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From Metagenomics to Ecogenomics: NGS-Based Approaches for Discovery of New Circular DNA Single-Stranded Viral Species

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Viral Metagenomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2732))

Abstract

Viruses comprise the most abundant genetic material in the biosphere; however, global viral genomic population (virome) has been largely underestimated. Recently, high-throughput sequencing (HTS) has provided a powerful tool for the detection of known viruses and the discovery of novel viral species from environmental and individual samples using metagenomics and ecogenomics approaches, respectively. Viruses with circular DNA single-stranded (ssDNA) genomes belonging to the begomovirus genera (family Geminiviridae) constitute the largest group of emerging plant viruses worldwide. The knowledge of begomoviruses viromes is mostly restricted to crop plant systems; nevertheless, it has been described that noncultivated plants specifically at the interface between wild and cultivated plants are important reservoirs leading to viral evolution and the emergence of new diseases. Here we present a protocol that allows the identification and isolation of known and novel begomoviruses species infecting cultivated and noncultivated plant species. The method consists of circular viral molecules enrichment by rolling circle amplification (RCA) from begomovirus-positive total plant DNA, followed by NGS-based metagenomic sequencing. Subsequently, metagenomic reads are processed for taxonomic classification using Viromescan software and a customized Geminiviridae family database, and begomovirus-related reads are used for contigs assembly and annotation using Spades software and Blastn algorithm, respectively. Then, the obtained begomovirus-related signatures are used as templates for specific primers design and implemented for PCR-based ecogenomic identification of individual samples harboring the corresponding viral species. Lastly, full-length begomovirus genomes are obtained by RCA-based amplification from total plant DNA of selected individual samples, cloning, and viral molecular identity corroborated by Sanger sequencing. Conclusively, the identification and isolation of a novel monopartite begomovirus species native to the New World (NW) named Gallium leaf deformation virus (GLDV) is shown.

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Acknowledgments

This research was funded by Consejo Nacional de Ciencia y Tecnología (CONACyT-PDCPN No. 214950) and Instituto Politécnico Nacional (SIP 20131613, SIP20141282, SIP20151969, and SIP20164812). EAG-R was supported by a fellowship from the CONACyT and BEIFI programs of IPN.

Author information

Authors and Affiliations

  1. Departamento de Biotecnología Agrícola, Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, Guasave, Sinaloa, Mexico

    Enrique A. Guevara-Rivera, Edgar A. Rodríguez-Negrete, Ángela P. Arce-Leal, Norma E. Leyva-López & Jesús Méndez-Lozano

  2. Department of Plant Biochemistry, Center for Plant Molecular Biology (ZMBP), Eberhard Karls University, Tübingen, Germany

    Rosa Lozano-Durán

  3. Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain

    Eduardo R. Bejarano

  4. Forschungszentrum Jülich, IBG-4: Bioinformatics, Jülich, Germany

    Alan M. Torres-Calderón

Authors
  1. Enrique A. Guevara-Rivera
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  2. Edgar A. Rodríguez-Negrete
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  3. Rosa Lozano-Durán
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  4. Eduardo R. Bejarano
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  5. Alan M. Torres-Calderón
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  6. Ángela P. Arce-Leal
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  7. Norma E. Leyva-López
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  8. Jesús Méndez-Lozano
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Corresponding author

Correspondence to Jesús Méndez-Lozano .

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Editors and Affiliations

  1. Institute for Sustainable Plant Protection, National Research Council, Bari, Italy

    Vitantonio Pantaleo

  2. Institute for Sustainable Plant Protection, National Research Council, Torino, Italy

    Laura Miozzi

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Guevara-Rivera, E.A. et al. (2024). From Metagenomics to Ecogenomics: NGS-Based Approaches for Discovery of New Circular DNA Single-Stranded Viral Species. In: Pantaleo, V., Miozzi, L. (eds) Viral Metagenomics. Methods in Molecular Biology, vol 2732. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3515-5_7

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  • DOI: https://doi.org/10.1007/978-1-0716-3515-5_7

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3514-8

  • Online ISBN: 978-1-0716-3515-5

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