Muscle5: High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Nov. 15, 2022

Abstract Multiple sequence alignments are widely used to infer evolutionary relationships, enabling inferences of structure, function, and phylogeny. Standard practice is construct one alignment by some preferred method use it in further analysis; however, undetected bias can be problematic. I describe Muscle5, a novel algorithm which constructs an ensemble high-accuracy with diverse biases perturbing hidden Markov model permuting its guide tree. Confidence inference assessed as the fraction supports it. Applied phylogenetic tree estimation, show that ensembles confidently resolve topologies low bootstrap according standard methods, conversely high bootstraps incorrect. phylogeny RNA viruses, analysis shows recently adopted taxonomic phyla probably polyphyletic. Ensemble improve confidence assessment any from alignment.

Language: Английский

---

RdRp-scan: A bioinformatic resource to identify and annotate divergent RNA viruses in metagenomic sequence data

Virus Evolution, Journal Year: 2022, Volume and Issue: 8(2)

Published: July 1, 2022

Despite a rapid expansion in the number of documented viruses following advent metagenomic sequencing, identification and annotation highly divergent RNA remain challenging, particularly from poorly characterized hosts environmental samples. Protein structures are more conserved than primary sequence data, such that structure-based comparisons provide an opportunity to reveal viral 'dusk matter': sequences with low, but detectable, levels identity known available protein structures. Here, we present new open computational resource-RdRp-scan-that contains standardized bioinformatic toolkit identify annotate data based on detection RNA-dependent polymerase (RdRp) sequences. By combining RdRp-specific hidden Markov models (HMMs) structural comparisons, show RdRp-scan can efficiently detect RdRp as low 10 per cent those not identifiable using standard sequence-to-sequence comparisons. In addition, facilitate placement newly detected virus-like into diversity viruses, provides custom curated databases core motifs, well pre-built multiple alignments. parallel, our analysis by revealed while most taxonomically unassigned RdRps fell pre-established clusters, some potentially orders related Wolframvirales Tolivirales. Finally, survey A, B, C motifs within database additional variations both position might insights structure, function, evolution polymerases.

Language: Английский

---

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

---

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

---

Identification of RNA Virus–Derived RdRp Sequences in Publicly Available Transcriptomic Data Sets

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(4)

Published: April 1, 2023

RNA viruses are abundant and highly diverse infect all or most eukaryotic organisms. However, only a tiny fraction of the number diversity virus species have been catalogued. To cost-effectively expand known sequences, we mined publicly available transcriptomic data sets. We developed 77 family-level Hidden Markov Model profiles for viral RNA-dependent polymerase (RdRp)-the universal "hallmark" gene viruses. By using these to search National Center Biotechnology Information Transcriptome Shotgun Assembly database, identified 5,867 contigs encoding RdRps fragments thereof analyzed their diversity, taxonomic classification, phylogeny, host associations. Our study expands viruses, curated RdRp Profile Models provide useful resource discovery community.

Language: Английский

---

Beneath the surface: Unsolved questions in soil virus ecology

Soil Biology and Biochemistry, Journal Year: 2025, Volume and Issue: unknown, P. 109780 - 109780

Published: March 1, 2025

Language: Английский

---

Using artificial intelligence to document the hidden RNA virosphere

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

---

Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians

Virus Evolution, Journal Year: 2022, Volume and Issue: 9(1)

Published: Dec. 26, 2022

The flavivirids (family

Language: Английский

---

Three new clades of putative viral RNA-dependent RNA polymerases with rare or unique catalytic triads discovered in libraries of ORFans from powdery mildews and the yeast of oenological interest Starmerella bacillaris

Virus Evolution, Journal Year: 2022, Volume and Issue: 8(1)

Published: Jan. 1, 2022

High throughput sequencing allowed the discovery of many new viruses and viral organizations increasing our comprehension virus origin evolution. Most RNA are currently characterized through similarity searches annotated databases. This approach limits possibility to detect completely virus-encoded proteins with no detectable similarities existing ones, i.e. ORFan proteins. A strong indication in a metatranscriptome is lack DNA corresponding an assembled sequence biological sample. Furthermore, homology among ORFans evidence co-occurrence these specific host individuals provides further origin. Here, we use this theoretical framework report finding three conserved clades protein-coding segments without fungi. Protein structural alignment suggest distantly related RNA-dependent polymerases (RdRP). In putative RdRP clades, GDD catalytic triad present, but most common NDD clade GDQ, previously unreported at that site. SDD, HDD, ADD also represented. For members were able associate second genomic segment, coding for protein unknown function. We provisionally named group ormycovirus. Interestingly, all one sub-clades (gammaormycovirus) accumulate more minus sense than plus during infection.

Language: Английский

---

Evidence for an ancient aquatic origin of the RNA viral order Articulavirales

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(45)

Published: Oct. 31, 2023

The emergence of previously unknown disease-causing viruses in mammals is part the result a long-term evolutionary process. Reconstructing deep phylogenetic histories helps identify major transitions and contextualizes new hosts. We used combination total RNA sequencing transcriptome data mining to extend diversity history virus order Articulavirales, which includes influenza viruses. identified instances Articulavirales invertebrate phylum Cnidaria (including corals), constituting novel divergent family that we provisionally named "Cnidenomoviridae." further extended lineage by identifying four divergent, fish-associated influenza-like viruses, thereby supporting hypothesis fish were among first hosts In addition, substantially expanded quaranjaviruses proposed this genus be reclassified as family-the "Quaranjaviridae." Within putative family, arachnid-infecting genus, "Cheliceravirus." Notably, observed close relationship between Crustacea- Chelicerata-infecting "Quaranjaviridae" inconsistent with virus-host codivergence. Together, these suggest has evolved over at least 600 million years, emerging aquatic animals. Importantly, evolution was likely shaped multiple aquatic-terrestrial substantial host jumps, some are still observable today.

Language: Английский

---