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

Abstract

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.ImportanceVirus-virus interactions in plants can modify host symptoms. As a result, disease management strategies may be unsuccessful if they are based solely on visual assessment and diagnostic assays for known individual viruses. Papaya ringspot virus is an important limiting factor for papaya production, and likely has interactions with other viruses that are not yet known. Using high-throughput sequencing, we recovered known and novel RNA and DNA viruses from papaya orchards in Chiapas, Mexico, categorized by host and, in the case of papaya, symptom type: asymptomatic papaya, papaya with ringspot virus symptoms, papaya with non-ringspot symptoms, weeds, and insects. Using network analysis, we demonstrated virus associations within and among host types, and described the ecological community patterns. Recovery of viruses from weeds and asymptomatic papaya suggests the need for additional management attention. These analyses contribute to the understanding of the community structure of viruses in the agroecological landscape.

First report of begomoviruses infecting Cucumis sativus L. in North America and identification of a proposed new begomovirus species

“…At the time of writing this article, the genome sequence of a BGV isolated from an unidentified weed in Chiapas, Mexico was released ( ) ( Alcalá-Briseño et al, 2020 ). When we compared the DNA-A of this virus with those of CuChLV, we found that both DNA-A share a high pairwise identity.…”

A glimpse into the DNA virome of the unique “living fossil” Welwitschia mirabilis

“…WGS DNA datasets have received less attention in virus discovery studies, perhaps given its higher complexity in terms of database size and technical difficulties during processing. However, given their widespread transcription or RNA intermediates it is also possible to detect signatures of DNA viruses from RNAseq datasets, in some cases allowing its characterization and the assembly of complete virus genomes [6,[16][17][18]…”

The Plant Negative-Sense RNA Virosphere: Virus Discovery Through New Eyes

“…In addition, the characterization of a tomato virome resulted in the identification of 22 viruses belonging to 12 genera, but only three genomes corresponded to NSR viruses (Xu et al, 2017). Moreover, the characterization of a papaya virome resulted in the identification of 52 viruses, but only one was a NSR virus (Alcalá-Briseño et al, 2020). It is worth mentioning that typically, virome studies based on HTS generate a significant amount of sequence contigs that lack detectable homology to both the sampled host and any microorganism.…”

“…Thus, it would be useful to apply HTS to complete the genome characterization of these viruses to increase our understanding of plant rhabdovirus diversity. Furthermore, since a tentative nucleorhabdovirus associated with papaya was recently discovered in a papaya virome ( Alcalá-Briseño et al, 2020 ), it would be useful to employ HTS to characterize the molecular properties of papaya apical necrosis virus, a putative nucleorhabdovirus associated with papaya, which was only characterized biologically almost four decades ago ( Lastra and Quintero, 1981 ), to determine if both viruses are related.…”