Mixed infection of ITPase-encoding potyvirid and secovirid in Mercurialis perennis: evidences for a convergent euphorbia-specific viral counterstrike DOI Creative Commons
Mathieu Mahillon, Justine Brodard,

Nathalie Dubuis

et al.

Virology Journal, Journal Year: 2024, Volume and Issue: 21(1)

Published: Jan. 4, 2024

Abstract Background In cellular organisms, inosine triphosphate pyrophosphatases (ITPases) prevent the incorporation of mutagenic deaminated purines into nucleic acids. These enzymes have also been detected in genomes several plant RNA viruses infecting two euphorbia species. particular, ipomoviruses produce replicase-associated ITPases to cope with high concentration non-canonical nucleotides found cassava tissues. Method Using high-throughput sequencing on wild species Mercurialis perennis , new members families Potyviridae and Secoviridae were identified. Both encode for a putative ITPase, mixed infection partitivirid. Following biological genomic characterization these viruses, origin function phytoviral investigated. Results While potyvirid was shown be pathogenic, secovirid partitivirid could not transmitted. The belonging proposed Comovirinae genus tentatively named "Mercomovirus", which accommodates other identified through transcriptome mining, an asymptomatic pollen-associated lifestyle is suspected. Homology phylogenetic analyses inferred that encoded by likely acquired independent horizontal gene transfer events, forming lineages distinct from ipomoviruses. Possible origins organisms are discussed proteins. parallel, endogenous ITPase M. predicted C-terminal nuclear localization signal, appears conserved among euphorbias but absent families. This subcellular line idea acids remain protected nucleus, while accumulate cytoplasm where they act as antiviral molecules. Conclusion Three described, encoding ITPases. origins, required circumvent level cytoplasmic nucleotides. defense mechanism has emerged early evolution euphorbias, seems specifically target certain groups perennial hosts. Graphical

Language: Английский

Using artificial intelligence to document the hidden RNA virosphere DOI Creative Commons
Xin Hou, Yong He,

Pan Fang

et al.

Cell, Journal Year: 2024, Volume and Issue: 187(24), P. 6929 - 6942.e16

Published: Oct. 9, 2024

Highlights•AI-based metagenomic mining greatly expands the diversity of global RNA virosphere•Developed a deep learning model that integrates sequence and structural information•161,979 putative virus species 180 supergroups were identified•RNA viruses are ubiquitous even found in most extreme environmentsSummaryCurrent tools can fail to identify highly divergent viruses. We developed algorithm, termed LucaProt, discover RNA-dependent polymerase (RdRP) sequences 10,487 metatranscriptomes generated from diverse ecosystems. LucaProt both predicted information, enabling accurate detection RdRP sequences. Using this approach, we identified 161,979 potential supergroups, including many previously poorly studied groups, as well genomes exceptional length (up 47,250 nucleotides) genomic complexity. A subset these novel was confirmed by RT-PCR RNA/DNA sequencing. Newly discovered present environments, air, hot springs, hydrothermal vents, with abundance varying substantially among This study advances discovery, highlights scale virosphere, provides computational better document virome.Graphical abstract

Language: Английский

Citations

29
Using artificial intelligence to document the hidden RNA virosphere DOI Creative Commons
Xin Hou, Yong He, Pan Fang

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: April 18, 2023

Current metagenomic tools can fail to identify highly divergent RNA viruses. We developed a deep learning algorithm, termed LucaProt, discover RNA-dependent polymerase (RdRP) sequences in 10,487 metatranscriptomes generated from diverse global ecosystems. LucaProt integrates both sequence and predicted structural information, enabling the accurate detection of RdRP sequences. Using this approach we identified 161,979 potential virus species 180 supergroups, including many previously poorly studied groups, as well genomes exceptional length (up 47,250 nucleotides) genomic complexity. A subset these novel viruses were confirmed by RT-PCR RNA/DNA sequencing. Newly discovered present environments, air, hot springs hydrothermal vents, diversity abundance varied substantially among This study advances discovery, highlights scale virosphere, provides computational better document virome.

Language: Английский

Citations

22
Metagenomic profiling of rhizosphere microbiota: Unraveling the plant-soil dynamics DOI
Atif Khurshid Wani, Farida Rahayu, Abdullah M. Alkahtani

et al.

Physiological and Molecular Plant Pathology, Journal Year: 2024, Volume and Issue: 133, P. 102381 - 102381

Published: Aug. 20, 2024

Language: Английский

Citations

7
Global phylogenetic analysis of soybean dwarf virus isolates and their associations with aphid vectors and severe disease in soybeans. DOI Creative Commons
Andrew L. Stone,

V. D. Damsteegt,

Oney P. Smith

et al.

Virology, Journal Year: 2024, Volume and Issue: 591, P. 109984 - 109984

Published: Jan. 6, 2024

Soybean dwarf virus (SbDV) was first described in Japan as an agent of severe soybean disease transmitted by the foxglove aphid, Aulacorthum solani, with separable yellowing (Y) and dwarfing (D) strains. SbDV both Y D genotypes were later documented other countries. For three decades, isolates assessed to evaluate risk U.S. production. pea aphid Acyrthosiphum pisum showed limited soybeans, suggesting it not a major threat Here we report 21 new full-length genome sequences including those originally Japanese isolates, from Syria New Zealand associated disease, 17 field collections. Using these genomes, global phylogeny assembled used revisit assessment based on sequence similarities, isolate pathogenicity, vector specificity.

Language: Английский

Citations

5
Managing the deluge of newly discovered plant viruses and viroids: an optimized scientific and regulatory framework for their characterization and risk analysis DOI Creative Commons
Núria Fontdevila Pareta, Maryam Khalili, Ayoub Maachi

et al.

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14

Published: May 30, 2023

The advances in high-throughput sequencing (HTS) technologies and bioinformatic tools have provided new opportunities for virus viroid discovery diagnostics. Hence, sequences of viral origin are being discovered published at a previously unseen rate. Therefore, collective effort was undertaken to write propose framework prioritizing the biological characterization steps needed after discovering plant evaluate its impact different levels. Even though proposed approach widely used, revision these guidelines prepared consider trends integrate novel approaches recently or under development. This updated is more adapted current rate provides an improved prioritization filling knowledge data gaps. It consists four distinct include multi-stakeholder feedback loop. Key improvements better organization various steps, earlier sharing among researchers involved stakeholders, public database screening, exploitation genomic information predict properties.

Language: Английский

Citations

12
Novel Tri-Segmented Rhabdoviruses: A Data Mining Expedition Unveils the Cryptic Diversity of Cytorhabdoviruses DOI Creative Commons
Nicolás Bejerman, Ralf G. Dietzgen, Humberto Debat

et al.

Viruses, Journal Year: 2023, Volume and Issue: 15(12), P. 2402 - 2402

Published: Dec. 10, 2023

Cytorhabdoviruses (genus Cytorhabdovirus, family Rhabdoviridae) are plant-infecting viruses with enveloped, bacilliform virions. Established members of the genus Cytorhabdovirus have unsegmented single-stranded negative-sense RNA genomes (ca. 10–16 kb) which encode four to ten proteins. Here, by exploring large publicly available metatranscriptomics datasets, we report identification and genomic characterization 93 novel genetic evolutionary cues cytorhabdoviruses. Strikingly, five unprecedented tri-segmented were also identified. This finding represents first in Rhabdoviridae, they should be classified a within this for suggest name “Trirhavirus”. Interestingly, nucleocapsid polymerase only typical rhabdoviral proteins encoded those viruses, whereas three them, protein similar emaravirus (family Fimoviridae) silencing suppressor was found, while other predicted had no matches any sequence databases. Genetic distance insights that all these may represent species. Phylogenetic analyses, both previously plant rhabdoviruses, provide compelling support division into distinct genera. proposed reclassification not enhances our understanding dynamics group rhabdoviruses but illuminates remarkable diversity encompass. study significant expansion genomics cytorhabdoviruses will enable future research on peculiarity shows plasticity rhabdovirus genome organization discovery unique trajectory.

Language: Английский

Citations

12
Revisiting a pollen-transmitted ilarvirus previously associated with angular mosaic of grapevine DOI Creative Commons
Mathieu Mahillon, Justine Brodard, R. Schoen

et al.

Virus Research, Journal Year: 2024, Volume and Issue: 344, P. 199362 - 199362

Published: March 22, 2024

We report the characterization of a novel tri-segmented RNA virus infecting Mercurialis annua, common crop weed and model species in plant science. The virus, named "Mercurialis latent virus" (MeLaV) was first identified mixed infection with recently described orthotospovirus 1 (MerV1) on symptomatic plants grown glasshouses Lausanne (Switzerland). Both viruses were found to be transmitted by Thrips tabaci, which presumably help inoculation infected pollen case MeLaV. Complete genome sequencing latter revealed typical ilarviral architecture close phylogenetic relationship members Ilarvirus subgroup 1. Surprisingly, short portion MeLaV replicase identical partial sequence grapevine angular mosaic (GAMV) reported Greece early 1990s. However, we have compiled data that challenge involvement GAMV grapevine, propose alternative causal agents for this disorder. In parallel, three highly-conserved isolates leaf samples Netherlands, including herbarium sample collected 1991. also traced diverse datasets from 2013 2020, corresponding transcriptomic analyses M. annua other five European countries, as well metaviromics bees Belgium. Additional hosts are thus expected MeLaV, yet argue grains likely contaminated several may caused initial GAMV.

Language: Английский

Citations

4
Comparative Transcriptomic and Physiological Analysis of Extremophilic and Non-Extremophilic Fungi in Bioremediation of Cadmium (Cd) and Strontium (Sr) DOI
Toquier Azam, X. J. Dai, Xiaohong Chen

et al.

Environmental Pollution, Journal Year: 2025, Volume and Issue: unknown, P. 125678 - 125678

Published: Jan. 1, 2025

Language: Английский

Citations

0
In-depth analysis of 17,115 rice transcriptomes reveals extensive viral diversity in rice plants DOI Creative Commons

Yu Zhu,

Ali Raza, Qing Bai

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Feb. 12, 2025

Rice viruses seriously threaten rice cultivation and cause significant economic losses, but they have not yet been systematically identified, with only 20 rice-infecting reported. Here, we perform a large-scale analysis of 17,115 RNA-seq libraries spanning 24 Oryza species across 51 countries. Using de novo assembly homology-based methods, identify 810 complete or near-complete viruses, including 276 known 534 novel viruses. Given the high divergence atypical genome organizations more than half them are tentatively assigned to 1 new order, 61 families, at least 104 genera. Utilizing homology-independent approaches, additionally 49 divergent RNA-dependent RNA polymerases (RdRPs), which confirmed by protein structural alignment. Furthermore, analyze metadata related Sequence Read Archive (SRA) estimated viral abundance in each library, leading screening 427 closely associated plants. Overall, our study vastly expands diversity plants, providing insights for prevention control disease. Large-scale metagenomic approach is used viromes into extensive diversity.

Language: Английский

Citations

0
Discovery of novel mycoviruses from fungi associated with mango leaf spots DOI Creative Commons
Qihua Wang, Mengyi Chen, Yanling Xie

et al.

Frontiers in Microbiology, Journal Year: 2025, Volume and Issue: 16

Published: Feb. 26, 2025

Mango (Mangifera indica) is a commercially significant fruit crop cultivated globally. However, leaf spot diseases are common in mango orchards, which severely impact the yield. Mycoviruses hold promise as potential biocontrol agents. To investigate this possibility, fungi were isolated from lesions, resulting identification of six strains that contained double-stranded RNA (dsRNA). Through BLASTx analysis NCBI non-redundant database, 27 mycovirus-related contigs identified, corresponded to 10 distinct viruses grouped into 8 lineages: Alternaviridae, Chrysoviridae, Partitiviridae, Polymycoviridae, Orthototiviridae, Deltaflexiviridae, Narnaviridae, and Bunyaviricetes. Full genomic sequences these characterized confirmed be associated with their host fungi. The findings included novel mycoviruses, three previously unreported discovered new hosts, one virus strain. These results highlight diversity taxonomy mycoviruses found spots.

Language: Английский

Citations

0