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. We evaluated the viromes of papaya orchards, including weed and insect viromes, to identify common viruses in intensive production of papaya in the Pacific Coastal Plain and the Central Depression of Chiapas, Mexico. Samples of papaya cultivar Maradol, susceptible to papaya ringspot virus (PRSV), were categorized by symptoms by local farmers (papaya ringspot symptoms, non-PRSV symptoms, or asymptomatic). These analyses revealed the presence of 61 viruses, where only 4 species were shared among both regions, 16 showed homology to known viruses, and 36 were homologous with 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, revealing ecological properties of the network, such as an asymmetric nested pattern, and compared the observed network to null models of network association. Understanding the network structure informs management strategies, for example, revealing the potential role of PRSV in asymptomatic papaya and that weeds may be an important pathogen reservoir. We identify three key management implications: (i) each region may need a customized management strategy; (ii) visual assessment of papaya may be insufficient for PRSV, requiring diagnostic assays; and (iii) weed control within orchards may reduce the risk of virus spread to papaya. Network analysis advances understanding of host-pathogen interactions in the agroecological landscape. IMPORTANCE Virus-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, and categorized them by host and, in the case of papaya, symptom type: asymptomatic papaya, papaya with ringspot virus symptoms, papaya with nonringspot 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.

Use of High-Throughput Sequencing and Two RNA Input Methods to Identify Viruses Infecting Tomato Crops

“…One of the main methodological decisions for pool sequencing is the balance between the number of samples to be pooled and the sequencing depth required to detect all viruses present in the pool. According to the literature, the pool composition of different metagenomic studies for plant viromes varied from four to 50 individual samples per pool [ 9 , 12 , 35 , 36 , 37 , 38 , 39 ]. Skums et al [ 40 ] provided a mathematical approach for a pooling strategy for the massive sequencing of human viruses, since the complex nature of these samples imposed restrictions on the pool design [ 40 ].…”

Differential Accumulation of Innate- and Adaptive-Immune-Response-Derived Transcripts during Antagonism between Papaya Ringspot Virus and Papaya Mosaic Virus

“…Mixed infections in papaya plants were documented for some years and more recently in Mexico with up to 15 viruses [21]. However, the mechanisms that underlay the production of symptoms under different viral combinations of mixed infections require further analysis.…”

Global Advances in Tomato Virome Research: Current Status and the Impact of High-Throughput Sequencing

“…Furthermore, the use of long-read (or single molecule) portable sequencing platforms, such as Oxford Nanopore Technologies MinIon, is expected to bring HTS even closer to the end-users (e.g., small research and diagnostics laboratories) and contribute to new viral discoveries in plants, including tomato (Bronzato Badial et al, 2018;Boykin et al, 2019;Chalupowicz et al, 2019). Approaches such as virome network analysis can finally be used to, e.g., associate viromes of the crops to that of the insect vectors or wild plants and can consider biogeographical features of the cropping area (Alcalá-Briseño et al, 2020). With such analyses, new insights can be generated that could be useful in possible forecasting and eventual prevention of virus disease emergence and outbreaks in the future (Garrett et al, 2018;McLeish et al, 2020a).…”