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High molecular diversity and divergent subpopulations of the begomovirus cnidoscolus mosaic leaf deformation virus associated with Cnidoscolus urens

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Abstract

Begomoviruses have circular, single-stranded DNA genomes encapsidated into twinned quasi-icosahedral particles and are transmitted by whiteflies of the Bemisia tabaci sibling group. Begomoviruses infect cultivated and non-cultivated plants, causing great losses in economically important crops worldwide. To better understand the genetic diversity of begomoviruses infecting the non-cultivated host Cnidoscolus urens, leaf samples exhibiting virus-like symptoms were collected in different localities in the state of Alagoas, Brazil, during 2015 and 2016. Forty-two complete DNA-A sequences were cloned and sequenced by the Sanger method. Based on nucleotide sequence comparisons, the 42 new isolates were identified as the bipartite begomovirus cnidoscolus mosaic leaf deformation virus (CnMLDV). The CnMLDV isolates were clustered in two phylogenetic groups (clusters I and II) corresponding to their sampling areas, and the high value of Wright’s F fixation index observed for the DNA-A sequences suggests population structuring. At least seven independent intraspecies recombination events were predicted among CnMLDV isolates, with recombination breakpoints located in the common region (CR) and in the CP and Rep genes. Also, a high per site nucleotide diversity (π) was observed for CnMLDV isolates, with CP being significantly more variable than Rep. Despite the high genetic variability, strong negative or purifying selection was identified as the main selective force acting upon CP and Rep.

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Data availability

The sequences described in this study were deposited in the GenBank database under accession numbers MW600734-MW600775.

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Acknowledgements

The authors wish to thank the Brazilian agencies Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) for supporting this research.

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Author notes

  1. Camila G. Ferro

    Present address: Departamento de Fitopatologia e Nematologia, Universidade de São Paulo, Piracicaba, 13418-900, Brazil

Authors and Affiliations

  1. Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil

    Adso L. S. F. Mendes, Aline M. Melo, Sarah J. C. Silva, Mayra M. M. Ferro, Gaus S. A. Lima & Iraildes P. Assunção

  2. School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA

    Roberto Ramos-Sobrinho

  3. Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil

    Camila G. Ferro & F. Murilo Zerbini

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Mendes, A.L.S.F., Melo, A.M., Ramos-Sobrinho, R. et al. High molecular diversity and divergent subpopulations of the begomovirus cnidoscolus mosaic leaf deformation virus associated with Cnidoscolus urens. Arch Virol 166, 3289–3299 (2021). https://doi.org/10.1007/s00705-021-05245-1

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