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In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem

Rivarez, M. P. S., Pecman, A., Bačnik, K., Maksimović Carvalho Ferreira, O., Vučurović, A., Seljak, G., Mehle, N., Gutiérrez-Aguirre, I., Ravnikar, M., & Kutnjak, D. (2022). In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem. BioRxiv, 2022.06.30.498278. https://doi.org/10.1101/2022.06.30.498278 In this comprehensive virome study of tomato agroecosystems in Slovenia, we have investigated presence of viruses in tomatoes and weeds and discovered a high amount of virus diversity in these two sample types. Most strikingly, a high amount of previously unknown viruses were detected in wild plant species (“weeds”) that surrounded tomato farming sites.

We detected 125 viruses, including 79 novel species, wherein 65 were found exclusively in weeds. This spanned 21 higher-level plant virus taxa dominated by Potyviridae, Rhabdoviridae, and Tombusviridae. We detected viruses of non-plant hosts and viroid-like sequences, and demonstrated infectivity of a novel tobamovirus in plants of Solanaceae family.This shows that even in relatively well studied agroecosystems, such as tomato farms, a large part of very diverse plant viromes can still be unknown and is mostly present in understudied non-crop plants. The overlapping presence of viruses in tomatoes and weeds implicate possible presence of virus reservoir and possible exchange between the weed and crop compartments. The extensive insights we generated from such in-depth agroecosystem virome exploration will be valuable in anticipating possible emergences of plant virus diseases, and would serve as baseline for further post-discovery characterization studies. 




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