. Based on their biological and genetic properties, the 41956, Cosimar, Galaxy, ND2492-2R, and Q1 isolates were identified as PVS O . PVS-FL206-1D and the two Chilean isolates (PVS-Q3 and PVS-Q5) could not be identified based on phenotype alone; however, based on sequence comparisons, PVS-FL206-1D was identified as PVS O , while Q3 and Q5 clustered with known PVS A strains. C. quinoa may not be a reliable indicator for distinguishing PVS strains. Sequences of the CP gene should be used as an additional criterion for delineating PVS strains. A global genetic analysis of known PVS sequences from GenBank was carried out to investigate nucleotide substitution, population selection, and genetic recombination and to assess the genetic diversity and evolution of PVS. A higher degree of nucleotide diversity (π value) of the CP gene compared to that of the 11K gene suggested greater variation in the CP gene. When comparing PVS A and PVS O strains, a higher π value was found for PVS A . Statistical tests of the neutrality hypothesis indicated a negative selection pressure on both the CP and 11K proteins of PVS O , whereas a balancing selection pressure was found on PVS A . http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Archives of Virology Springer Journals

Molecular characterization of domestic and exotic potato virus S isolates and a global analysis of genomic sequences

Loading next page...
 
/lp/springer_journal/molecular-characterization-of-domestic-and-exotic-potato-virus-s-9dBmXegbgg
Publisher
Springer Journals
Copyright
Copyright © 2014 by Springer-Verlag Wien
Subject
Biomedicine; Virology; Medical Microbiology; Infectious Diseases
ISSN
0304-8608
eISSN
1432-8798
D.O.I.
10.1007/s00705-014-2022-6
Publisher site
See Article on Publisher Site

Abstract

Five potato virus S (PVS) isolates from the USA and three isolates from Chile were characterized based on biological and molecular properties to delineate these PVS isolates into either ordinary (PVS O ) or Andean (PVS A ) strains. Five isolates – 41956, Cosimar, Galaxy, ND2492-2R, and Q1 – were considered ordinary strains, as they induced local lesions on the inoculated leaves of Chenopodium quinoa , whereas the remaining three (FL206-1D, Q3, and Q5) failed to induce symptoms. Considerable variability of symptom expression and severity was observed among these isolates when tested on additional indicator plants and potato cv. Defender. Additionally, all eight isolates were characterized by determining the nucleotide sequences of their coat protein (CP) genes. Based on their biological and genetic properties, the 41956, Cosimar, Galaxy, ND2492-2R, and Q1 isolates were identified as PVS O . PVS-FL206-1D and the two Chilean isolates (PVS-Q3 and PVS-Q5) could not be identified based on phenotype alone; however, based on sequence comparisons, PVS-FL206-1D was identified as PVS O , while Q3 and Q5 clustered with known PVS A strains. C. quinoa may not be a reliable indicator for distinguishing PVS strains. Sequences of the CP gene should be used as an additional criterion for delineating PVS strains. A global genetic analysis of known PVS sequences from GenBank was carried out to investigate nucleotide substitution, population selection, and genetic recombination and to assess the genetic diversity and evolution of PVS. A higher degree of nucleotide diversity (π value) of the CP gene compared to that of the 11K gene suggested greater variation in the CP gene. When comparing PVS A and PVS O strains, a higher π value was found for PVS A . Statistical tests of the neutrality hypothesis indicated a negative selection pressure on both the CP and 11K proteins of PVS O , whereas a balancing selection pressure was found on PVS A .

Journal

Archives of VirologySpringer Journals

Published: Aug 1, 2014

References

  • An exact nonparametric method for inferring mosaic structure in sequence triplets
    Boni, MF; Posada, D; Feldman, MW
  • Genetic variability in the coat protein gene of Potato virus S isolates and distinguishing its biologically distinct strains
    Cox, BA; Jones, RAC
  • Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology
    Delport, W; Poon, AFY; Frost, SDW; Kosakovsky Pond, SL
  • Maximum likelihood estimation of population parameters
    Fu, YX; Li, WH

You’re reading a free preview. Subscribe to read the entire article.


DeepDyve is your
personal research library

It’s your single place to instantly
discover and read the research
that matters to you.

Enjoy affordable access to
over 18 million articles from more than
15,000 peer-reviewed journals.

All for just $49/month

Explore the DeepDyve Library

Search

Query the DeepDyve database, plus search all of PubMed and Google Scholar seamlessly

Organize

Save any article or search result from DeepDyve, PubMed, and Google Scholar... all in one place.

Access

Get unlimited, online access to over 18 million full-text articles from more than 15,000 scientific journals.

Your journals are on DeepDyve

Read from thousands of the leading scholarly journals from SpringerNature, Elsevier, Wiley-Blackwell, Oxford University Press and more.

All the latest content is available, no embargo periods.

See the journals in your area

DeepDyve

Freelancer

DeepDyve

Pro

Price

FREE

$49/month
$360/year

Save searches from
Google Scholar,
PubMed

Create lists to
organize your research

Export lists, citations

Read DeepDyve articles

Abstract access only

Unlimited access to over
18 million full-text articles

Print

20 pages / month

PDF Discount

20% off