Book ChapterDOI
Eukaryotic Circular Rep-Encoding Single-Stranded DNA (CRESS DNA) Viruses: Ubiquitous Viruses With Small Genomes and a Diverse Host Range
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TLDR
The explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade is surveyed, similarities between the well-studied geminiviruses and circoviruses with newly identified groups known only through their genome sequences are highlighted, and the ecology and evolution of eUKaryoticCRESS DNA viruses are discussed.Abstract:
While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for viruses, modern metagenomics sequencing has revealed circular ssDNA viruses in most environments and in association with diverse hosts. In particular, circular ssDNA viruses encoding a homologous replication-associated protein (Rep) have been identified in the majority of eukaryotic supergroups, generating interest in the ecological effects and evolutionary history of circular Rep-encoding ssDNA viruses (CRESS DNA) viruses. This review surveys the explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade, highlights similarities between the well-studied geminiviruses and circoviruses with newly identified groups known only through their genome sequences, discusses the ecology and evolution of eukaryotic CRESS DNA viruses, and speculates on future research horizons.read more
Citations
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Journal ArticleDOI
Global Organization and Proposed Megataxonomy of the Virus World
Eugene V. Koonin,Valerian V. Dolja,Mart Krupovic,Arvind Varsani,Arvind Varsani,Yuri I. Wolf,Natalya Yutin,F. Murilo Zerbini,Jens H. Kuhn +8 more
TL;DR: Phylogenetic analyses of virus hallmark genes combined with analyses of gene-sharing networks show that replication modules of five BCs evolved from a common ancestor that encoded an RNA-directed RNA polymerase or a reverse transcriptase, and propose a comprehensive hierarchical taxonomy of viruses.
Journal ArticleDOI
Origin of viruses: primordial replicators recruiting capsids from hosts.
TL;DR: A ‘chimeric’ scenario under which different types of primordial, selfish replicons gave rise to viruses by recruiting host proteins for virion formation is outlined, suggesting that new groups of viruses have repeatedly emerged at all stages of the evolution of life.
Journal ArticleDOI
Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome
Yuri I. Wolf,Sukrit Silas,Yongjie Wang,Shuang Wu,Michael J. Bocek,Darius Kazlauskas,Mart Krupovic,Andrew Fire,Valerian V. Dolja,Eugene V. Koonin +9 more
TL;DR: Analysis of a single RNA virome from the Yangshan Deep-Water Harbour in China enabled the recovery of more than 4,500 distinct RNA viruses, doubling the known set of RNA viruses to date, and provided insights into their biology.
Journal ArticleDOI
Discovery of several thousand highly diverse circular DNA viruses.
Michael J. Tisza,Diana V. Pastrana,Nicole L. Welch,Brittany Stewart,Alberto Peretti,Gabriel J. Starrett,Yuk Ying S. Pang,Siddharth R. Krishnamurthy,Patricia A. Pesavento,David H. McDermott,Philip M. Murphy,Jessica L. Whited,Jessica L. Whited,Bess M. Miller,Bess M. Miller,Jason M. Brenchley,Stephan P. Rosshart,Barbara Rehermann,John Doorbar,Blake A Ta'ala,Olga Pletnikova,Juan C. Troncoso,Susan M. Resnick,Ben Bolduc,Matthew B. Sullivan,Arvind Varsani,Arvind Varsani,Anca M. Segall,Christopher B. Buck +28 more
TL;DR: This work selectively enriched for the genomes of circular DNA viruses in over 70 animal samples, ranging from nematodes to human tissue specimens, to further the understanding of viral sequence diversity and allow for high throughput documentation of the virosphere.
Journal ArticleDOI
Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids
TL;DR: It is shown that viral Reps evolved from Reps of bacterial and archaeal plasmids on multiple independent occasions, shedding light on the complex evolutionary history of a major class of viruses revealing its polyphyletic origins.
References
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TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
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Virus taxonomy: classification and nomenclature of viruses. Seventh report of the International Committee on Taxonomy of Viruses.
TL;DR: This report builds on the accumulated taxonomic construction of the eight previous reports dating back to 1971 and records the proceedings of the Committee since publication of the last report in 2005.
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