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Genome sequence analysis of five Canadian isolates of strawberry mottle virus reveals extensive intra-species diversity and a longer RNA2 with increased coding capacity compared to a previously characterized European isolate

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Abstract

In this study, we report the genome sequence of five isolates of strawberry mottle virus (family Secoviridae, order Picornavirales) from strawberry field samples with decline symptoms collected in Eastern Canada. The Canadian isolates differed from the previously characterized European isolate 1134 in that they had a longer RNA2, resulting in a 239-amino-acid extension of the C-terminal region of the polyprotein. Sequence analysis suggests that reassortment and recombination occurred among the isolates. Phylogenetic analysis revealed that the Canadian isolates are diverse, grouping in two separate branches along with isolates from Europe and the Americas.

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Acknowledgments

We thank Cinta Hernandez Sebastia, Xiaofei Cheng and Patrick Chapman for help with NGS work and data analysis. We also acknowledge Michael Celetti, Pam Fisher, Mathuresh Singh and John Lewis for assistance in sampling.

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    Authors and Affiliations

    1. Summerland Research and Development Centre, Agriculture and Agri-Food Canada, 4200 Highway 97, Summerland, BC, V0H 1Z0, Canada

      Basdeo Bhagwat, Melanie Walker, Michael Bernardy, Michel Bouthillier, Robyn DeYoung, Yu Xiang & Hélène Sanfaçon

    2. Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, P.O. Box 20280, 850 Lincoln Road, Fredericton, NB, E3B 4Z7, Canada

      Virginia Dickison, Alexa Creelman & Xianzhou Nie

    3. Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People’s Republic of China

      Xinlun Ding

    4. London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sanford St., London, ON, N5V 4T3, Canada

      Xinlun Ding, Yinzi Li & Aiming Wang

    5. Biology Program, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada

      Alexa Creelman

    Authors
    1. Basdeo Bhagwat
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    2. Virginia Dickison
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    3. Xinlun Ding
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    4. Melanie Walker
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    5. Michael Bernardy
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    6. Michel Bouthillier
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    7. Alexa Creelman
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    8. Robyn DeYoung
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    9. Yinzi Li
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    10. Xianzhou Nie
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    11. Aiming Wang
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    12. Yu Xiang
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    13. Hélène Sanfaçon
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    Corresponding authors

    Correspondence to Xianzhou Nie, Aiming Wang, Yu Xiang or Hélène Sanfaçon.

    Ethics declarations

    This study was funded by Agriculture and Agri-Food Canada (project J-000051 awarded to XN, AW, YX and HS). XD was a recipient of a visiting scholarship from Fujian Agriculture and Forestry University, China. All authors declare that they have no conflict of interest. This article does not contain any studies with human participants or animals performed by any of the authors.

    Additional information

    B. Bhagwat, V. Dickison, X. Ding and M. Walker contributed equally to this study and should be considered joint first authors.

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    Bhagwat, B., Dickison, V., Ding, X. et al. Genome sequence analysis of five Canadian isolates of strawberry mottle virus reveals extensive intra-species diversity and a longer RNA2 with increased coding capacity compared to a previously characterized European isolate. Arch Virol 161, 1657–1663 (2016). https://doi.org/10.1007/s00705-016-2799-6

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    • DOI: https://doi.org/10.1007/s00705-016-2799-6

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