Network analysis of the papaya orchard virome from two agroecological regions of Chiapas, Mexico

The study of complex ecological interactions - such as those among host, pathogen, and vector communities - can help to explain host ranges and the emergence of novel pathogens. The analysis of community structures using bipartite networks describe the associations between two trophic levels, for ex...

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Published inbioRxiv
Main Authors Alcalá-Briseño, Ricardo Ivan, Casarrubias-Castillo, Kena, López-Ley, Diana, Garrett, Karen, Silva-Rosales, Laura
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 20.07.2019
Subjects
Cultivars
DNA viruses
Genomes
Homology
Host-parasite interactions
Orchards
Pathogens
Pollinators
RNA viruses
Trophic levels
Viruses
Mexico
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Summary:The study of complex ecological interactions - such as those among host, pathogen, and vector communities - can help to explain host ranges and the emergence of novel pathogens. The analysis of community structures using bipartite networks describe the associations between two trophic levels, for example plants and pollinators, or hosts and parasitoids. Bipartite networks represent interactions (links) occurring only between nodes in different levels - in our case, between viruses and hosts. We evaluated the viromes of papaya orchards (papaya, weeds, and insects) from intensive production of papaya in the Pacific Coastal Plain and the Central Depression of Chiapas, Mexico. Samples of papaya cultivar Maradol, which, like most cultivars, is susceptible to papaya ringspot virus (PRSV), were categorized by symptoms by local farmers (papaya ringspot symptoms, non-PRSV symptoms, or no symptoms). These analyses revealed the presence of 61 viruses, where only four species were shared among both physiographic regions. Nearly 52 complete viral genome sequences were recovered, of which 16 showed homology to known viruses, and 36 shared similarities with different genera including Potyvirus, Comovirus and Tombusvirus (RNA viruses), and Begomovirus and Mastrevirus (DNA viruses). We analyzed the network of associations between viruses and host-location combinations, and described ecological properties of the network, such as asymmetry in interactions and nestedness compared to null models. Understanding the network structure informs management strategies, and advances understanding of interactions of hosts and viruses in the agroecological landscape.
DOI:10.1101/708479