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Genetic diversity and recombination between turnip yellows virus strains in Australia

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Abstract

Disease outbreaks caused by turnip yellows virus (TuYV), a member of the genus Polerovirus, family Luteoviridae, regularly occur in canola and pulse crops throughout Australia. To understand the genetic diversity of TuYV for resistance breeding and management, genome sequences of 28 TuYV isolates from different hosts and locations were determined using high-throughput sequencing (HTS). We aimed to identify the parts of the genome that were most variable and clarify the taxonomy of viruses related to TuYV. Poleroviruses contain seven open reading frames (ORFs): ORF 0–2, 3a, and 3–5. Phylogenetic analysis based on the genome sequences, including isolates of TuYV and brassica yellows virus (BrYV) from the GenBank database, showed that most genetic variation among isolates occurred in ORF 5, followed by ORF 0 and ORF 3a. Phylogenetic analysis of ORF 5 revealed three TuYV groups; P5 group 1 and group 3 shared 45–49% amino acid sequence identity, and group 2 is a recombinant between the other two. Phylogenomic analysis of the concatenated ORFs showed that TuYV is paraphyletic with respect to BrYV, and together these taxa form a well-supported monophyletic group. Our results support the hypothesis that TuYV and BrYV belong to the same species and that the phylogenetic topologies of ORF 0, 3a and 5 are incongruent and may not be informative for species demarcation. A number of beet western yellow virus (BWYV)- and TuYV-associated RNAs (aRNA) were also identified by HTS for the first time in Australia.

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Acknowledgements

This study was funded by the Queensland Department of Agriculture and Fisheries and the Australian Grains Research and Development Corporation projects DAN00202, DAQ00186 and DAQ00154. We thank Dr. Joop Van Leur and Dr. Brenda Coutts for discussions about the project and assistance with sample collection, and Dr. Paul Campbell for discussions about the results.

GenBank accession numbers MT586571– MT586598 and MT642436–MT642445.

Funding

This study was funded by the Queensland Department of Agriculture and Fisheries and the Australian Grains Research and Development Corporation (projects DAN00202, DAQ00186 and DAQ00154).

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Authors and Affiliations

  1. Department of Agriculture and Fisheries, Ecosciences Precinct, GPO Box 267, Brisbane, Queensland, 4001, Australia

    Fiona Filardo & Murray Sharman

  2. Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, GPO Box 267, Brisbane, Queensland, 4001, Australia

    Alistair R. McTaggart & John Thomas

  3. Department of Jobs, Precincts and Regions, Agriculture Victoria, Grains Innovation Park, 110 Natimuk Road, Horsham, Victoria, 3400, Australia

    Narelle Nancarrow, Mohammad Aftab & Piotr Trębicki

  4. Department of Jobs, Precincts and Regions, Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, 3083, Australia

    Brendan Rodoni

  5. School of Applied Systems Biology, La Trobe University, Bundoora, 3083, Australia

    Brendan Rodoni

  6. Department of Primary Industries and Regional Development, DPIRD Diagnostic Laboratory Services, South Perth, WA, Australia

    Monica Kehoe

  7. Department of Primary Industries and Regional Development, Industry and Economic Development, 3 Baron-Hay Court, Kensington, Western Australia, 6151, Australia

    Benjamin Congdon

  8. Terbol Station, International Center for Agricultural Research in the Dry Areas (ICARDA), Beqaa valley, Zahle, Lebanon

    Safaa Kumari

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Filardo, F., Nancarrow, N., Kehoe, M. et al. Genetic diversity and recombination between turnip yellows virus strains in Australia. Arch Virol 166, 813–829 (2021). https://doi.org/10.1007/s00705-020-04931-w

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