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Table 1 The major monophyletic classes of viruses and selfish genetic elements

From: The ancient Virus World and evolution of cells

Class of viruses Constituent virus lineages Hosts Support for monophyly Refs
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]
  1. 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.