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In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem [Elektronski vir]Rivarez, Mark Paul Selda ...Background: In agroecosystems, viruses are well known to influence crop health and some cause phytosanitary and economic problems, but their diversity in non-crop plants and role outside the disease ... perspective is less known. Extensive virome explorations that include both crop and diverse weed plants are therefore needed to better understand roles of viruses in agroecosystems. Such unbiased exploration is available through viromics, which could generate biological and ecological insights from immense high-throughput sequencing (HTS) data. Results: Here, we implemented HTS-based viromics to explore viral diversity in tomatoes and weeds in farming areas at a nation-wide scale. 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, and four non-plant virus families. We detected viruses of non-plant hosts and viroid-like sequences and demonstrated infectivity of a novel tobamovirus in plants of Solanaceae family. Diversities of predominant tomato viruses were variable, in some cases, comparable to that of global isolates of the same species. We phylogenetically classified novel viruses and showed links between a subgroup of phylogenetically related rhabdoviruses to their taxonomically related host plants. Ten classified viruses detected in tomatoes were also detected in weeds, which might indicate possible role of weeds as their reservoirs and that these viruses could be exchanged between the two compartments. Conclusions: We showed 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, which may influence weed management decisions. The observed variability and widespread presence of predominant tomato viruses and the infectivity of a novel tobamovirus in solanaceous plants, provided foundation for further investigation of virus disease dynamics and their effect on tomato health. 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.Source: Microbiome [Elektronski vir]. - ISSN 2049-2618 (Vol. 11, art. 60, 2023, str. [1]-24)Type of material - e-article ; adult, seriousPublish date - 2023Language - englishCOBISS.SI-ID - 148647683
Author
Rivarez, Mark Paul Selda |
Pecman, Anja, 1988- |
Bačnik, Katarina |
Maksimović, Olivera |
Vučurović, Ana |
Seljak, Gabrijel |
Mehle, Nataša, biologinja |
Gutiérrez-Aguirre, Ion |
Ravnikar, Maja |
Kutnjak, Denis
Topics
tomato |
weed |
virus |
viroid |
virome |
virus discovery |
virus diversity |
phylogenetics |
metagenomics |
viromics |
paradižnik |
trava |
virusi |
viroidi |
metagenomika
Author | Rivarez, Mark Paul Selda ... |
Title | In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem [Elektronski vir] |
Publication date | 2023-03-28 |
COBISS.SI-ID | 148647683 |
Publication version in repository | Publisher's version |
Publication licence | Creative Commons Attribution 4.0 International |
Embargo | Immediate publication for public |
Project(s) from which the publication was funded
Title | Acronym | Project ID | Funder |
---|---|---|---|
Innovative Network for Next Generation Training and Sequencing of Virome | INEXTVIR | 813542 |
European Commission |
Biotehnologija in sistemska biologija rastlin | P4-0165-2022 |
Javna agencija za znanstvenoraziskovalno in inovacijsko dejavnost Republike Slovenije |
|
Okoljska in aplikativna virologija: virusi, prijatelji in sovražniki | P4-0407-2019 |
Javna agencija za znanstvenoraziskovalno in inovacijsko dejavnost Republike Slovenije |
|
Nanopore visokozmogljivo sekvenciranje mikrobnih genomov za razrešitev epidemioloških in diagnostičnih vprašanj v rastlinski patologiji | L7-2632-2020 |
Javna agencija za znanstvenoraziskovalno in inovacijsko dejavnost Republike Slovenije |
|
Odkrivanje in z vodo povezana epidemiologija porajajočih se tobamovirusov, ki okužujejo kmetijske rastline | L4-3179-2021 |
Javna agencija za znanstvenoraziskovalno in inovacijsko dejavnost Republike Slovenije |
Files that belong to the publication
Link |
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https://doi.org/10.1186/s40168-023-01500-6 |
https://d.cobiss.net/repository/si/files/148647683/116553/Rivarez_et_al-2023-Microbiome.pdf |
https://dirros.openscience.si/IzpisGradiva.php?id=16442 |
Costs of publication
Cost type | Total cost | Payments |
---|---|---|
APC – Article Processing Charge | 3745.00 € |
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Database name | Field | Year |
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Links to authors' personal bibliographies | Links to information on researchers in the SICRIS system |
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Rivarez, Mark Paul Selda | 54044 |
Pecman, Anja, 1988- | 38081 |
Bačnik, Katarina | 50563 |
Maksimović, Olivera | 53180 |
Vučurović, Ana | 54287 |
Seljak, Gabrijel | 07442 |
Mehle, Nataša, biologinja | 23610 |
Gutiérrez-Aguirre, Ion | 27827 |
Ravnikar, Maja | 05229 |
Kutnjak, Denis | 35384 |
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