Biology Direct

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The ancient Virus World and evolution of cells

Eugene V Koonin*, Tatiana G Senkevich and Valerian V Dolja

Biology Direct 2006, 1:29 doi:10.1186/1745-6150-1-29

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

Huiquan Liu, Yanping Fu, Bo Li, Xiao Yu, Jiatao Xie, Jiasen Cheng, Said A Ghabrial, Guoqing Li, Xianhong Yi, Daohong Jiang BMC Evolutionary Biology 2011, 11:276 (26 September 2011)

Research   Open Access

Evolution of DNA ligases of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes: a case of hidden complexity

Natalya Yutin, Eugene V Koonin Biology Direct 2009, 4:51 (18 December 2009)

Research   Open Access

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

Natalya Yutin, Yuri I Wolf, Didier Raoult, Eugene V Koonin Virology Journal 2009, 6:223 (17 December 2009)

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The fundamental units, processes and patterns of evolution, and the Tree of Life conundrum

Eugene V Koonin, Yuri I Wolf Biology Direct 2009, 4:33 (29 September 2009)

This article is part of a collection on Evolutionary Biology 150...

A tree is a natural representation of evolution owing to the inherent tree-like character of the replication process but the fundamental units of evolution amenable to tree analysis seem to be individual genetic elements rather than complete genomes.

Hypothesis   Open Access

Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements

Kira S Makarova, Yuri I Wolf, John van der Oost, Eugene V Koonin Biology Direct 2009, 4:29 (25 August 2009)

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On the origin of life in the Zinc world: 1. Photosynthesizing, porous edifices built of hydrothermally precipitated zinc sulfide as cradles of life on Earth

Armen Y Mulkidjanian Biology Direct 2009, 4:26 (24 August 2009)

Life may have emerged owing to the ability of porous, hydrothermal zinc sulfide precipitates to store solar energy and reduce atmospheric carbon dioxide, providing nourishment and shelter for the first organisms.

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Geminiviruses: a tale of a plasmid becoming a virus

Mart Krupovic, Janne J Ravantti, Dennis H Bamford BMC Evolutionary Biology 2009, 9:112 (21 May 2009)

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Phylogenetic evidence for extensive lateral acquisition of cellular genes by Nucleocytoplasmic large DNA viruses

Jonathan Filée, Noëlle Pouget, Mick Chandler BMC Evolutionary Biology 2008, 8:320 (26 November 2008)

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The genome of the brown alga Ectocarpus siliculosus contains a series of viral DNA pieces, suggesting an ancient association with large dsDNA viruses

Nicolas Delaroque, Wilhelm Boland BMC Evolutionary Biology 2008, 8:110 (12 April 2008)

The genome of the brown alga Ectocarpus siliculosus contains fragments of the ESV-1 viral genome, which is similar to the nucleocytoplasmic large DNA viruses, and could intriguingly represent the ancestor of extant forms of this virus.

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Marine mimivirus relatives are probably large algal viruses

Adam Monier, Jens Larsen, Ruth-Anne Sandaa, Gunnar Bratbak, Jean-Michel Claverie, Hiroyuki Ogata Virology Journal 2008, 5:12 (23 January 2008)

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Giant viruses, giant chimeras: The multiple evolutionary histories of Mimivirus genes

David Moreira, Céline Brochier-Armanet BMC Evolutionary Biology 2008, 8:12 (18 January 2008)

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Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses

Adam Monier, Jean-Michel Claverie, Hiroyuki Ogata BMC Genomics 2007, 8:456 (10 December 2007)

Large genome sizes in DNA viruses are unexpectedly not explained by 'borrowed' host genes, as virus and host DNA composition differs and the number of genes with anomalous composition bears no relation to viral genome size.

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The new biology: beyond the Modern Synthesis

Michael R Rose, Todd H Oakley Biology Direct 2007, 2:30 (24 November 2007)

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The Biological Big Bang model for the major transitions in evolution

Eugene V Koonin Biology Direct 2007, 2:21 (20 August 2007)

Research article   Open Access

Evolutionary genomics of plant genes encoding N-terminal-TM-C2 domain proteins and the similar FAM62 genes and synaptotagmin genes of metazoans

Molly Craxton BMC Genomics 2007, 8:259 (31 July 2007)

Research article   Open Access

Putative prophages related to lytic tailless marine dsDNA phage PM2 are widespread in the genomes of aquatic bacteria

Mart Krupovič, Dennis H Bamford BMC Genomics 2007, 8:236 (16 July 2007)

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On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization

Yuri I Wolf, Eugene V Koonin Biology Direct 2007, 2:14 (31 May 2007)

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Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases

Eugene V Koonin Biology Direct 2006, 1:39 (18 December 2006)

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Did the last common ancestor have a biological membrane?

Gáspár Jékely Biology Direct 2006, 1:35 (27 November 2006)