UF graduate student Ricardo I. Alcalá-Briseño and his mentor plant epidemiologist Karen Garrett earned the distinction of having a “top-viewed” poster at the Plant Health virtual annual meeting of the American Phytopathological Society. The poster, entitled, “A network analysis framework for complex virome data,” folds together three ideas at three different scales, concepts that Alcalá-Briseño has refined during his doctoral studies with Garrett, a UF preeminence professor. The pair are affiliated with UF’s Institute of Food and Agricultural Systems department of plant pathology and Food Systems Institute, and UF’s Emerging Pathogens Institute. They collaborated on the poster with Jan F. Kreuze, of the CGIAR Research Program on Roots, Tubers and Bananas and the International Potato Center.
The team’s work looks at plant diseases threatening crops at the continental and individual host scale but also takes a deep dive into the minutia of viral contigs. These are series of short DNA sequences within a sample that can be matched up to create a physical map of an original viral sequence, not unlike pasting together the shreds of a document to recreate the original whole. Alcalá-Briseño used new machine learning approaches to apply current taxonomic standards for contig classification within a sample. At the scale of a host, they probed how viruses co-occur in virome networks, and how current disease management strategies may not adequately address interactions between virus species if management is based only on a single species. And at the continental scale, the poster addresses cropland connectivity as a factor that may support virus distribution, and the implementation of virus community ecology to inform regional management strategies.
The Virome Network Analysis package being developed by the team incorporates these concepts across multiple scales to analyze viromes in agroecological landscapes using data generated through viral metagenomics.
Written by: DeLene Beeland