Hybrids of RNA viruses and viroid-like elements replicate in fungi

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: May 5, 2023

Earth's life may have originated as self-replicating RNA, and it has been argued that RNA viruses viroid-like elements are remnants of such pre-cellular world. defined by linear genomes encoding an RNA-dependent polymerase (RdRp), whereas consist small, single-stranded, circular that, in some cases, encode paired self-cleaving ribozymes. Here we show the number candidate occurring geographically ecologically diverse niches is much higher than previously thought. We report amongst these genomes, fungal ambiviruses undergo rolling circle replication their own viral RdRp. Thus, distinct infectious RNAs showing hybrid features viruses. also detected similar RNAs, containing active ribozymes RdRps, related to mitochondrial-like viruses, highlighting fungi evolutionary hub for elements. Our findings point a deep co-evolutionary history between subviral offer new perspectives origin evolution primordial agents, life.

Language: Английский

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

Microbiome, Journal Year: 2023, Volume and Issue: 11(1)

Published: March 28, 2023

Abstract Background In agroecosystems, viruses are well known to influence crop health and some cause phytosanitary economic problems, but their diversity in non-crop plants role outside the disease perspective is less known. Extensive virome explorations that include both diverse weed therefore needed better understand roles of agroecosystems. Such unbiased exploration available through viromics, which could generate biological ecological insights from immense high-throughput sequencing (HTS) data. Results Here, we implemented HTS-based viromics explore viral tomatoes weeds farming areas at a nation-wide scale. We detected 125 viruses, including 79 novel species, wherein 65 were found exclusively weeds. This spanned 21 higher-level plant virus taxa dominated by Potyviridae , Rhabdoviridae Tombusviridae four non-plant families. hosts viroid-like sequences demonstrated infectivity tobamovirus Solanaceae family. Diversities predominant tomato variable, cases, comparable global isolates same species. phylogenetically classified showed links between subgroup related rhabdoviruses taxonomically host plants. Ten also weeds, might indicate possible as reservoirs these be exchanged two compartments. Conclusions even relatively studied such farms, large part very viromes can still unknown mostly present understudied The overlapping presence implicate reservoir exchange compartments, may management decisions. observed variability widespread solanaceous plants, provided foundation for further investigation dynamics effect on health. extensive generated in-depth agroecosystem will valuable anticipating emergences diseases would serve baseline post-discovery characterization studies.

Language: Английский

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You can move, but you can't hide: identification of mobile genetic elements with geNomad

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

Published: March 6, 2023

Identifying and characterizing mobile genetic elements (MGEs) in sequencing data is essential for understanding their diversity, ecology, biotechnological applications, impact on public health. Here, we introduce geNomad, a classification annotation framework that combines information from gene content deep neural network to identify sequences of plasmids viruses. geNomad uses large dataset marker proteins provide functional taxonomic assignment viral genomes. Using conditional random field model, also detects proviruses integrated into host genomes with high precision. In benchmarks included diverse MGE chromosome sequences, significantly outperformed other tools all evaluated clades Leveraging geNomad's speed scalability, were able process metagenomes metatranscriptomes, leading the discovery millions new viruses are available through IMG/VR IMG/PR databases. We anticipate will enable further advancements research, it at https://portal.nersc.gov/genomad.

Language: Английский

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SingleM and Sandpiper: Robust microbial taxonomic profiles from metagenomic data

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 31, 2024

Determining the taxonomy and relative abundance of microorganisms in metagenomic data is a foundational problem microbial ecology. To address limitations existing approaches, we developed ‘SingleM’, which estimates community composition using conserved regions within universal marker genes. SingleM accurately profiles complex communities known species, only tool that detects species without genomic representation, even those representing novel phyla. Given SingleM’s computational efficiency, applied it to 248,559 publicly available metagenomes show vast majority samples from marine, freshwater, sediment soil environments are dominated by lacking representation (median 75.0%). also provides way identify for recovery metagenome-assembled genomes lineages interest, can incorporate user-recovered into its reference database improve profiling resolution. Quantifying full diversity Bacteria Archaea shows genome databases far saturated.

Language: Английский

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High-quality metagenome assembly from long accurate reads with metaMDBG

Nature Biotechnology, Journal Year: 2024, Volume and Issue: 42(9), P. 1378 - 1383

Published: Jan. 2, 2024

Abstract We introduce metaMDBG, a metagenomics assembler for PacBio HiFi reads. MetaMDBG combines de Bruijn graph assembly in minimizer space with an iterative over sequences of minimizers to address variations genome coverage depth and abundance-based filtering strategy simplify strain complexity. For complex communities, we obtained up twice as many high-quality circularized prokaryotic metagenome-assembled genomes existing methods had better recovery viruses plasmids.

Language: Английский

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Using artificial intelligence to document the hidden RNA virosphere

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

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Megataxonomy and global ecology of the virosphere

The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)

Published: Jan. 1, 2024

Nearly all organisms are hosts to multiple viruses that collectively appear be the most abundant biological entities in biosphere. With recent advances metagenomics and metatranscriptomics, known diversity of substantially expanded. Comparative analysis these using advanced computational methods culminated reconstruction evolution major groups enabled construction a virus megataxonomy, which has been formally adopted by International Committee on Taxonomy Viruses. This comprehensive taxonomy consists six realms, aspired monophyletic assembled based conservation hallmark proteins involved capsid structure formation or genome replication. The different taxa differ host range accordingly ecological niches. In this review article, we outline latest developments megataxonomy discoveries will likely lead reassessment some taxa, particular, split three current realms into two more independent realms. We then discuss correspondence between distribution among niches, as well abundance versus cells habitats. across environments appears primarily determined ranges, i.e. virome is shaped composition biome given habitat, itself affected abiotic factors.

Language: Английский

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Viroid-like colonists of human microbiomes

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 21, 2024

Here, we describe the "Obelisks," a previously unrecognised class of viroid-like elements that first identified in human gut metatranscriptomic data. "Obelisks" share several properties: (i) apparently circular RNA ~1kb genome assemblies, (ii) predicted rod-like secondary structures encompassing entire genome, and (iii) open reading frames coding for novel protein superfamily, which call "Oblins". We find Obelisks form their own distinct phylogenetic group with no detectable sequence or structural similarity to known biological agents. Further, are prevalent tested microbiome metatranscriptomes representatives detected ~7% analysed stool (29/440) ~50% oral (17/32). Obelisk compositions appear differ between anatomic sites capable persisting individuals, continued presence over >300 days observed one case. Large scale searches 29,959 (clustered at 90% nucleotide identity), examples from all seven continents diverse ecological niches. From this search, subset code Obelisk-specific variants hammerhead type-III self-cleaving ribozyme. Lastly, case bacterial species (Streptococcus sanguinis) defined laboratory strains harboured specific population. As such, comprise RNAs have colonised, gone unnoticed in, human, global microbiomes.

Language: Английский

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Diverse and abundant phages exploit conjugative plasmids

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: April 12, 2024

Phages exert profound evolutionary pressure on bacteria by interacting with receptors the cell surface to initiate infection. While majority of phages use chromosomally encoded structures as receptors, plasmid-dependent exploit plasmid-encoded conjugation proteins, making their host range dependent horizontal transfer plasmid. Despite unique biology and biotechnological significance, only a small number have been characterized. Here we systematically search for new targeting IncP IncF plasmids using targeted discovery platform, find that they are common abundant in wastewater, largely unexplored terms genetic diversity. Plasmid-dependent enriched non-canonical types phages, all but one 65 isolated were non-tailed, members lipid-containing tectiviruses, ssDNA filamentous or ssRNA phages. We show tectiviruses exhibit differences which is associated variation phage holin protein. relatively high abundance missed metaviromic analyses, underscoring continued importance culture-based discovery. Finally, identify tailed plasmid, related structural genes orthogonal type 4 pilus receptor, highlighting evolutionarily promiscuous these distinct contractile multiple groups Taken together, results indicate play an under-appreciated role constraining gene via conjugative plasmids.

Language: Английский

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Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer

Cell Systems, Journal Year: 2021, Volume and Issue: 12(10), P. 958 - 968.e6

Published: Sept. 14, 2021

DNA sequencing data continue to progress toward longer reads with increasingly lower error rates. Here, we define an algorithmic approach, mdBG, that makes use of minimizer-space de Bruijn graphs enable long-read genome assembly. mdBG achieves orders-of-magnitude improvement in both speed and memory usage over existing methods without compromising accuracy. A human is assembled under 10 min using 8 cores GB RAM, 60 Gbp metagenome are 4 1 RAM. In addition, constructed a graph-based representation 661,405 bacterial genomes, comprising 16 million nodes 45 edges, successfully search it for anti-microbial resistance (AMR) genes 12 min. We expect our advances be essential sequence analysis, given the rise genomics, metagenomics, pangenomics. Code constructing mdBGs freely available download at https://github.com/ekimb/rust-mdbg/.

Language: Английский

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