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Two new umbravirus-like associated RNAs (ulaRNAs) discovered in maize and johnsongrass from Ecuador

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Abstract

Two new umbravirus-like associated RNAs (ulaRNAs) were found, respectively, in maize and Johnsongrass samples from Ecuador. The complete sequences consist of 3,053 and 3,025 nucleotides, respectively, and contain four open reading frames (ORFs). Their genome sequences were 58% identical to each other and 28 to 60% identical to the most closely related viruses. Phylogenetic analysis using full genome sequences and amino acid sequence of the RNA-dependent-RNA polymerase (RdRp) placed both sequences in a clade sharing the most recent common ancestor with ulaRNAs from sugarcane and maize, suggesting that they belong to a monophyletic grass-infecting lineage. Their terminal regions exhibit features common to umbraviruses and ulaRNAs.

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Data availability

The genomic sequences of the two viruses reported here have been deposited in the GenBank database under the accession numbers OM937759 and OM937760.

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Acknowledgements

The contribution of Viola Weichelt and Dennis Knierim (Leibniz Institute DSMZ) in library preparation and bioinformatics analysis is deeply acknowledged.

Funding

Funding was received from the European Virus Archive Global (EVAg) project, through the European Union’s Horizon 2020 research and innovation program under grant agreement no. 871029. Additional funding was received from the National Science Foundation EAGER 1912025 to AES, the National Science Foundation MCB-1818229 to AES, and the USDA NIFA Emergency Citrus Disease Research and Extension Program 2020-08455 to AES.

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Authors and Affiliations

  1. Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Km 30.5 Vía Perimetral Campus Gustavo Galindo, Guayaquil, Ecuador

    Diego F. Quito-Avila & Edison G. Reyes-Proaño

  2. Centro de Investigaciones Biotecnológicas del Ecuador, CIBE, Escuela Superior Politécnica del Litoral, Km 30.5 Vía Perimetral Campus Gustavo Galindo, Guayaquil, Ecuador

    Diego F. Quito-Avila

  3. INIAP, Estación Experimental Portoviejo, Km 12, Via a Santa Ana, Manabí, Ecuador

    Alma Mendoza

  4. Plant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, Braunschweig, Germany

    Paolo Margaria & Wulf Menzel

  5. Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, MD, 20742, USA

    Sayanta Bera & Anne E. Simon

Authors
  1. Diego F. Quito-Avila
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  2. Edison G. Reyes-Proaño
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  3. Alma Mendoza
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  4. Paolo Margaria
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  5. Wulf Menzel
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  6. Sayanta Bera
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  7. Anne E. Simon
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Contributions

Study conception and design: DFQ-A. Material preparation and data collection were performed by EGR-P and AM. HTS and bioinformatics analyses were performed under the supervision of PM and WM. Sequence and phylogenetic analyses were performed by DFQ-A, SB, and AES. The first draft of the manuscript was written by DFQ-A and AES; all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Diego F. Quito-Avila.

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Conflict of interest

The authors declare no conflict of interest.

Ethics approval

This article does not contain any studies with human participants or animals performed by any of the authors. Plant samples were collected under Genetic Resource Access Permit # MAE–DNB–CM–2018–0098 granted by the Department of Biodiversity of the Ecuadorean Ministry of the Environment.

Additional information

Handling Editor: Massimo Turina .

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Supplementary Information

Below is the link to the electronic supplementary material.

Online resource 1

Summary of virus- or virus-like contigs obtained from high-throughput sequencing based on BLAST searches (BLAST search done on November 3, 2021). (DOCX 17 KB)

Online resource 2

Reverse transcription PCR confirmation of three selected contigs relevant to this study. ‘X’ denotes a positive result. (DOCX 17 KB)

Online resource 3

Maximum-likelihood phylogenetic tree constructed based on the complete nucleotide sequence of the RNA-dependent RNA polymerase (RdRp). Branch numbers indicate bootstrap support as a percentage of 1000 replicates. The scale bar denotes nucleotide substitutions per site. The tree is rooted at the midpoint. The name of each ulaRNA isolate is followed by an underscore and its accession number. (PDF 100 KB)

Supplementary file4 (TXT 6 KB)

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Quito-Avila, D.F., Reyes-Proaño, E.G., Mendoza, A. et al. Two new umbravirus-like associated RNAs (ulaRNAs) discovered in maize and johnsongrass from Ecuador. Arch Virol 167, 2093–2098 (2022). https://doi.org/10.1007/s00705-022-05525-4

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  • DOI: https://doi.org/10.1007/s00705-022-05525-4

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