Widespread Horizontal Gene Transfer Among Animal Viruses

Published: June 5, 2024

The initial objective of this study was to shed light on the evolution small DNA tumor viruses by analyzing de novo assemblies publicly available deep sequencing datasets. survey generated a searchable database contig snapshots representing more than 100,000 Sequence Read Archive records. Using modern structure-aware search tools, we iteratively broadened include an increasingly wide range other virus families. analysis revealed surprisingly diverse chimeras involving different groups. In some instances, genes resembling known DNA-replication modules or virion protein operons were paired with unrecognizable sequences that structural predictions suggest may represent previously unknown replicases and novel architectures. Discrete clades emerging group called adintoviruses discovered in datasets humans primates. As proof concept, show is also useful for discovering RNA candidate archaeal phages. ancillary searches additional examples chimerization between observations support gene-centric taxonomic framework should be future virus-hunting efforts.

Language: Английский

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Single-cell RNA-seq of the rare virosphere reveals the native hosts of giant viruses in the marine environment

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(6), P. 1619 - 1629

Published: April 11, 2024

Language: Английский

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Investigations into the Diversity and Distribution of tRNA and Phylogenetics of Translation Factors in Amoebozoa-Infecting Nucleocytoviricota

Viruses, Journal Year: 2025, Volume and Issue: 17(3), P. 328 - 328

Published: Feb. 27, 2025

Translation is a sine qua non process for life as we know it. factors (TFs) and tRNAs are rare among viruses but commonly found in giant of the class Megaviricetes. In this study, explored diversity distribution that were isolated replicated amoebae (phylum Amoebozoa), investigated evolutionary history TFs to gain insights into their origins these viruses. We analyzed genomes 77 viruses, 52 which contained at least 1 tRNA. most tRNA sequences dispersed throughout genome, except Tupanviruses Yasmineviruses, where clustered specific genomic islands. The often contain introns, with 73.1% exhibiting one intronic region genes. Codon usage bias (CUB) analysis various revealed two distinct patterns codon preferences closely related did not observe clear correlation between presence CUB Due limited size genes, could confidently investigate phylogenetic relationships. However, position sister groups or embedded different eukaryotic taxa high statistical support. Overall, our findings reinforce complexity key components translation apparatus members Nucleocytoviricota from regions Earth.

Language: Английский

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Widespread Horizontal Gene Transfer Among Animal Viruses

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

Published: March 26, 2024

The initial objective of this study was to shed light on the evolution small DNA tumor viruses by analyzing

Language: Английский

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A taxonomic proposal for cedratviruses, orpheoviruses, and pithoviruses

Archives of Virology, Journal Year: 2024, Volume and Issue: 169(6)

Published: June 1, 2024

Orpheoviruses, cedratviruses, and pithoviruses are large DNA viruses that cluster together taxonomically within the order Pimascovirales of phylum Nucleocytoviricota. However, they were not classified previously by International Committee on Taxonomy Viruses (ICTV). Here, we present a comprehensive analysis gene content, morphology, phylogenomics these viruses, providing data underpinned recent proposal to establish new taxa for their initial classification. The taxonomy, which has now been ratified ICTV, includes family Orpheoviridae genus Alphaorpheovirus, Pithoviridae Alphapithovirus, Cedratviridae Alphacedratvirus, aiming formally catalogue isolates covered in this study. Additionally, as per newly adopted rules, applied standardized binomial names virus species created classify with complete genome sequences available public databases at time proposal. specific epithet each was chosen reference location where exemplar isolated.

Language: Английский

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Genomics and evolutionary analysis of Chlorella variabilis- infecting viruses demarcate criteria for defining species of giant viruses

Journal of Virology, Journal Year: 2024, Volume and Issue: 98(11)

Published: Oct. 15, 2024

ABSTRACT Chloroviruses exhibit a close relationship with their hosts the phenotypic aspect of ability to form lytic plaques having primarily guided taxonomy. However, isolation viruses that are only able complete replication cycle in one strain Chlorella variabilis , systematic challenges emerged. In this study, we described genomic features 53 new chlorovirus isolates and used them elucidate part evolutionary history taxonomy clade. Our analysis revealed chloroviruses largest genomes date (>400 kbp) indicated four statistically different infect Syngen 2–3 C. (OSy viruses). We found large regions dissimilarity PBCV-1 OSy-NE5 when compared other genomes. These contained genes related interaction host cell machinery viral capsid proteins, which provided insights into evolution replicative structural modules these giant viruses. Phylogenetic using hallmark Nucleocytoviricota OSy-viruses evolved from NC64A-viruses, possibly emerging as result strict hosts. Merging phylogenetics nucleotide identity analyses, propose strategies demarcate species, resulting seven species chloroviruses. Collectively, our results show how data can be lines evidence species. Using case expect similar initiatives will emerge basis exhibited here. IMPORTANCE group long dsDNA Chlorella- like green algae. They host-specific, some replicate within single . The genomics is still poorly explored, characterization provides important on genetic diversity evolution. work, describe genomes, including many isolated alkaline lakes for first time. Through comparative molecular phylogeny, provide gigantism subset became highly specific at particular point history. criteria chloroviruses, paving way an update groups This study piece complex puzzle algal

Language: Английский

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A long-term prospecting study on giant viruses in terrestrial and marine Brazilian biomes

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

Published: June 10, 2024

Language: Английский

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Proteome-scale structural prediction of the giant Marseillevirus reveals conserved folds and putative homologs of the hypothetical proteins

Archives of Virology, Journal Year: 2024, Volume and Issue: 169(11)

Published: Oct. 16, 2024

Language: Английский

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Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses

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

Published: Nov. 6, 2024

ABSTRACT Borgs are huge extrachromosomal elements of anaerobic methane-oxidizing archaea. They exist in exceedingly complex microbiomes, lack cultivated hosts and have few protein functional annotations, precluding their classification as plasmids, viruses or other. Here, we used silico structure prediction methods to investigate potential roles for ∼10,000 Borg proteins. Prioritizing analysis multicopy genes that could signal importance lifestyles, uncovered highly represented de-ubiquitination-like Zn-metalloproteases may counter host targeting proteins proteolysis. Also prevalent clusters production diverse glycoconjugates contribute decoration the cell surface, putative capsid predict multimerize into hexagonal arrays. Features including megabase-scale linear genomes with inverted terminal repeats, genomic repertoires energy metabolism, central carbon compound transformations translation, pervasive direct repeat regions shared giant eukaryotes, although analyses suggest these parallels arose via convergent evolution. If archaeal they would fill gap tri(um)virate all three domains life. One Sentence Summary Protein analyses, informed by prediction, revealed share numerous features eukaryotic viruses, suggesting a viral-like lifestyle evolutionary convergence large across Domains Life.

Language: Английский

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Cytogenetic characterization of EPSPS gene amplification in glyphosate‐resistant Hordeum glaucum and Bromus diandrus from Australia

The Plant Journal, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 14, 2024

As a result of extensive selection, two polyploid grass weeds, Hordeum glaucum (northern barley grass; 2n = 4x 28) and Bromus diandrus (ripgut brome; 8x 56), have evolved resistance to glyphosate, in Australia. Previous research suggested amplification 5-enolpyruvylshikimate-3-Phosphate synthase (EPSPS) gene confers these weed species. The objective this was investigate the genomic organization EPSPS species through molecular cytogenetic analyses fluorescence situ hybridization (FISH) understand possible mechanism gene. copy number H. B. plants estimated via quantitative polymerase chain reaction. susceptible both had one EPSPS, whereas resistant 14-17 16-32 copies, respectively. FISH analysis glyphosate-susceptible (Hg-RWS) glaucum, revealed four faint signals pairs homologous chromosomes, at telomeric region. glyphosate-resistant (Hg-YP1) also showed regions but were brighter appeared as cluster genes. Similarly, (Bd-S) on position. However, samples glyphosate-resistant, diandrus, Bd-SA988 Bd-Vic much gene, located telomere suggesting an increase copies Overall, unequal crossover during meiosis may triggered initial duplication sparking evolution glyphosate resistance.

Language: Английский

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