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Naslov:In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem
Avtorji:ID Rivarez, Mark Paul Selda (Avtor)
ID Pecman, Anja (Avtor)
ID Bačnik, Katarina (Avtor)
ID Maksimović, Olivera (Avtor)
ID Vučurović, Ana (Avtor)
ID Seljak, Gabrijel (Avtor)
ID Mehle, Nataša (Avtor)
ID Gutiérrez-Aguirre, Ion (Avtor)
ID Ravnikar, Maja (Avtor)
ID Kutnjak, Denis (Avtor)
Datoteke:URL URL - Izvorni URL, za dostop obiščite https://doi.org/10.1186/s40168-023-01500-6
 
Jezik:Angleški jezik
Tipologija:1.01 - Izvirni znanstveni članek
Organizacija:Logo NIB - Nacionalni inštitut za biologijo
Povzetek: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.
Ključne besede:tomato, weed, virus, viroid, virome, virus discovery, virus diversity, phylogenetics, metagenomics, viromics
Status publikacije:Objavljeno
Verzija publikacije:Objavljena publikacija
Datum objave:28.03.2023
Leto izida:2023
Št. strani:str. [1]-24
Številčenje:Vol. 11, art. 60
PID:20.500.12556/DiRROS-16442 Novo okno
UDK:632
ISSN pri članku:2049-2618
DOI:10.1186/s40168-023-01500-6 Novo okno
COBISS.SI-ID:148647683 Novo okno
Opomba:Nasl. z nasl. zaslona; Opis vira z dne 13. 4. 2023; Soavtorji: Anja Pecman, Katarina Bačnik, Olivera Maksimović, Ana Vučurović, Gabrijel Seljak, Nataša Mehle, Ion Gutiérrez-Aguirre, Maja Ravnikar & Denis Kutnjak; Št. članka: 60;
Datum objave v DiRROS:13.04.2023
Število ogledov:1011
Število prenosov:242
Metapodatki:XML DC-XML DC-RDF
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Gradivo je del revije

Naslov:Microbiome
Skrajšan naslov:Microbiome
Založnik:BioMed Central
ISSN:2049-2618
COBISS.SI-ID:523276313 Novo okno

Gradivo je financirano iz projekta

Financer:EC - European Commission
Program financ.:European Commission
Številka projekta:813542
Naslov:Innovative Network for Next Generation Training and Sequencing of Virome
Akronim:INEXTVIR

Financer:ARRS - Agencija za raziskovalno dejavnost Republike Slovenije
Številka projekta:P4-0165-2022
Naslov:Biotehnologija in sistemska biologija rastlin

Financer:ARRS - Agencija za raziskovalno dejavnost Republike Slovenije
Številka projekta:P4-0407-2019
Naslov:Okoljska in aplikativna virologija: virusi, prijatelji in sovražniki

Financer:ARRS - Agencija za raziskovalno dejavnost Republike Slovenije
Številka projekta:L7-2632-2020
Naslov:Nanopore visokozmogljivo sekvenciranje mikrobnih genomov za razrešitev epidemioloških in diagnostičnih vprašanj v rastlinski patologiji

Financer:ARRS - Agencija za raziskovalno dejavnost Republike Slovenije
Številka projekta:L4-3179-2021
Naslov:Odkrivanje in z vodo povezana epidemiologija porajajočih se tobamovirusov, ki okužujejo kmetijske rastline

Financer:Drugi - Drug financer ali več financerjev
Program financ.:Balik Scientist Program
Številka projekta:Republic Act 11035

Financer:Drugi - Drug financer ali več financerjev
Program financ.:Natural Resources Research and Development
Številka projekta:DOST–PCAARRD

Licence

Licenca:CC BY 4.0, Creative Commons Priznanje avtorstva 4.0 Mednarodna
Povezava:http://creativecommons.org/licenses/by/4.0/deed.sl
Opis:To je standardna licenca Creative Commons, ki daje uporabnikom največ možnosti za nadaljnjo uporabo dela, pri čemer morajo navesti avtorja.

Sekundarni jezik

Jezik:Slovenski jezik
Ključne besede:paradižnik, trava, virusi, viroidi, metagenomika


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