Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements

The Wonderful World of Archaeal Viruses

(2013) David Prangishvili   Annual Review of Microbiology

“Megavirales”, a proposed new order for eukaryotic nucleocytoplasmic large DNA viruses

(2013) Philippe Colson et al.   ARCHIVES OF VIROLOGY

Mechanisms for RNA Capture by ssDNA Viruses: Grand Theft RNA

(2013) Kenneth Stedman   JOURNAL OF MOLECULAR EVOLUTION

Diversity of Virophages in Metagenomic Data Sets

(2013) J. Zhou et al.   JOURNAL OF VIROLOGY

Breaking and joining single-stranded DNA: the HUH endonuclease superfamily

(2013) Michael Chandler et al.   NATURE REVIEWS MICROBIOLOGY

On the concept and elucidation of endogenous retroviruses

(2013) R. A. Weiss   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

LTR-Retrotransposons in R. exoculata and Other Crustaceans: The Outstanding Success of GalEa-Like Copia Elements

(2013) Mathieu Piednoël et al.   PLoS One

A Superfamily of DNA Transposons Targeting Multicopy Small RNA Genes

(2013) Kenji K. Kojima et al.   PLoS One

Structure of the archaeal head-tailed virus HSTV-1 completes the HK97 fold story

(2013) M. K. Pietila et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes

(2013) N. Philippe et al.   SCIENCE

The Molecular Virology of Hepatitis B Virus

(2013) Corinna Bremer et al.   SEMINARS IN LIVER DISEASE

Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies

(2013) Natalya Yutin et al.   Virology Journal

Mimiviridae: clusters of orthologous genes, reconstruction of gene repertoire evolution and proposed expansion of the giant virus family

(2013) Natalya Yutin et al.   Virology Journal

Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses

(2013) Simon Roux et al.   Nature Communications

Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses

(2013) Mart Krupovic   Current Opinion in Virology

A virocentric perspective on the evolution of life

(2013) Eugene V Koonin et al.   Current Opinion in Virology

Structure Unifies the Viral Universe

(2012) Nicola G.A. Abrescia et al.   Annual Review of Biochemistry

A field guide to eukaryotic circular single-stranded DNA viruses: insights gained from metagenomics

(2012) Karyna Rosario et al.   ARCHIVES OF VIROLOGY

A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses

(2012) Geoffrey S Diemer et al.   Biology Direct

Regulation of transposable elements in maize

(2012) Damon Lisch   CURRENT OPINION IN PLANT BIOLOGY

Reclassification of Giant Viruses Composing a Fourth Domain of Life in the New Order Megavirales

(2012) Philippe Colson et al.   INTERVIROLOGY

Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes

(2012) D. M. Kristensen et al.   JOURNAL OF BACTERIOLOGY

Studies of endogenous retroviruses reveal a continuing evolutionary saga

(2012) Jonathan P. Stoye   NATURE REVIEWS MICROBIOLOGY

Related haloarchaeal pleomorphic viruses contain different genome types

(2012) Ana Senčilo et al.   NUCLEIC ACIDS RESEARCH

Evolutionary dynamics of RNA-like replicator systems: A bioinformatic approach to the origin of life

(2012) Nobuto Takeuchi et al.   Physics of Life Reviews

Evolution and Diversity of the Microviridae Viral Family through a Collection of 81 New Complete Genomes Assembled from Virome Reads

(2012) Simon Roux et al.   PLoS One

Provirophages and transpovirons as the diverse mobilome of giant viruses

(2012) C. Desnues et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Viroids and Hepatitis Delta Virus

(2012) Ricardo Flores et al.   SEMINARS IN LIVER DISEASE

Temperate membrane-containing halophilic archaeal virus SNJ1 has a circular dsDNA genome identical to that of plasmid pHH205

(2012) Ziqian Zhang et al.   VIROLOGY

Evolution of microbes and viruses: a paradigm shift in evolutionary biology?

(2012) Eugene V. Koonin et al.   Frontiers in Cellular and Infection Microbiology

A member of the virus family Narnaviridae from the plant pathogenic oomycete Phytophthora infestans

(2011) Guohong Cai et al.   ARCHIVES OF VIROLOGY

Plasmids, viruses and virus-like membrane vesicles from Thermococcales

(2011) Nicolas Soler et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

On the alleged origin of geminiviruses from extrachromosomal DNAs of phytoplasmas

(2011) Federica Saccardo et al.   BMC EVOLUTIONARY BIOLOGY

Widespread Horizontal Gene Transfer from Circular Single-stranded DNA Viruses to Eukaryotic Genomes

(2011) Huiquan Liu et al.   BMC EVOLUTIONARY BIOLOGY

The remarkable evolutionary history of endornaviruses

(2011) M. J. Roossinck et al.   JOURNAL OF GENERAL VIROLOGY

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

(2011) M. Krupovic et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

A widespread class of reverse transcriptase-related cellular genes

(2011) E. A. Gladyshev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Virophage control of antarctic algal host-virus dynamics

(2011) S. Yau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Virophage at the Origin of Large DNA Transposons

(2011) M. G. Fischer et al.   SCIENCE

Rapidly expanding genetic diversity and host range of the Circoviridae viral family and other Rep encoding small circular ssDNA genomes

(2011) Eric Delwart et al.   VIRUS RESEARCH

Double-stranded DNA viruses: 20 families and only five different architectural principles for virion assembly

(2011) Mart Krupovic et al.   Current Opinion in Virology

Common origins and host-dependent diversity of plant and animal viromes

(2011) Valerian V Dolja et al.   Current Opinion in Virology

On the Origin of DNA Genomes: Evolution of the Division of Labor between Template and Catalyst in Model Replicator Systems

(2011) Nobuto Takeuchi et al.   PLoS Computational Biology

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

Presence of a classical RRM-fold palm domain in Thg1-type 3'- 5'nucleic acid polymerases and the origin of the GGDEF and CRISPR polymerase domains

(2010) Vivek Anantharaman et al.   Biology Direct

Repetitive elements in parasitic protozoa

(2010) Christine Clayton   BMC BIOLOGY

Origin of hepatitis δ virus

(2010) John Taylor et al.   Future Microbiology

Origin and Evolution of Eukaryotic Large Nucleo-Cytoplasmic DNA Viruses

(2010) Eugene V. Koonin et al.   INTERVIROLOGY

A Dimeric Rep Protein Initiates Replication of a Linear Archaeal Virus Genome: Implications for the Rep Mechanism and Viral Replication

(2010) M. Oke et al.   JOURNAL OF VIROLOGY

New, Closely Related Haloarchaeal Viral Elements with Different Nucleic Acid Types

(2010) E. Roine et al.   JOURNAL OF VIROLOGY

The energetics of genome complexity

(2010) Nick Lane et al.   NATURE

Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison

(2010) Jianchang Du et al.   PLANT JOURNAL

N15: The linear phage–plasmid

(2010) Nikolai V. Ravin   PLASMID

Giant virus with a remarkable complement of genes infects marine zooplankton

(2010) M. G. Fischer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mimivirus: the emerging paradox of quasi-autonomous viruses

(2010) Jean-Michel Claverie et al.   TRENDS IN GENETICS

Group II Introns: Mobile Ribozymes that Invade DNA

(2010) A. M. Lambowitz et al.   Cold Spring Harbor Perspectives in Biology

The origin and early evolution of eukaryotes in the light of phylogenomics

(2010) Eugene V Koonin   GENOME BIOLOGY

Ginger DNA transposons in eukaryotes and their evolutionary relationships with long terminal repeat retrotransposons

(2010) Weidong Bao et al.   Mobile DNA

Cellular Genes Derived from Gypsy/Ty3 Retrotransposons in Mammalian Genomes

(2009) Jean-Nicolas Volff   Annals of the New York Academy of Sciences

The Great Billion-year War between Ribosome- and Capsid-encoding Organisms (Cells and Viruses) as the Major Source of Evolutionary Novelties

(2009) Patrick Forterre et al.   Annals of the New York Academy of Sciences

Viruses of Plant Pathogenic Fungi

(2009) Said A. Ghabrial et al.   Annual Review of Phytopathology

The classification and nomenclature of endogenous viruses of the family Caulimoviridae

(2009) Andrew D. W. Geering et al.   ARCHIVES OF VIROLOGY

Geminiviruses: a tale of a plasmid becoming a virus

(2009) Mart Krupovic et al.   BMC EVOLUTIONARY BIOLOGY

Hydrogenosomes and Mitosomes: Conservation and Evolution of Functions

(2009) MARK VAN DER GIEZEN   JOURNAL OF EUKARYOTIC MICROBIOLOGY

A novel putative virus of Gremmeniella abietina type B (Ascomycota: Helotiaceae) has a composite genome with endornavirus affinities

(2009) T. T. Tuomivirta et al.   JOURNAL OF GENERAL VIROLOGY

Molecular characterization of the plant virus genus Ourmiavirus and evidence of inter-kingdom reassortment of viral genome segments as its possible route of origin

(2009) M. Rastgou et al.   JOURNAL OF GENERAL VIROLOGY

A Broadscale Phylogenetic Analysis of Group II Intron RNAs and Intron-Encoded Reverse Transcriptases

(2009) D. M. Simon et al.   MOLECULAR BIOLOGY AND EVOLUTION

An ssDNA virus infecting archaea: a new lineage of viruses with a membrane envelope

(2009) Maija K. Pietilä et al.   MOLECULAR MICROBIOLOGY

New dimensions of the virus world discovered through metagenomics

(2009) David M. Kristensen et al.   TRENDS IN MICROBIOLOGY

Eukaryotic large nucleo-cytoplasmic DNA viruses: Clusters of orthologous genes and reconstruction of viral genome evolution

(2009) Natalya Yutin et al.   Virology Journal

The Take and Give Between Retrotransposable Elements and their Hosts

(2008) Arthur Beauregard et al.   Annual Review of Genetics

Genomics and Evolution of Heritable Bacterial Symbionts

(2008) Nancy A. Moran et al.   Annual Review of Genetics

Taxonomy, molecular phylogeny and evolution of plant reverse transcribing viruses (family Caulimoviridae) inferred from full-length genome and reverse transcriptase sequences

(2008) M. Bousalem et al.   ARCHIVES OF VIROLOGY

Evolution of complexity in RNA-like replicator systems

(2008) Nobuto Takeuchi et al.   Biology Direct

Relationships of Gag-pol Diversity between Ty3/Gypsy and Retroviridae LTR retroelements and the three kings hypothesis

(2008) Carlos Llorens et al.   BMC EVOLUTIONARY BIOLOGY

A Novel Mycovirus That Is Related to the Human Pathogen Hepatitis E Virus and Rubi-Like Viruses

(2008) H. Liu et al.   JOURNAL OF VIROLOGY

Mitochondrial DNA of Vitis vinifera and the Issue of Rampant Horizontal Gene Transfer

(2008) V. V. Goremykin et al.   MOLECULAR BIOLOGY AND EVOLUTION

The virophage as a unique parasite of the giant mimivirus

(2008) Bernard La Scola et al.   NATURE

The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups

(2008) Eugene V. Koonin et al.   NATURE REVIEWS MICROBIOLOGY

Virus evolution: how far does the double β-barrel viral lineage extend?

(2008) Mart Krupovič et al.   NATURE REVIEWS MICROBIOLOGY

Redefining viruses: lessons from Mimivirus

(2008) Didier Raoult et al.   NATURE REVIEWS MICROBIOLOGY

A diversity of uncharacterized reverse transcriptases in bacteria

(2008) Dawn M. Simon et al.   NUCLEIC ACIDS RESEARCH

The diversity of retrotransposons and the properties of their reverse transcriptases

(2008) Thomas H. Eickbush et al.   VIRUS RESEARCH

Linear plasmids in plant mitochondria: Peaceful coexistences or malicious invasions?

(2007) Hirokazu Handa   MITOCHONDRION