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Characterization of yam mosaic viruses from Brazil reveals a new phylogenetic group and possible incursion from the African continent

Abstract

Yam (Dioscorea spp.) is an important crop for smallholder farmers in the Northeast region of Brazil. Wherever yam is grown, diseases caused by yam mosaic virus (YMV) are prevalent. In the present study, the diversity of YMV infecting Dioscorea cayennensis-rotundata was analyzed. In addition, five species of Dioscorea (D. alata, D. altissima, D. bulbifera, D. subhastata, and D. trifida) commonly found in Brazil were analyzed using ELISA and high-throughput sequencing (HTS). YMV was detected only in D. cayennensis-rotundata, of which 66.7% of the samples tested positive in ELISA. Three YMV genome sequences were assembled from HTS and one by Sanger sequencing to group the sequences in a clade phylogenetically distinct from YMV from other origins. Temporal phylogenetic analyses estimated the mean evolutionary rate for the CP gene of YMV as 1.76 × 10–3 substitutions per site per year, and the time to the most recent common ancestor as 168.68 years (95% Highest Posterior Density, HPD: 48.56–363.28 years), with a most likely geographic origin in the African continent. The data presented in this study contribute to reveal key aspects of the probable epidemiological history of YMV in Brazil.

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Acknowledgements

The authors acknowledge the financial support given by CNPq (Project 408709/2018-9), CAPES-PrInt-UFRPE, and the Rural Federal University of Pernambuco (Edital 015/2018, UFRPE-PRPPG). Thanks to the yam farmers who allowed access to their fields to collect samples of study material. Also to professionals, for providing samples (yam tubers) and support in the sample collections in non-cultivated areas: Master in Plant Biology, Gabriel Pavan Sabino, Universidade Estadual Pulista (UNESP), Rio Claro, São Paulo. Botanical Biologist Dr. Diogo Amorim de Araújo, Permanbuco. Botanical Biologist Dr. Jones Clebson R. Mendez, Universidade Federal Rural de Pernambuco (UFRPE), Plant Taxonomy Laboratory, Pernambuco. Thanks to the researchers of the Agronomic Institute of Pernambuco (IPA) Dr. José Nildo Tabosa, and MSc. Almir Dias Alves da Silva for providing us with access to Yam's production fields.

Funding

This work was supported by funding from CNPq (Project 408709/2018–9), CAPES-PrInt-UFRPE, and the Rural Federal University of Pernambuco (Edital 015/2018, UFRPE-PRPPG).

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Mendoza, A.R., Margaria, P., Nagata, T. et al. Characterization of yam mosaic viruses from Brazil reveals a new phylogenetic group and possible incursion from the African continent. Virus Genes 58, 294–307 (2022). https://doi.org/10.1007/s11262-022-01903-x

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Keywords

  • Yam mosaic virus
  • Dioscorea
  • HTS
  • Phylogeographic
  • Geospatial studies