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