Table 5 Evolutionary connections between prokaryotic and eukaryotic viruses and related selfish genetic elements

Positive-strand RNA viruses

Positive-strand RNA bacteriophages (MS2, etc)

RdRp

Possible direct vertical link (monophyly) although capsid proteins of RNA phages are unrelated to those of eukaryotic viruses

[87]

Retroid viruses and elements

Retrons, group II introns

RT

Possible direct vertical relationship although eukaryotic viruses/elements have many additional genes including proteases and virion components; none of the prokaryotic elements have capsids.

[32, 103, 104]

Parvoviruses, papovaviruses, circoviruses, geminiviruses, helitron transposons

Small DNA bacteriophages (e.g., φX174) and plasmids

RCRE

Generic evolutionary relationship linked to the common mode of replication

[17–19]

Adenoviruses

Tailed bacteriophages with genome-linked terminal proteins (e.g., PRD1)

JRC, DNA polymerase, terminal protein, packaging ATPase

Possible direct relationship suggested by the coherent set of conserved proteins

[116]

Herpesviruses

Tailed bacteriophages

JRC, large terminase subunit, UL9 helicase, DNA polymerase, assemblin (virion morphogenetic protease)

Possible direct relationship suggested by the coherent set of conserved proteins. However, a more complex relationship with different phages might be more likely

[109, 117]

Nucleo-Cytoplasmic Large DNA viruses (NCLDV)

Tailed bacteriophages, plasmids

JRC, S3H, primase, packaging ATPase, Holliday junction resolvase, helicases

Complex relationships with different groups of phages and plasmids; in particular, the fusion primase-S3H protein most closely resembles a homolog from archaeal plasmids.

[53, 107]