scholarly journals Phylogeny of the Varidnaviria Morphogenesis Module: Congruence and Incongruence With the Tree of Life and Viral Taxonomy

2021 ◽  
Vol 12 ◽  
Author(s):  
Anthony C. Woo ◽  
Morgan Gaia ◽  
Julien Guglielmini ◽  
Violette Da Cunha ◽  
Patrick Forterre
Keyword(s):  
Evolutionary History ◽  
International Committee ◽  
Tree Of Life ◽  
Dna Viruses ◽  
Origin And Evolution ◽  
Double Stranded Dna ◽  
Domains Of Life ◽  
History Of ◽  
Recent Classification ◽  
Jelly Roll

Double-stranded DNA viruses of the realm Varidnaviria (formerly PRD1-adenovirus lineage) are characterized by homologous major capsid proteins (MCPs) containing one (kingdom: Helvetiavirae) or two β-barrel domains (kingdom: Bamfordvirae) known as the jelly roll folds. Most of them also share homologous packaging ATPases (pATPases). Remarkably, Varidnaviria infect hosts from the three domains of life, suggesting that these viruses could be very ancient and share a common ancestor. Here, we analyzed the evolutionary history of Varidnaviria based on single and concatenated phylogenies of their MCPs and pATPases. We excluded Adenoviridae from our analysis as their MCPs and pATPases are too divergent. Sphaerolipoviridae, the only family in the kingdom Helvetiavirae, exhibit a complex history: their MCPs are very divergent from those of other Varidnaviria, as expected, but their pATPases groups them with Bamfordvirae. In single and concatenated trees, Bamfordvirae infecting archaea were grouped with those infecting bacteria, in contradiction with the cellular tree of life, whereas those infecting eukaryotes were organized into three monophyletic groups: the Nucleocytoviricota phylum, formerly known as the Nucleo-Cytoplasmic Large DNA Viruses (NCLDVs), Lavidaviridae (virophages) and Polintoviruses. Although our analysis mostly supports the recent classification proposed by the International Committee on Taxonomy of Viruses (ICTV), it also raises questions, such as the validity of the Adenoviridae and Helvetiavirae ranking. Based on our phylogeny, we discuss current hypotheses on the origin and evolution of Varidnaviria and suggest new ones to reconcile the viral and cellular trees.

scholarly journals Evolution of the PRD1-adenovirus lineage: a viral tree of life incongruent with the cellular universal tree of life

2019 ◽  
Author(s):  
Anthony C. Woo ◽  
Morgan Gaia ◽  
Julien Guglielmini ◽  
Violette Da Cunha ◽  
Patrick Forterre
Keyword(s):  
Evolutionary History ◽  
Common Ancestor ◽  
Tree Of Life ◽  
Capsid Proteins ◽  
Dna Viruses ◽  
Universal Tree ◽  
Double Stranded Dna ◽  
Domains Of Life ◽  
History Of ◽  
Jelly Roll

AbstractDouble-stranded DNA viruses of the PRD1-adenovirus lineage are characterized by homologous major capsid proteins containing one or two β-barrel domains known as the jelly roll folds. Most of them also share homologous packaging ATPases of the FtsK/HerA superfamily P-loop ATPases. Remarkably, members of this lineage infect hosts from the three domains of life, suggesting that viruses from this lineage could be very ancient and share a common ancestor. Here we analyzed the evolutionary history of these cosmopolitan viruses by inferring phylogenies based on single or concatenated genes. These viruses can be divided into two supergroups infecting either eukaryotes or prokaryotes. The latter can be further divided into two groups of bacterioviruses and one group of archaeoviruses. This viral tree is thus incongruent with the cellular tree of life in which Archaea are closer to Eukarya and more divergent from Bacteria. We discuss various evolutionary scenarios that could explain this paradox.

scholarly journals Crustacean Genome Exploration Reveals the Evolutionary Origin of White Spot Syndrome Virus

2018 ◽  
Vol 93 (3) ◽  
Author(s):  
Satoshi Kawato ◽  
Aiko Shitara ◽  
Yuanyuan Wang ◽  
Reiko Nozaki ◽  
Hidehiro Kondo ◽  
...  
Keyword(s):  
Evolutionary History ◽  
White Spot Syndrome Virus ◽  
Genomic Data ◽  
White Spot ◽  
Viral Pathogen ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
History Of ◽  
Phylogenetic Origin ◽  
White Spot Syndrome

ABSTRACT White spot syndrome virus (WSSV) is a crustacean-infecting, double-stranded DNA virus and is the most serious viral pathogen in the global shrimp industry. WSSV is the sole recognized member of the family Nimaviridae, and the lack of genomic data on other nimaviruses has obscured the evolutionary history of WSSV. Here, we investigated the evolutionary history of WSSV by characterizing WSSV relatives hidden in host genomic data. We surveyed 14 host crustacean genomes and identified five novel nimaviral genomes. Comparative genomic analysis of Nimaviridae identified 28 “core genes” that are ubiquitously conserved in Nimaviridae; unexpected conservation of 13 uncharacterized proteins highlighted yet-unknown essential functions underlying the nimavirus replication cycle. The ancestral Nimaviridae gene set contained five baculoviral per os infectivity factor homologs and a sulfhydryl oxidase homolog, suggesting a shared phylogenetic origin of Nimaviridae and insect-associated double-stranded DNA viruses. Moreover, we show that novel gene acquisition and subsequent amplification reinforced the unique accessory gene repertoire of WSSV. Expansion of unique envelope protein and nonstructural virulence-associated genes may have been the key genomic event that made WSSV such a deadly pathogen. IMPORTANCE WSSV is the deadliest viral pathogen threatening global shrimp aquaculture. The evolutionary history of WSSV has remained a mystery, because few WSSV relatives, or nimaviruses, had been reported. Our aim was to trace the history of WSSV using the genomes of novel nimaviruses hidden in host genome data. We demonstrate that WSSV emerged from a diverse family of crustacean-infecting large DNA viruses. By comparing the genomes of WSSV and its relatives, we show that WSSV possesses an expanded set of unique host-virus interaction-related genes. This extensive gene gain may have been the key genomic event that made WSSV such a deadly pathogen. Moreover, conservation of insect-infecting virus protein homologs suggests a common phylogenetic origin of crustacean-infecting Nimaviridae and other insect-infecting DNA viruses. Our work redefines the previously poorly characterized crustacean virus family and reveals the ancient genomic events that preordained the emergence of a devastating shrimp pathogen.

scholarly journals A novel lineage of polyomaviruses identified in bark scorpions

2021 ◽  
Author(s):  
Kara Schmidlin ◽  
Simona Kraberger ◽  
Chelsea Cook ◽  
Dale F DeNardo ◽  
Rafaela S Fontenele ◽  
...  
Keyword(s):  
Evolutionary History ◽  
High Throughput Sequencing ◽  
Gene Array ◽  
Molecular Techniques ◽  
Dna Viruses ◽  
Circular Dna ◽  
Important Group ◽  
Double Stranded Dna ◽  
Centruroides Sculpturatus ◽  
History Of

Polyomaviruses are nonenveloped viruses with circular double stranded DNA genomes that range in size from ~4 to 7 kilobasepairs. Initially identified in mammals, polyomaviruses have now been identified in birds and a few fish species. Although fragmentary polyomavirus-like sequences have been detected as apparent 'hitchhikers' in shotgun genomics datasets for various arthropods, the possible diversity of these viruses in invertebrates remains unclear. In general, polyomaviruses are host-specific, showing strong evidence of host virus coevolution. Identification of polyomaviruses in a broader range of animals could shed useful light on the evolutionary history of this medically important group of viruses. Scorpions are predatory arachnids that are among the oldest terrestrial animals. Thus far, viromes of arachnids have been under sampled and understudied. Here, high throughput sequencing and traditional molecular techniques were used to explore the diversity of circular DNA viruses associated with bark scorpions (Centruroides sculpturatus) from the greater Phoenix area, Arizona, USA. The complete genomes of eight novel polyomaviruses were identified. Analysis of Centruroides transcriptomic datasets elucidated the splicing of the viral late gene array, which is more complex than that of vertebrate polyomaviruses. Phylogenetic analysis provides further evidence of co-divergence of polyomaviruses with their hosts, suggesting that at least one ancestral species of polyomaviruses was circulating amongst the primitive common ancestors of arthropods and chordates.

scholarly journals Origin and evolution of the Yangtze River reconstructed from the largest molecular phylogeny of Cyprinidae

2021 ◽  
Author(s):  
Feng Chen ◽  
Ge Xue ◽  
Yeke Wang ◽  
Hucai Zhang ◽  
Peter D. Clift ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
East Asia ◽  
Time Resolution ◽  
Yangtze River ◽  
Evolutionary History ◽  
East Asian ◽  
The Yangtze River ◽  
Origin And Evolution ◽  
History Of ◽  
Lacustrine Ecosystem

Abstract The Yangtze River is the longest river in Asia, but its evolutionary history has long been debated. So far no robust biological evidences can be found to crack this mystery. Here we reconstruct spatiotemporal and diversification dynamics of endemic East Asian cyprinids based on a largest molecular phylogeny of Cyprinidae, including 1420 species, and show that their ancestors laying adhesive eggs were distributed in southern East Asia before ~24 Ma, subsequently dispersed to the Yangtze River to spawn semi-buoyant eggs at ~19 Ma. This indicates that the Yangtze River diverted eastward around the Oligocene-Miocene boundary. Some of these cyprinids evolved again into fishes producing adhesive eggs at ~13 Ma, together with a peaked net diversification rate, indicating that the river formed a potamo-lacustrine ecosystem during the Mid-Miocene. Our reconstruction of the history of the Yangtze River has higher time resolution and much better continuity than those deriving from geological studies.

scholarly journals Yaravirus: A novel 80-nm virus infectingAcanthamoeba castellanii

2020 ◽  
Vol 117 (28) ◽  
pp. 16579-16586 ◽  
Author(s):  
Paulo V. M. Boratto ◽  
Graziele P. Oliveira ◽  
Talita B. Machado ◽  
Ana Cláudia S. P. Andrade ◽  
Jean-Pierre Baudoin ◽  
...  
Keyword(s):  
Major Capsid Protein ◽  
Amino Acid Level ◽  
Three Dimensional ◽  
Genomic Diversity ◽  
Phylogenetic Distance ◽  
Preliminary Assessment ◽  
Dna Viruses ◽  
Origin And Evolution ◽  
Viral Genomes ◽  
Jelly Roll

Here we report the discovery of Yaravirus, a lineage of amoebal virus with a puzzling origin and evolution. Yaravirus presents 80-nm-sized particles and a 44,924-bp dsDNA genome encoding for 74 predicted proteins. Yaravirus genome annotation showed that none of its genes matched with sequences of known organisms at the nucleotide level; at the amino acid level, six predicted proteins had distant matches in the nr database. Complimentary prediction of three-dimensional structures indicated possible function of 17 proteins in total. Furthermore, we were not able to retrieve viral genomes closely related to Yaravirus in 8,535 publicly available metagenomes spanning diverse habitats around the globe. The Yaravirus genome also contained six types of tRNAs that did not match commonly used codons. Proteomics revealed that Yaravirus particles contain 26 viral proteins, one of which potentially representing a divergent major capsid protein (MCP) with a predicted double jelly-roll domain. Structure-guided phylogeny of MCP suggests that Yaravirus groups together with the MCPs ofPleurochrysisendemic viruses. Yaravirus expands our knowledge of the diversity of DNA viruses. The phylogenetic distance between Yaravirus and all other viruses highlights our still preliminary assessment of the genomic diversity of eukaryotic viruses, reinforcing the need for the isolation of new viruses of protists.

scholarly journals Genomic Sequence of Spodoptera frugiperda Ascovirus 1a, an Enveloped, Double-Stranded DNA Insect Virus That Manipulates Apoptosis for Viral Reproduction

2006 ◽  
Vol 80 (23) ◽  
pp. 11791-11805 ◽  
Author(s):  
Dennis K. Bideshi ◽  
Marie-Véronique Demattei ◽  
Florence Rouleux-Bonnin ◽  
Karine Stasiak ◽  
Yeping Tan ◽  
...  
Keyword(s):  
Spodoptera Frugiperda ◽  
Genomic Sequence ◽  
Open Reading Frames ◽  
The Novel ◽  
Fatty Acid Elongase ◽  
Dna Viruses ◽  
Origin And Evolution ◽  
Iridescent Virus ◽  
Double Stranded Dna ◽  
New Hosts

ABSTRACT Ascoviruses (family Ascoviridae) are double-stranded DNA viruses with circular genomes that attack lepidopterans, where they produce large, enveloped virions, 150 by 400 nm, and cause a chronic, fatal disease with a cytopathology resembling that of apoptosis. After infection, host cell DNA is degraded, the nucleus fragments, and the cell then cleaves into large virion-containing vesicles. These vesicles and virions circulate in the hemolymph, where they are acquired by parasitic wasps during oviposition and subsequently transmitted to new hosts. To develop a better understanding of ascovirus biology, we sequenced the genome of the type species Spodoptera frugiperda ascovirus 1a (SfAV-1a). The genome consisted of 156,922 bp, with a G+C ratio of 49.2%, and contained 123 putative open reading frames coding for a variety of enzymes and virion structural proteins, of which tentative functions were assigned to 44. Among the most interesting enzymes, due to their potential role in apoptosis and viral vesicle formation, were a caspase, a cathepsin B, several kinases, E3 ubiquitin ligases, and especially several enzymes involved in lipid metabolism, including a fatty acid elongase, a sphingomyelinase, a phosphate acyltransferase, and a patatin-like phospholipase. Comparison of SfAV-1a proteins with those of other viruses showed that 10% were orthologs of Chilo iridescent virus proteins, the highest correspondence with any virus, providing further evidence that ascoviruses evolved from a lepidopteran iridovirus. The SfAV-1a genome sequence will facilitate the determination of how ascoviruses manipulate apoptosis to generate the novel virion-containing vesicles characteristic of these viruses and enable study of their origin and evolution.

scholarly journals Evolutionary history and metabolic insights of ancient mammalian uricases

2014 ◽  
Vol 111 (10) ◽  
pp. 3763-3768 ◽  
Author(s):  
James T. Kratzer ◽  
Miguel A. Lanaspa ◽  
Michael N. Murphy ◽  
Christina Cicerchi ◽  
Christina L. Graves ◽  
...  
Keyword(s):  
Uric Acid ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Tumor Lysis Syndrome ◽  
Integrated Approach ◽  
Last Common Ancestor ◽  
Evolutionary Models ◽  
Monosodium Urate ◽  
Domains Of Life ◽  
History Of

Uricase is an enzyme involved in purine catabolism and is found in all three domains of life. Curiously, uricase is not functional in some organisms despite its role in converting highly insoluble uric acid into 5-hydroxyisourate. Of particular interest is the observation that apes, including humans, cannot oxidize uric acid, and it appears that multiple, independent evolutionary events led to the silencing or pseudogenization of the uricase gene in ancestral apes. Various arguments have been made to suggest why natural selection would allow the accumulation of uric acid despite the physiological consequences of crystallized monosodium urate acutely causing liver/kidney damage or chronically causing gout. We have applied evolutionary models to understand the history of primate uricases by resurrecting ancestral mammalian intermediates before the pseudogenization events of this gene family. Resurrected proteins reveal that ancestral uricases have steadily decreased in activity since the last common ancestor of mammals gave rise to descendent primate lineages. We were also able to determine the 3D distribution of amino acid replacements as they accumulated during evolutionary history by crystallizing a mammalian uricase protein. Further, ancient and modern uricases were stably transfected into HepG2 liver cells to test one hypothesis that uricase pseudogenization allowed ancient frugivorous apes to rapidly convert fructose into fat. Finally, pharmacokinetics of an ancient uricase injected in rodents suggest that our integrated approach provides the foundation for an evolutionarily-engineered enzyme capable of treating gout and preventing tumor lysis syndrome in human patients.

scholarly journals Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yoichiro Nakatani ◽  
Prashant Shingate ◽  
Vydianathan Ravi ◽  
Nisha E. Pillai ◽  
Aravind Prasad ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Gene Loss ◽  
De Novo ◽  
Genome Structure ◽  
Origin And Evolution ◽  
Long Read ◽  
History Of ◽  
And Function ◽  
Genome Assemblies ◽  
Key Questions

AbstractAncient polyploidization events have had a lasting impact on vertebrate genome structure, organization and function. Some key questions regarding the number of ancient polyploidization events and their timing in relation to the cyclostome-gnathostome divergence have remained contentious. Here we generate de novo long-read-based chromosome-scale genome assemblies for the Japanese lamprey and elephant shark. Using these and other representative genomes and developing algorithms for the probabilistic macrosynteny model, we reconstruct high-resolution proto-vertebrate, proto-cyclostome and proto-gnathostome genomes. Our reconstructions resolve key questions regarding the early evolutionary history of vertebrates. First, cyclostomes diverged from the lineage leading to gnathostomes after a shared tetraploidization (1R) but before a gnathostome-specific tetraploidization (2R). Second, the cyclostome lineage experienced an additional hexaploidization. Third, 2R in the gnathostome lineage was an allotetraploidization event, and biased gene loss from one of the subgenomes shaped the gnathostome genome by giving rise to remarkably conserved microchromosomes. Thus, our reconstructions reveal the major evolutionary events and offer new insights into the origin and evolution of vertebrate genomes.

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