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Next generation sequencing reveals past and current widespread occurrence of maize yellow mosaic virus in South Africa

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Abstract

Maize yellow mosaic virus (MaYMV) is a single-stranded RNA polerovirus first identified in China. MaYMV was recently reported from West and East Africa, however it had not yet been reported from southern Africa. RNA-seq data from South African field-grown fungal-infected maize was mined for viral sequences by de novo assembly of reads that did not map to the maize or fungal genomes. Predicted proteins from the de novo-assembled unmapped reads matched MaYMV proteins with regions of 96–100% identity. MaYMV was detected in maize RNAseq data from 2009, 2012 and 2013. Complete South African MaYMV genome sequences (5642 nt) were determined by RT-PCR and Sanger sequencing of samples from two different maize genotypes, years, and sites. Phylogenetic analysis confirmed the species identity as MaYMV, and showed separate clustering of isolates between Africa, Asia and South America. Some MaYMV positive samples had reads matching Potyviridae (Johnson grass mosaic virus and Sugarcane mosaic virus), and mycoviruses (Setosphaeria turcica hypovirus 1, Bipolaris maydis partitivirus 1, and Pleospora typhicola fusarivirus 1). A 2016/2017 RT-PCR survey of maize plants exhibiting virus-like symptoms, such as yellowing and streaking patterns, revealed MaYMV in 39 samples from six provinces in South Africa. This report documents the earliest known MaYMV infection world-wide, and indicates that the virus is widespread throughout Africa.

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Acknowledgements and funding

This work was funded by the National Research Foundation, South Africa (grant # 98977), the Department of Agriculture Forestry and Fisheries Research and Technology Fund, South Africa (grant # 98617), and the University of Pretoria, South Africa (Genomics Research Institute grant # A0U945). The funding agencies provided financial support only and had no role in the design, execution, interpretation or documentation of this study. The authors thank P. Tongoona and F. Middleton for assistance with maize field trials, local farmers for access to maize field sites, and M.Greve for assistance with Fig. 3.

Availability of data

All data is available in the manuscript and Electronic Supplementary Material. The MaYMV RSA BR1A and MaYMV RSA SCM genome sequences have been deposited in Genbank (Accessions MG570476; MN943641, respectively). RNA-seq data has been deposited at the NCBI GEO (Gene Expression Omnibus) repository (Accessions GSE94442, GSE99005).

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Authors and Affiliations

  1. Centre for Bioinformatics and Computational Biology, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa

    Tanya Welgemoed & Rian Pierneef

  2. Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa

    Tanya Welgemoed, Susanna E. Schulze, Gerhard Pietersen & Dave K. Berger

  3. Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa

    Tanya Welgemoed, Rian Pierneef, Susanna E. Schulze & Gerhard Pietersen

  4. Agricultural Research Council – Biotechnology Platform, Pretoria, 0110, South Africa

    Rian Pierneef & David A. Read

  5. Department of Genetics, Stellenbosch University, Stellenbosch, 7600, South Africa

    Gerhard Pietersen

  6. Department of Plant and Soil Sciences, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa

    Dave K. Berger

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  1. Tanya Welgemoed
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  2. Rian Pierneef
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Contributions

Conceived and designed experiments: DKB, GP. Bioinformatics analysis: TW, RP. Sample collection: DKB, SES, GP. Laboratory analyses: TW, SES, DAR. Wrote the manuscript: TW, DKB. Edited the manuscript: GP, RP, SES, DAR.

Corresponding author

Correspondence to Dave K. Berger.

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The authors declare no conflicts of interest. All authors consent to the submission of this manuscript. The manuscript has been prepared following principles of ethical and professional conduct. The research did not involve human participants or animal subjects, therefore neither statements concerning informed consent nor welfare of animals is applicable.

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Welgemoed, T., Pierneef, R., Read, D.A. et al. Next generation sequencing reveals past and current widespread occurrence of maize yellow mosaic virus in South Africa. Eur J Plant Pathol 158, 237–249 (2020). https://doi.org/10.1007/s10658-020-02070-1

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