A novel virus from Macrosiphum euphorbiae with similarities to members of the family Flaviviridae

Teixeira, Marcella; Sela, Noa; Ng, Jillian; Casteel, Clare L.; Peng, Hsuan‐Chieh; Bekal, Sadia; Girke, Thomas; Ghanim, Murad; Kaloshian, Isgouhi

doi:10.1099/jgv.0.000414

Cited by 26 publications

(32 citation statements)

References 48 publications

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“…To an even greater extent than in Branch 2, the apparent routes of virus evolution in Branch 3 involve lineage-specific gene capture resulting in evolution of complex genome architectures (Figure 4B). The most notable cases are closteroviruses and divergent flaviviruses that have genomes of up to 20-26 kb, rivalling coronaviruses in terms of genome length and the complexity of the gene repertoire (38, 88-90).…”

Section: Resultsmentioning

confidence: 99%

Origins and Evolution of the Global RNA Virome

Dolja¹,

Wolf

Kazlauskas³

et al. 2018

Preprint

118

197

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Viruses with RNA genomes dominate the eukaryotic virome, reaching enormous diversity in animals and plants. The recent advances of metaviromics prompted us to perform a detailed phylogenomic reconstruction of the evolution of the dramatically expanded global RNA virome. The only universal gene among RNA viruses is the RNA-dependent RNA polymerase (RdRp). We developed an iterative computational procedure that alternates the RdRp phylogenetic tree construction with refinement of the underlying multiple sequence alignments. The resulting tree encompasses 4,617 RNA virus RdRps and consists of 5 major branches, 2 of which include positive-sense RNA viruses, 1 is a mix of positive-sense (+) RNA and double-stranded (ds) RNA viruses, and 2 consist of dsRNA and negative-sense (−) RNA viruses, respectively. This tree topology implies that dsRNA viruses evolved from +RNA viruses on at least two independent occasions, whereas -RNA viruses evolved from dsRNA viruses. Reconstruction of RNA virus evolution using the RdRp tree as the scaffold suggests that the last common ancestors of the major branches of +RNA viruses encoded only the RdRp and a single jelly-roll capsid protein. Subsequent evolution involved independent capture of additional genes, particularly, those encoding distinct RNA helicases, enabling replication of larger RNA genomes and facilitating virus genome expression and virus-host interactions. Phylogenomic analysis reveals extensive gene module exchange among diverse viruses and horizontal virus transfer between distantly related hosts. Although the network of evolutionary relationships within the RNA virome is bound to further expand, the present results call for a thorough reevaluation of the RNA virus taxonomy.IMPORTANCEThe majority of the diverse viruses infecting eukaryotes have RNA genomes, including numerous human, animal, and plant pathogens. Recent advances of metagenomics have led to the discovery of many new groups of RNA viruses in a wide range of hosts. These findings enable a far more complete reconstruction of the evolution of RNA viruses than what was attainable previously. This reconstruction reveals the relationships between different Baltimore Classes of viruses and indicates extensive transfer of viruses between distantly related hosts, such as plants and animals. These results call for a major revision of the existing taxonomy of RNA viruses.

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Section: Resultsmentioning

confidence: 99%

Origins and Evolution of the Global RNA Virome

Dolja¹,

Wolf

Kazlauskas³

et al. 2018

Preprint

118

197

View full text Add to dashboard Cite

show abstract

“…4B). The most notable cases are the closteroviruses and divergent flaviviruses that have genomes of up to 20 to 26 kb, rivalling coronaviruses in terms of genome length and the complexity of the gene repertoire (38,(88)(89)(90).…”

Section: Evolution Of the 5 Major Branches Of Rna Viruses And Reconstmentioning

confidence: 99%

Origins and Evolution of the Global RNA Virome

Wolf

Kazlauskas

Iranzo

et al. 2018

mBio

442

333

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Viruses with RNA genomes dominate the eukaryotic virome, reaching enormous diversity in animals and plants. The recent advances of metaviromics prompted us to perform a detailed phylogenomic reconstruction of the evolution of the dramatically expanded global RNA virome. The only universal gene among RNA viruses is the gene encoding the RNA-dependent RNA polymerase (RdRp). We developed an iterative computational procedure that alternates the RdRp phylogenetic tree construction with refinement of the underlying multiple-sequence alignments. The resulting tree encompasses 4,617 RNA virus RdRps and consists of 5 major branches; 2 of the branches include positive-sense RNA viruses, 1 is a mix of positive-sense (ϩ) RNA and double-stranded RNA (dsRNA) viruses, and 2 consist of dsRNA and negative-sense (Ϫ) RNA viruses, respectively. This tree topology implies that dsRNA viruses evolved from ϩRNA viruses on at least two independent occasions, whereas ϪRNA viruses evolved from dsRNA viruses. Reconstruction of RNA virus evolution using the RdRp tree as the scaffold suggests that the last common ancestors of the major branches of ϩRNA viruses encoded only the RdRp and a single jelly-roll capsid protein. Subsequent evolution involved independent capture of additional genes, in particular, those encoding distinct RNA helicases, enabling replication of larger RNA genomes and facilitating virus genome expression and virus-host interactions. Phylogenomic analysis reveals extensive gene module exchange among diverse viruses and horizontal virus transfer between distantly related hosts. Although the network of evolutionary relationships within the RNA virome is bound to further expand, the present results call for a thorough reevaluation of the RNA virus taxonomy. IMPORTANCE The majority of the diverse viruses infecting eukaryotes have RNA genomes, including numerous human, animal, and plant pathogens. Recent advances of metagenomics have led to the discovery of many new groups of RNA viruses in a wide range of hosts. These findings enable a far more complete reconstruction of the evolution of RNA viruses than was attainable previously. This reconstruction reveals the relationships between different Baltimore classes of viruses and indicates extensive transfer of viruses between distantly related hosts, such as plants and animals. These results call for a major revision of the existing taxonomy of RNA viruses.

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“…Other aphid viruses include the following: (i) Brevicoryne brassicae virus of the family Iflaviridae (Picornavirales), which infects cabbage aphid (Brevicoryne brassicae) (Ryabov 2007), (ii) a virus resembling those in the family Flaviviridae, but with a genome twice as large, in Macrosiphum euphorbiae (Teixeira et al 2016), (iii) a pea aphid virus (Acyrthosiphon pisum virus) (van den Heuvel et al 1997) distantly related to the Picornaviridae; and (iv) a rosy apple aphid virus (Dysaphis plantaginea, Rosy apple aphid virus) (Ryabov et al 2009), distantly related to the family Caliciviridae. Small DNA viruses in the genus Densovirus (Parvoviridae) have been discovered in Acyrthosiphon pisum, D. plantaginea (Ryabov et al 2009), andMyzus persicae (van Munster et al 2003).…”

mentioning

confidence: 99%

Discovery of Known and Novel Viral Genomes in Soybean Aphid by Deep Sequencing

Feng

Krueger

Liu

et al. 2017

Phytobiomes Journal

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The phytobiome includes not just cellular microorganisms, but also all viruses associated with plants: the virome. Plants and aphids exchange viruses regularly and efficiently; thus, the plant virome is tightly linked with the aphid virome. Yet, little is known about aphid viromes, particularly that of the soybean aphid (Aphis glycines), one of the most economically important pest insects of soybean. To sample the soybean aphid virome, and to seek new viruses as potential biological control agents, we employed next-generation sequencing. Genomes isolated from viruses in soybean aphids collected at four sites revealed many viruses, and six complete or nearly complete genomes were assembled. Most abundant were the picornavirus-like dicistroviruses Aphid lethal paralysis virus and Rhopalosiphum padi virus. We also sequenced the genome of a new dicistrovirus, Big Sioux River virus, fragments of which had been found previously in honey bee. Genome sequences that represent two entirely new virus families were obtained. These include an abundant tetravirus-like virus and a virus distantly related to cileviruses of plants and negeviruses of insects. Surprisingly, Cotton leafroll dwarf virus, a member of the genus Polerovirus, was found in soybean aphids from China, suggesting that the soybean aphid may be a vector of this virus. This virus had not been reported previously in China or in soybean. This study provides a peek into the rapidly expanding, largely unexplored world of insect viromes that will provide valuable knowledge for future understanding of plant−virus−vector interactions. [Formula: see text] Copyright © 2017 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

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A novel virus from Macrosiphum euphorbiae with similarities to members of the family Flaviviridae

Cited by 26 publications

References 48 publications

Origins and Evolution of the Global RNA Virome

Origins and Evolution of the Global RNA Virome

Origins and Evolution of the Global RNA Virome

Discovery of Known and Novel Viral Genomes in Soybean Aphid by Deep Sequencing

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