The diversity of endogenous viral elements in insects

Bracoviruses represent the most complex endogenous viral elements (EVEs) described to date. Nudiviral genes have been hosted within parasitoid wasp genomes since approximately 100 Ma. They play a crucial role in the wasp life cycle as they produce bracovirus particles, which are injected into parasitized lepidopteran hosts during wasp oviposition. Bracovirus particles encapsidate multiple dsDNA circles encoding virulence genes. Their expression in parasitized caterpillars is essential for wasp parasitism success. Here, we report on the genomic organization of the proviral segments (i.e. master sequences used to produce the encapsidated dsDNA circles) present in the Cotesia congregata parasitoid wasp genome. The provirus is composed of a macrolocus, comprising two-thirds of the proviral segments and of seven dispersed loci, each containing one to three segments. Comparative genomic analyses with closely related species gave insights into the evolutionary dynamics of bracovirus genomes. Conserved synteny in the different wasp genomes showed the orthology of the proviral macrolocus across different species. The nudiviral gene odv-e66-like1 is conserved within the macrolocus, suggesting an ancient co-localization of the nudiviral genome and bracovirus proviral segments. By contrast, the evolution of proviral segments within the macrolocus has involved a series of lineage-specific duplications.

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Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a fragmented IHHNV EVE sequence

10.1101/2021.11.11.468259 ◽

2021 ◽

Author(s):

Roger Huerlimann ◽

Jeff A Cowley ◽

Nicholas M Wade ◽

Yinan Wang ◽

Naga Kasinadhuni ◽

...

Keyword(s):

Genome Assembly ◽

Draft Genome ◽

Penaeus Monodon ◽

Penaeid Shrimp ◽

Protein Coding ◽

Black Tiger Shrimp ◽

Draft Genome Assembly ◽

Repeat Content ◽

Tiger Shrimp ◽

Endogenous Viral Elements

Shrimp are a valuable aquaculture species globally; however, disease remains a major hindrance to shrimp aquaculture sustainability and growth. Mechanisms mediated by endogenous viral elements (EVEs) have been proposed as a means by which shrimp that encounter a new virus start to accommodate rather than succumb to infection over time. However, evidence on the nature of such EVEs and how they mediate viral accommodation is limited. More extensive genomic data on Penaeid shrimp from different geographical locations should assist in exposing the diversity of EVEs. In this context, reported here is a PacBio Sequel-based draft genome assembly of an Australian black tiger shrimp (Penaeus monodon) inbred for one generation. The 1.89 Gbp draft genome is comprised of 31,922 scaffolds (N50: 496,398 bp) covering 85.9% of the projected genome size. The genome repeat content (61.8% with 30% representing simple sequence repeats) is almost the highest identified for any species. The functional annotation identified 35,517 gene models, of which 25,809 were protein-coding and 17,158 were annotated using interproscan. Scaffold scanning for specific EVEs identified an element comprised of a 9,045 bp stretch of repeated, inverted and jumbled genome fragments of Infectious hypodermal and hematopoietic necrosis virus (IHHNV) bounded by a repeated 591/590 bp host sequence. As only near complete linear ~4 kb IHHNV genomes have been found integrated in the genome of P. monodon previously, its discovery has implications regarding the validity of PCR tests designed to specifically detect such linear EVE types. The existence of conjoined inverted IHHNV genome fragments also provides a means by which hairpin dsRNAs could be expressed and processed by the shrimp RNA interference (RNAi) machinery.

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In and Outs of Chuviridae Endogenous Viral Elements: Origin of a Potentially New Retrovirus and Signature of Ancient and Ongoing Arms Race in Mosquito Genomes

Frontiers in Genetics ◽

10.3389/fgene.2020.542437 ◽

2020 ◽

Vol 11 ◽

Cited By ~ 1

Author(s):

Filipe Zimmer Dezordi ◽

Crhisllane Rafaele dos Santos Vasconcelos ◽

Antonio Mauro Rezende ◽

Gabriel Luz Wallau

Keyword(s):

Arms Race ◽

Endogenous Viral Elements

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Evolution of dependoparvoviruses across geological timescales—implications for design of AAV-based gene therapy vectors

Virus Evolution ◽

10.1093/ve/veaa043 ◽

2020 ◽

Vol 6 (2) ◽

Author(s):

Evin Hildebrandt ◽

Judit J Penzes ◽

Robert J Gifford ◽

Mavis Agbandje-Mckenna ◽

Robert M Kotin

Keyword(s):

Gene Therapy ◽

In Silico Analysis ◽

Biological Properties ◽

Variable Regions ◽

Evolution Of Viruses ◽

Extant Species ◽

Gene Therapy Vectors ◽

Endogenous Viral Elements ◽

High Degree ◽

A2 Domain

Abstract Endogenous viral elements (EVEs) are genetic remnants of viruses that have integrated into host genomes millions of years ago and retained as heritable elements passed on to offspring until present-day. As a result, EVEs provide an opportunity to analyse the genomes of extinct viruses utilizing these genomic viral fossils to study evolution of viruses over large timescales. Analysis of sequences from near full-length EVEs of dependoparvoviral origin identified within three mammalian taxa, Whippomorpha (whales and hippos), Vespertilionidae (smooth-nosed bats), and Lagomorpha (rabbits, hares, and pikas), indicates that distinct ancestral dependoparvovirus species integrated into these host genomes approximately 77 to 23 million years ago. These ancestral viruses are unique relative to modern adeno-associated viruses (AAVs), and distinct from extant species of genus Dependoparvovirus. These EVE sequences show characteristics previously unseen in modern, mammalian AAVs, but instead appear more similar to the more primitive, autonomously replicating and pathogenic waterfowl dependoparvoviruses. Phylogeny reconstruction suggests that the whippomorph EVE orthologue derives from exogenous ancestors of autonomous and highly pathogenic dependoparvovirus lineages, believed to have uniquely co-evolved with waterfowl birds to present date. In contrast, ancestors of the two other mammalian orthologues (Lagomorpha and Vespertilionidae) likely shared the same lineage as all other known mammalian exogenous AAVs. Comparative in silico analysis of the EVE genomes revealed remarkable overall conservation of AAV rep and cap genes, despite millions of years of integration within the host germline. Modelling these proteins identified unexpected variety, even between orthologues, in previously defined capsid viral protein (VP) variable regions, especially in those related to the three- and fivefold symmetry axes of the capsid. Moreover, the normally well-conserved phospholipase A2 domain of the predicted minor VP1 also exhibited a high degree of sequence variance. These findings may indicate unique biological properties for these virus ‘fossils’ relative to extant dependoparvoviruses and suggest key regions to explore within capsid sequences that may confer novel properties for engineered gene therapy vectors based on paleovirology data.

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Fighting Fire with Fire: Endogenous Retrovirus Envelopes as Restriction Factors

Journal of Virology ◽

10.1128/jvi.03653-14 ◽

2015 ◽

Vol 89 (8) ◽

pp. 4047-4050 ◽

Cited By ~ 49

Author(s):

Ray Malfavon-Borja ◽

Cédric Feschotte

Keyword(s):

Viral Infection ◽

Domain Architecture ◽

Endogenous Retrovirus ◽

Endogenous Retroviruses ◽

Gene Products ◽

Restriction Factors ◽

Host Protection ◽

Considerable Portion ◽

Endogenous Viral Elements ◽

Host Development

A considerable portion of vertebrate genomes are made up of endogenous retroviruses (ERVs). While aberrant or uncontrolled ERV expression has been perceived as a potential cause of disease, there is mounting evidence that some ERVs have become integral components of normal host development and physiology. Here, we revisit the longstanding concept that some of the gene products encoded by ERVs and other endogenous viral elements may offer to the host protection against viral infection. Notably, proteins produced fromenvelope(env) genes have been shown to act as restriction factors against related exogenous retroviruses in chickens, sheep, mice, and cats. Based on the proposed mode of restriction and the domain architecture of known antiretroviralenv, we argue that many moreenvgene-derived restriction factors await discovery in vertebrate genomes, including the human genome.

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Hidden diversity and macroevolutionary mode of Caulimoviridae uncovered by euphyllophyte paleoviruses

10.1101/170415 ◽

2017 ◽

Cited By ~ 2

Author(s):

Zhen Gong ◽

Guan-Zhu Han

Keyword(s):

Large Scale ◽

Phylogenetic Analyses ◽

Repetitive Elements ◽

Molecular Fossils ◽

Copy Numbers ◽

Minor Part ◽

Endogenous Viral Elements ◽

A Minor ◽

Endogenous Plant

AbstractFew viruses have been documented in plants outside angiosperms. Endogenous viral elements (paleoviruses) provide ‘molecular fossils’ for studying the deep history and macroevolution of viruses. Endogenous plant pararetroviruses (EPRVs) are widespread across angiosperms, but little is known about EPRVs in earlier branching plants. Here we use a large-scale phylogenomic approach to investigate the diversity and macroevolution of plant pararetroviruses (formally known as Caulimoviridae). We uncover an unprecedented and unappreciated diversity of EPRVs in the genomes of gymnosperms and ferns. The known angiosperm viruses only constitute a minor part of the Caulimoviridae diversity. By characterizing the distribution of EPRVs, we show that no major euphyllophyte lineages escape the activity of Caulimoviridae, raising the possibility that many exogenous Caulimoviridae remain to be discovered in euphyllophytes. We find that the copy numbers of EPRVs are generally high, suggesting that EPRVs define a unique group of repetitive elements and represent major components of euphyllophyte genomes. Phylogenetic analyses reveal an ancient monilophyte origin of Caulimoviridae and at least three independent origins of Caulimoviridae in angiosperms by cross-division transmissions. Our findings uncover the remarkable diversity of Caulimoviridae and have important implications in understanding the origin and macroevolution of plant pararetroviruses.

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Non-retroviral endogenous viral element limits cognate virus replication in Aedes aegypti ovaries

10.1101/2020.03.28.013441 ◽

2020 ◽

Cited By ~ 2

Author(s):

Yasutsugu Suzuki ◽

Artem Baidaliuk ◽

Pascal Miesen ◽

Lionel Frangeul ◽

Anna B. Crist ◽

...

Keyword(s):

Aedes Aegypti ◽

Virus Replication ◽

Insect Virus ◽

Functional Link ◽

Naturally Occurring ◽

Specific Virus ◽

Virus Interaction ◽

Endogenous Viral Elements ◽

Viral Sequences

SummaryEndogenous viral elements (EVEs) are viral sequences integrated in host genomes. A large number of non-retroviral EVEs was recently detected in Aedes mosquito genomes, leading to the hypothesis that mosquito EVEs may control exogenous infections by closely related viruses. Here, we experimentally investigated the role of an EVE naturally found in Aedes aegypti populations and derived from the widespread insect-specific virus, cell-fusing agent virus (CFAV). Using CRISPR/Cas9 genome editing, we created an Ae. aegypti line lacking the CFAV EVE. Absence of the EVE resulted in increased CFAV replication in ovaries, possibly modulating vertical transmission of the virus. Viral replication was controlled by targeting of viral RNA by EVE-derived piRNAs. Our results provide evidence that antiviral piRNAs are produced in the presence of a naturally occurring EVE and its cognate virus, demonstrating a functional link between non-retroviral EVEs and antiviral immunity in a natural insect-virus interaction.

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Genome-wide identification of endogenous viral sequences in alfalfa (Medicago sativa L.)

Virology Journal ◽

10.1186/s12985-021-01650-9 ◽

2021 ◽

Vol 18 (1) ◽

Author(s):

Alexander M. Boutanaev ◽

Lev G. Nemchinov

Keyword(s):

Medicago Sativa ◽

Genetic Material ◽

Virus Species ◽

Functional Roles ◽

Genome Wide ◽

Chlorotic Mottle Virus ◽

Chlorotic Mottle ◽

Recent Developments ◽

Living Organisms ◽

Endogenous Viral Elements

AbstractEndogenous viral elements (EVEs) have been for the most part described in animals and to a less extent in plants. The endogenization was proposed to contribute toward evolution of living organisms via horizontal gene transfer of novel genetic material and resultant genetic diversity. During the last two decades, several full-length and fragmented EVEs of pararetroviral and non-retroviral nature have been identified in different plant genomes, both monocots and eudicots. Prior to this work, no EVEs have been reported in alfalfa (Medicago sativa L.), the most cultivated forage legume in the world. In this study, taking advantage of the most recent developments in the field of alfalfa research, we have assessed alfalfa genome on the presence of viral-related sequences. Our analysis revealed segmented EVEs resembling two dsDNA reverse-transcribing virus species: Soybean chlorotic mottle virus (family Caulimoviridae, genus Soymovirus) and Figwort mosaic virus (family Caulimoviridae, genus Caulimovirus). The EVEs appear to be stable constituents of the host genome and in that capacity could potentially acquire functional roles in alfalfa’s development and response to environmental stresses.

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Analysis of the RNA virome of basal hexapods

PeerJ ◽

10.7717/peerj.8336 ◽

2020 ◽

Vol 8 ◽

pp. e8336 ◽

Cited By ~ 1

Author(s):

Sabina Ott Rutar ◽

Dusan Kordis

Keyword(s):

Rna Viruses ◽

Genome Databases ◽

Endogenous Viral Elements ◽

Insight Into ◽

High Diversity

The diversity and evolution of RNA viruses has been well studied in arthropods and especially in insects. However, the diversity of RNA viruses in the basal hexapods has not been analysed yet. To better understand their diversity, evolutionary histories and genome organizations, we searched for RNA viruses in transcriptome and genome databases of basal hexapods. We discovered 40 novel RNA viruses, some of which are also present as endogenous viral elements derived from RNA viruses. Here, we demonstrated that basal hexapods host 14 RNA viral clades that have been recently identified in invertebrates. The following RNA viral clades are associated with basal hexapods: Reo, Partiti-Picobirna, Toti-Chryso, Mono-Chu, Bunya-Arena, Orthomyxo, Qinvirus, Picorna-Calici, Hepe-Virga, Narna-Levi, Tombus-Noda, Luteo-Sobemo, Permutotetra and Flavi. We have found representatives of the nine RNA viral clades that are present as endogenous genomic copies in the genomes of Machilis (Monocondylia) and Catajapyx (Diplura). Our study provided a first insight into the diversity of RNA viruses in basal hexapods and demonstrated that the basal hexapods possess quite high diversity of RNA viral clades.

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