Phylogenetic analysis of New Zealand tomato spotted wilt virus isolates suggests likely incursion history scenarios and mechanisms for population evolution

Phylogenetic analysis of New Zealand tomato spotted wilt virus isolates suggests likely incursion... Tomato spotted wilt virus (TSWV) is an internationally significant pathogen with a wide host range, vectored by thrips. We have studied the sequence variation and evolutionary mechanisms at play in parts of the L, M and S subgenomes of 23 New Zealand TSWV isolates collected between 1992 and 2009, aiming to identify the possible geographic origins of isolates. Maximum-likelihood-based phylogenetic analyses of New Zealand and overseas TSWV isolates placed the L and M subgenome sequences of two isolates (MAF04 and PFR04) in distinct clades composed primarily of Korean, Japanese and Chinese isolates, in contrast to the remaining 21 isolates, which clustered with a cosmopolitan group of isolates. The nucleocapsid (N) gene sequences of MAF04 and PFR04 plus MAF02 clustered with Japanese isolates. Consequently, we postulate that these isolates may represent a distinct incursion into New Zealand, but we do not have enough evidence to indicate an incursion pathway. Alternately, these isolates may have arrived with an incursion that included a mixture of TSWV isolates of diverse international origins. The sequences of four of the TSWV isolates contained a number of sites with a mixture of nucleotides, suggesting that these isolates either consisted of several sequence variants or were from plants with mixed infections. One isolate (MAF02) was shown to be a either a reassortant or an S subgenome recombinant. Large amounts of low-level polymorphism were detected with low amino acid change fixation rates (purifying selection). Negative selection was indicated at four amino acid sites in the New Zealand TSWV N gene sequences. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Archives of Virology Springer Journals

Phylogenetic analysis of New Zealand tomato spotted wilt virus isolates suggests likely incursion history scenarios and mechanisms for population evolution

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Publisher
Springer Vienna
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/s00705-013-1909-y
Publisher site
See Article on Publisher Site

Abstract

Tomato spotted wilt virus (TSWV) is an internationally significant pathogen with a wide host range, vectored by thrips. We have studied the sequence variation and evolutionary mechanisms at play in parts of the L, M and S subgenomes of 23 New Zealand TSWV isolates collected between 1992 and 2009, aiming to identify the possible geographic origins of isolates. Maximum-likelihood-based phylogenetic analyses of New Zealand and overseas TSWV isolates placed the L and M subgenome sequences of two isolates (MAF04 and PFR04) in distinct clades composed primarily of Korean, Japanese and Chinese isolates, in contrast to the remaining 21 isolates, which clustered with a cosmopolitan group of isolates. The nucleocapsid (N) gene sequences of MAF04 and PFR04 plus MAF02 clustered with Japanese isolates. Consequently, we postulate that these isolates may represent a distinct incursion into New Zealand, but we do not have enough evidence to indicate an incursion pathway. Alternately, these isolates may have arrived with an incursion that included a mixture of TSWV isolates of diverse international origins. The sequences of four of the TSWV isolates contained a number of sites with a mixture of nucleotides, suggesting that these isolates either consisted of several sequence variants or were from plants with mixed infections. One isolate (MAF02) was shown to be a either a reassortant or an S subgenome recombinant. Large amounts of low-level polymorphism were detected with low amino acid change fixation rates (purifying selection). Negative selection was indicated at four amino acid sites in the New Zealand TSWV N gene sequences.

Journal

Archives of VirologySpringer Journals

Published: May 1, 2014

References

  • Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences
    Gibbs, MJ; Armstrong, JS; Gibbs, AJ
  • A new statistic for detecting genetic differentiation
    Hudson, RR
  • Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
    Kosakovsky Pond, SL; Frost, SDW
  • DnaSP v5: a software for comprehensive analysis of DNA polymorphism data
    Librado, P; Rozas, J
  • RDP: detection of recombination amongst aligned sequences
    Martin, D; Rybicki, E
  • RDP3: a flexible and fast computer program for analyzing recombination
    Martin, D; Lemey, P; Lott, M; Moulton, V; Posada, D; Lefeuvre, P
  • Top 10 plant viruses in molecular plant pathology
    Scholthof, K-B; Adkins, S; Czosnek, H; Palukaitis, P; Jacquot, E; Hohn, T; Hohn, B; Saunders, K; Candresse, T; Ahlquist, P; Hemenway, C; Foster, GD
  • Evolutionary relationship of DNA sequences in finite populations
    Tajima, F
  • The molecular population genetics of the Tomato spotted wilt virus genome
    Tsompana, M; Abad, J; Purugganan, M; Moyer, JW

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