|
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]
|
