|
The major monophyletic classes of viruses and selfish genetic elements |
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| Class of viruses |
Constituent virus lineages |
Hosts |
Support for monophyly |
Refs |
|
|
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| Positive-strand RNA viruses |
Superfamily I: picorna-like; superfamily II: alpha-like; superfamily III: flavi-like; the exact affinity of RNA bacteriophages within this class of viruses remains uncertain (possibly, a fourth lineage) |
Animals, plants, protists, bacteria (one family of bacteriophages) |
Conserved RdRp; JRC in most superfamily 1 viruses, and subsets of superfamilies 2 and 3 viruses. Reconstructed ancestor with RdRp and JRC |
[87] |
| Retroid viruses and elements |
Retroviruses, hepadnaviruses, caulimoviruses, badnaviruses; LTR- and nonLTR retroelements; retrons; group II self-splicing introns – the progenitors of eukaryotic spliceosomal introns |
Animals, fungi, plants, protists, bacteria, archaea |
Conserved RT |
[103, 104] |
| Small DNA viruses, plasmids, and transposons with rolling circle replication |
Gemini-, circo-, parvo-, papovaviruses, phages (e.g., φX174), archaeal and bacterial plasmids, eukaryotic helitron transposons |
Animals, plants, archaea, bacteria |
Conserved RCRE, JRC, S3H (in eukaryotic viruses) |
[17, 18, 20] |
| Tailed bacteriophages (Caudovirales) |
Families: Myoviridae (e.g., T4), Podoviridae (e.g., T7), Siphoviridae (e.g., λ) |
Bacteria, euryarchaea |
Complex, overlapping arrays of genes conserved in subsets of tailed phages; genes of all tailed phages thought to comprise a single pool |
[11, 93, 94, 105, 106] |
| Nucleo-cytoplasmic large DNA viruses (NCLDV) |
Poxviruses, asfarviruses, iridoviruses, phycodnaviruses, mimiviruses |
Animals, algae, protests |
Core set of 11 conserved genes, including JRC, S3H, and a FtsK-like packaging ATPase, found in all NCLDVs; reconstructed ancestor with ~40 genes |
[50–53, 107] |
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Abbreviations: JRC, Jelly-Roll Capsid protein; LTR, Long Terminal Repeat; RdRp, RNA-dependent RNA polymerase; RCRE, Rolling Circle Replication (initiation) Endonuclease; RT, Reverse Transcriptase; S3H, Superfamily 3 Helicase. | ||||
Koonin et al. Biology Direct 2006 1:29 doi:10.1186/1745-6150-1-29 |
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