Archives of Virology

, Volume 157, Issue 1, pp 147–153 | Cite as

Variability in the P1 gene helps to refine phylogenetic relationships among leek yellow stripe virus isolates from garlic

  • Naoto Yoshida
  • Hanako Shimura
  • Kazuo Yamashita
  • Masahiko Suzuki
  • Chikara Masuta
Brief Report


Nucleotide sequences from the P1 gene and the 5′ untranslated region of leek yellow stripe virus (LYSV), collected from several locations, were used to refine the phylogenetic relationships among the isolates. Multiple alignments revealed three distinct regions of insertions and deletions to classify LYSVs. In our phylogenetic analyses, the LYSV isolates separated into two major groups (N-type and S-type). S-type viruses had two large deletions compared to N-type viruses. Considering that the outgroup, onion yellow dwarf virus (OYDV) also has the sequences corresponding to the deletions in the S-type viruses, our study shows that the sequences missing in the S-type were present in the common ancestor of the N-type and S-type. In the phylogenetic trees, we found three distinct clades of isolates, from Uruguay (U), Okinawa (O) and Spain (Sp), suggesting that LYSVs have unique evolutionary histories depending on their garlic origins. The P1 gene of LYSV is thus quite suited to reflecting viral evolution, as recently suggested for other potyviruses.


Sequence Deletion Aomori Prefecture Onion Yellow Dwarf Virus Garlic Bulb Garlic Plant 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This study was partially supported by the A-STEP (AS2211387E) program of Japan Science and Technology Agency (JST). We thank Dr. Yoshihiko Shiga of Hokkaido Agricultural Laboratory for Business Development for providing garlic materials.


  1. 1.
    Chen J, Chen J, Adams MJ (2001) Molecular characterization of a complex mixture of viruses in garlic with mosaic symptoms in China. Arch Virol 146:1841–1853PubMedCrossRefGoogle Scholar
  2. 2.
    Chen J, Chen J, Adams MJ (2002) Characterisation of some carla- and potyviruses from bulb crops in China. Arch Virol 147:419–428PubMedCrossRefGoogle Scholar
  3. 3.
    Park KS, Bae YJ, Jung EJ, Kang SJ (2005) RT-PCR-based detection of six garlic viruses and their phylogenetic relationships. J Microbiol Biotechnol 15:1110–1114Google Scholar
  4. 4.
    Sumi S, Tsuneyoshi T, Suzuki A, Ayabe M (2001) Development and establishment of practical tissue culture methods for production of virus-free garlic seed bulbs, a novel field cultivation system and convenient methods for detecting garlic infecting viruses. Plant Biotechnol 18:179–190CrossRefGoogle Scholar
  5. 5.
    Tsuneyoshi T, Matsumi T, Natsuaki KT, Sumi S (1998) Nucleotide sequence analysis of virus isolates indicates the presence of three potyvirus species in Allium plants. Arch Virol 143:97–113PubMedCrossRefGoogle Scholar
  6. 6.
    Thompson JD, Higgins DG, Bibson TJ (1994) Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680PubMedCrossRefGoogle Scholar
  7. 7.
    Hall TA (1999) BIOEDIT: a user-friendly biological sequence alignment editor and analysis program fro WINDOWS 95/98/NT. Nucleic Acids Symp 41:95–98Google Scholar
  8. 8.
    Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. doi: 10.1093/molbev/msr121 Google Scholar
  9. 9.
    Valli A, Lopez-Moya J, Garcia A (2007) Recombination and gene duplication in the evolutionary diversification of P1 proteins in the family Potyviridae. J Gen Virol 88:1016–1026PubMedCrossRefGoogle Scholar
  10. 10.
    Takaki F, Sano T, Yamashita K, Fujita T, Ueda K, Kato T (2005) Complete nucleotide sequences of attenuated and severe isolates of Leek yellow stripe virus from garlic in northern Japan: identification of three distinct virus types in garlic and leek world-wide. Arch Virol 150:1135–1149PubMedCrossRefGoogle Scholar
  11. 11.
    Gu X, Li W-H (1995) The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment. J Molec Evol 40:464–473PubMedCrossRefGoogle Scholar
  12. 12.
    de Jong WW, Rydén L (1981) Causes of more frequent deletions than insertions in mutations and protein evolution. Nature 290:157–159PubMedCrossRefGoogle Scholar
  13. 13.
    Etoh T, Simon PW (2002) Diversity, fertility and seed production of garlic. In: Rabinowitch HO, Currah L (eds) Allium crop science: recent advances. CABI Publishing, Oxford, pp 101–117CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Naoto Yoshida
    • 1
  • Hanako Shimura
    • 1
  • Kazuo Yamashita
    • 2
  • Masahiko Suzuki
    • 1
  • Chikara Masuta
    • 1
  1. 1.Graduate School of AgricultureHokkaido UniversitySapporoJapan
  2. 2.Aomori Prefectural Industrial Technology Research CenterAomoriJapan

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