Origins and Evolution of the Global RNA Virome

mBio, Год журнала: 2018, Номер 9(6)

Опубликована: Ноя. 26, 2018

The majority of the diverse viruses infecting eukaryotes have RNA genomes, including numerous human, animal, and plant pathogens. Recent advances metagenomics led to discovery many new groups in a wide range hosts. These findings enable far more complete reconstruction evolution than was attainable previously. This reveals relationships between different Baltimore classes indicates extensive transfer distantly related hosts, such as plants animals. results call for major revision existing taxonomy viruses.

Язык: Английский

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Metagenomics reshapes the concepts of RNA virus evolution by revealing extensive horizontal virus transfer

Virus Research, Год журнала: 2017, Номер 244, С. 36 - 52

Опубликована: Ноя. 8, 2017

Virus metagenomics is a young research filed but it has already transformed our understanding of virus diversity and evolution, illuminated at new level the connections between evolution ecology hosts. In this review article, we examine picture RNA viruses, dominant component eukaryotic virome, that emerging from metagenomic data analysis. The major expansion many groups viruses through allowed construction substantially improved phylogenetic trees for conserved genes, primarily, RNA-dependent polymerases (RdRp). particular, superfamily widespread, small positive-strand was delineated unites tombus-like noda-like viruses. Comparison genome architectures discovered by traditional methods reveals an extent gene module shuffling among diverse genomes far exceeds previous appreciation evolutionary phenomenon. Most dramatically, inclusion in analyses RdRp resulted identification numerous, strongly supported encompass hosts including different protists, animals plants. Notwithstanding potential caveats, incomplete uneven sampling taxa, these highly unexpected findings reveal horizontal transfer (HVT) as central aspect evolution. vast virome invertebrates, particularly nematodes arthropods, appears to be reservoir, which viromes plants vertebrates evolved via multiple HVT events.

Язык: Английский

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A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations

Journal of Virology, Год журнала: 2017, Номер 91(16)

Опубликована: Май 18, 2017

ABSTRACT Understanding the diversity and consequences of viruses present in honey bees is critical for maintaining pollinator health managing spread disease. The viral landscape ( Apis mellifera ) has changed dramatically since emergence parasitic mite Varroa destructor , which increased virulent variants such as deformed wing virus. Previous genomic studies have focused on colonies suffering from infections by viruses, could mask other species bees, resulting a distorted view diversity. To capture within that are exposed to mites but do not suffer ultimate infestation, we examined populations evolved naturally or been selected resistance . This analysis revealed seven novel isolated sampled globally, including first identification negative-sense RNA bees. Notably, two rhabdoviruses were three geographically diverse locations also parasitizing characterize antiviral response, performed deep sequencing small mites. provided evidence Dicer-mediated immune response while profile was distinct observed Overall, show bee greater than previously thought, encourages additional virome global scale may ultimately improve disease management. IMPORTANCE Honey become increasingly susceptible colony losses due pathogenic date, 24 described with most belonging order Picornavirales Collapsing -infected often overwhelmed high levels picornaviruses. examine underlying employed metatranscriptomics analyses Varroa- resistant Europe, Africa, Pacific. We describe range families, all locations. In sequences indicate these processed Dicer interference pathway, whereas produce strikingly patterns. work increases number known will contribute improved management our important agricultural pollinator.

Язык: Английский

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Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses

Molecular Biology and Evolution, Год журнала: 2020, Номер 37(9), С. 2661 - 2678

Опубликована: Май 9, 2020

Genetic variation is the fuel of evolution, with standing genetic especially important for short-term evolution and local adaptation. To date, studies spatiotemporal patterns in natural populations have been challenging, as comprehensive sampling logistically difficult, sequencing entire costly. Here, we address these issues using a collaborative approach, 48 pooled population samples from 32 locations, perform first continent-wide genomic analysis European Drosophila melanogaster. Our analyses uncover longitudinal structure, provide evidence selective sweeps, identify candidate genes climate adaptation, document clines chromosomal inversion transposable element frequencies. We also characterize among composition fly microbiome, five new DNA viruses our samples.

Язык: Английский

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A planarian nidovirus expands the limits of RNA genome size

PLoS Pathogens, Год журнала: 2018, Номер 14(11), С. e1007314 - e1007314

Опубликована: Ноя. 1, 2018

RNA viruses are the only known RNA-protein (RNP) entities capable of autonomous replication (albeit within a permissive host environment). A 33.5 kilobase (kb) nidovirus has been considered close to upper size limit for such entities; conversely, minimal cellular DNA genome is in 100–300 kb range. This large difference presents daunting gap transition from primordial RNP contemporary DNA-RNP-based life. Whether or not represent transitional steps towards DNA-based life, studies larger advance our understanding constraints on and role virus adaptation. For example, emergence largest previously genomes (20–34 positive-stranded nidoviruses, including coronaviruses) associated with acquisition proofreading exoribonuclease (ExoN) encoded open reading frame 1b (ORF1b) monophyletic subset nidoviruses. However, apparent ORF1b, which encodes this other key replicative enzymes, have hypothesized further expansion these viral genomes. Here, we characterize novel (planarian secretory cell nidovirus; PSCNV) whose disproportionately ORF1b-like region unannotated domains, overall 41.1-kb genome, substantially extend presumed limits size. predicted 13,556-aa polyprotein an unconventional single ORF, yet retains canonical nidoviral organization expression, as well domains. These domains may include functionally relevant substitutions rarely never before observed highly conserved sites RdRp, NiRAN, ExoN 3CLpro. Our evolutionary analysis suggests that PSCNV diverged early multi-ORF acquired additional genes, those typical hosts, e.g. Ankyrin Fibronectin type II, might modulate virus-host interactions. PSCNV's greatly expanded proteomic complexity, unique features–impressive themselves–attest likelihood still-larger awaiting discovery.

Язык: Английский

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Mosquito Small RNA Responses to West Nile and Insect-Specific Virus Infections in Aedes and Culex Mosquito Cells

Viruses, Год журнала: 2019, Номер 11(3), С. 271 - 271

Опубликована: Март 18, 2019

Small RNA mediated responses are essential for antiviral defence in mosquitoes, however, they appear to differ per virus-vector combination. To further investigate the diversity of small against viruses we applied a deep sequencing approach on five mosquito cell lines: Culex tarsalis CT cells, Aedes albopictus U4.4 and C6/36 Ae. aegypti Aag2 cells (cleared from fusing agent virus Y (CYV) by repetitive dsRNA transfections) pseudoscutellaris AP-61 cells. De novo assembly RNAs revealed presence Phasi Charoen-like (PCLV), Calbertado virus, Flock House novel narnavirus CYV PCLV whereas no insect-specific (ISVs) were detected Next, investigated identified ISVs acute infection with arthropod-borne West Nile (WNV). We demonstrate that do not produce siRNAs WNV infection, suggesting AP-61, like C6/36, Dicer-2 deficient. produced strong siRNA response persistent infection. Interestingly, also viral PIWI-interacting (pi)RNAs PCLV, but or any other ISVs. In contrast, siRNAs, pi-like without typical ping-pong piRNA signature observed, while this was present piRNAs Together, our results strongly dependent both type and/or species family infecting virus.

Язык: Английский

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Ythdf is a N6‐methyladenosine reader that modulates Fmr1 target mRNA selection and restricts axonal growth in Drosophila

The EMBO Journal, Год журнала: 2021, Номер 40(4)

Опубликована: Янв. 11, 2021

Abstract N6‐methyladenosine (m 6 A) regulates a variety of physiological processes through modulation RNA metabolism. This modification is particularly enriched in the nervous system several species, and its dysregulation has been associated with neurodevelopmental defects neural dysfunctions. In Drosophila , loss m A alters fly behavior, albeit underlying molecular mechanism role during development have remained elusive. Here we find that impairment pathway leads to axonal overgrowth misguidance at larval neuromuscular junctions as well adult mushroom bodies. We identify Ythdf main reader system, being required limit growth. Mechanistically, show directly interacts Fmr1, homolog Fragile X mental retardation binding protein (FMRP), inhibit translation key transcripts involved growth regulation. Altogether, this study demonstrates controls modulates Fmr1 target transcript selection.

Язык: Английский

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Study of the Metatranscriptome of Eight Social and Solitary Wild Bee Species Reveals Novel Viruses and Bee Parasites

Frontiers in Microbiology, Год журнала: 2018, Номер 9

Опубликована: Фев. 14, 2018

Bees are associated with a remarkable diversity of microorganisms, including unicellular parasites, bacteria, fungi, and viruses. The application next-generation sequencing approaches enables the identification this rich species composition as well discovery previously unknown associations. Using high-throughput polyadenylated ribonucleic acid (RNA) sequencing, we investigated metatranscriptome eight wild bee (Andrena cineraria, Andrena fulva, haemorrhoa, Bombus terrestris, cryptarum, pascuorum, Osmia bicornis, cornuta) sampled from four different localities in Belgium. Across RNA libraries, 88-99% taxonomically informative reads were host transcriptome. Four viruses homology to insect pathogens found two (belonging families Iflaviridae Tymoviridae that harbor already honey bees), double stranded DNA virus (family Nudiviridae) single Parvoviridae). In addition, genomic sequences 11 unclassified arthropod (related negeviruses, sobemoviruses, totiviruses, rhabdoviruses, mononegaviruses), seven plant pathogenic viruses, one fungal virus. Interestingly, nege-like appear be widespread, host-specific, capable attaining high copy numbers inside bees. Next three novel parasite associations discovered bees, Crithidia pragensis tubulinosematid neogregarine parasite. Yeasts genus Metschnikowia identified solitary This study gives glimpse microorganisms social bees demonstrates their exceeds by far subset first

Язык: Английский

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Metagenomic analysis of Varroa-free Australian honey bees (Apis mellifera) shows a diverse Picornavirales virome

Journal of General Virology, Год журнала: 2018, Номер 99(6), С. 818 - 826

Опубликована: Май 11, 2018

The viral landscape of the honey bee (Apismellifera) has changed as a consequence global spread parasitic mite Varroa destructor and accompanying virulent strains iflavirus deformed wing virus (DWV), which vectors. presence DWV in populations is known to influence occurrence other viruses, suggesting that current virome A. mellifera may be undercharacterized. Here we tested this hypothesis by examining Australia, uniquely free mites or DWV. Using high-throughput sequencing (HTS) approach, examined RNA from nine pools across Australia. In addition previously reported several insect viruses were detected, including related aphid lethal paralysis (ALPV) Rhopalosiphum padi (RhPV), have recently been identified infecting bees USA, well found Drosophila spp. A further 42 putative novel genomes spanning order Picornavirales assembled, significantly increases diversity mellifera. Among these genomes, similar (but different) key such DWV, warrant investigation. We propose preferentially infected with diverse population representative Varroa-free landscape.

Язык: Английский

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The virome of Drosophila suzukii, an invasive pest of soft fruit

Virus Evolution, Год журнала: 2018, Номер 4(1)

Опубликована: Янв. 1, 2018

Drosophila suzukii (Matsumura) is one of the most damaging and costly pests to invade temperate horticultural regions in recent history. Conventional control this pest challenging, an environmentally benign microbial biopesticide highly desirable. A thorough exploration pathogens infecting not only first step on road development effective biopesticide, but also provides a valuable comparative dataset for study viruses model family Drosophilidae. Here we use metatransciptomic approach identify fly both its native (Japanese) invasive (British French) ranges. We describe eighteen new RNA viruses, including members Picornavirales, Mononegavirales, Bunyavirales, Chuviruses, Nodaviridae, Tombusviridae, Reoviridae, Nidovirales, discuss their phylogenetic relationships with previously known viruses. detect 18 described other species that appear be associated D. wild.

Язык: Английский

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