From: Hidden evolutionary complexity of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes
Vaccinia virus gene numbera | Functional category | # of viral families/ genomes | NCVOG annotation | Evolutionary scenario from constrained tree analysis | |
---|---|---|---|---|---|
NCVOG0038 | E9L | DNA replication, recombination and repair | 6/45 | DNA polymerase elongation subunit family B | Monophyletic NCLDV, common origin with baculoviruses and possibly herpesviruses |
NCVOG0023 | D5R | DNA replication, recombination and repair | 6/45 | D5-like helicase-primase | Monophyletic NCLDV but displaced by a bacteriophage homolog in phycodnaviruses. |
NCVOG1060 | G5R | DNA replication, recombination and repair | 5/35 | FLAP-like endonuclease XPG (cd00128) | Possibly monophyletic NCLDV although displacement by a phage homolog in poxviruses cannot be ruled out; loss in phycodnaviruses and subsequent acquisition of a eukaryotic homolog by E. huxlei virus |
NCVOG0036 | H6R | DNA replication, recombination and repair | 3/23 | DNA topoisomerase IB | Possibly monophyletic NCLDV |
NCVOG0037 | None | DNA replication, recombination and repair | 6/15 | DNA topoisomerase II | Polyphyletic NCLDV, gene acquired from different eukaryotes |
NCVOG0035 | None | DNA replication, recombination and repair | 3/7 | NAD + dependent DNA ligase (smart00532) | Monophyletic NCLDV |
NCVOG0034 | A50R | DNA replication, recombination and repair | 4/19 | ATP-dependent DNA ligase (pfam01068, PRK01109) | Polyphyletic NCLDV, gene acquired from different eukaryotes |
NCVOG0278 | A22R | DNA replication, recombination and repair | 5/36 | RuvC, Holliday junction resolvases (HJRs); cl00243. Extended Pox_A22, Poxvirus A22 family (pfam04848). Marseille virus protein lacks C-term conserved positions. | Insufficient sequence conservation for reliable phylogenetic analysis |
NCVOG0004_APa | None | DNA replication, recombination and repair | 4/6 | AP (apurinic) endonuclease family 2 | Strongly supported monophyly of NCLDV |
NCVOG0004_NTa | None | DNA replication, recombination and repair | 3/4 | Nucleotidyltransferase (DNA polymerase beta family) | Polyphyletic NCLDV, gene acquired from different eukaryotes |
NCVOG1192 | None | DNA replication, recombination and repair | 4/13 | YqaJ viral recombinase family (pfam09588) | Possibly monophyletic NCLDV |
NCVOG0024 | None | DNA replication, recombination and repair | ¾ | Superfamily II helicase related to herpesvirus replicative helicase (origin-binding protein UL9), pfam03121 | Limited sequence similarity between proteins from different NCLDV; probable polyphyletic origin; possibly not an ancestral NCLDV gene |
NCVOG1115 | D4R | DNA replication, recombination and repair | 3/23 | Uracil-DNA glycosylase | Present in only a few NCLDV; uncertain, monophyly of the NCLDV cannot be ruled out |
NCVOG0274 | J6R | Transcription and RNA processing | 6/36 | DNA-directed RNA polymerase subunit alpha | Displacement of ancestral NCLDV gene in mimivirus and ASFV with eukaryotic RNAP2 and RNAP1 subunit genes, respectively; loss in most phycodnaviruses. Ancestral NCLDV gene possibly derived from eukaryote RNAP I |
NCVOG0271 | A24R | Transcription and RNA processing | 6/36 | DNA-directed RNA polymerase subunit beta | Possibly polyphyletic NCLDV, with one subset derived from RNAP1. and another from RNAP2; likely more recent displacement with RNAP2 in mimivirus; however, monophyly of NCLDV cannot be ruled out; loss in most phycodnaviruses. |
NCVOG0273 | G5.5R | Transcription and RNA processing | 5/15 | DNA-directed RNA polymerase subunit 5 | Uncertain, not enough sequence conservation for reliable phylogenetic analysis |
NCVOG1164 | A1L | Transcription and RNA processing | 6/44 | A1L transcription factor/late transcription factor VLTF-2 | Uncertain, not enough sequence conservation for reliable phylogenetic analysis |
NCVOG0262 | A2L | Transcription and RNA processing | 6/45 | Poxvirus Late Transcription Factor VLTF3 like | No obvious homologs outside NCLDV (monophyly of NCLDV by default). |
NCVOG0261 | A7L | Transcription and RNA processing | 5/35 | Poxvirus early transcription factor (VETF), large subunit (pfam04441) | No obvious homologs outside NCLDV (monophyly of NCLDV by default). |
NCVOG0272 | E4L | Transcription and RNA processing | 6/39 | Transcription factor S-II (TFIIS)-domain-containing protein | Uncertain, not enough sequence conservation for reliable phylogenetic analysis |
NCVOG1127 | One | Transcription and RNA processing | 4/11 | transcription initiation factor IIB | Strongly supported monophyly of NCLDV |
NCVOG0076 | A18R | Transcription and RNA processing | 6/38 | DNA or RNA helicases of superfamily II (COG1061) | Monophyletic NCLDV except for displacement with a eukaryotic homolog in one phycodnavirus and acquisition of a distinct eukaryotic paralog in ASFV |
NCVOG0267 | I8R | Transcription and RNA processing | 3/23 | RNA-helicase DExH-NPH-II | Monophyletic NCLDV; independent losses in several NCLDV lineages |
NCVOG1117 | D1R | Transcription and RNA processing | 6/33 | mRNA capping enzyme large subunit | Complex, variable domain architecture; apparent monophyly of NCLDV for the conserved methyltransferase domain; guanylyltransferases of apparent distinct eukaryotic origin in a single iridovirus and a single phycodnavirus |
NCVOG0236 | D9R, D10R | Transcription and RNA processing | 6/29 | Nudix hydrolase | Uncertain, not enough sequence conservation for reliable phylogenetic analysis |
NCVOG1088 | None | Transcription and RNA processing | 3/13 | RNA ligase | Monophyletic NCLDV; common origin with baculovirus and possibly bacteriophage homologs |
- | J3R | Transcription and RNA processing | 2/16 | PolyA polymerase, regulatory subunit | Present only in poxviruses and one mimivirus; however, monophyly strongly supported; possible ancestral gene |
NCVOG0276 | F4L | Nucleotide metabolism | 6/29 | Ribonucleotide reductase small subunit | Polyphyletic NCLDV, complex evolutionary scenario; ancestral status uncertain; trees similar for the large and small subunits |
NCVOG1353 | I4L | Nucleotide metabolism | 6/24 | ribonucleoside diphosphate reductase, large subunit | Polyphyletic NCLDV, complex evolutionary scenario; ancestral status uncertain; trees similar for the large and small subunits |
NCVOG0319 | J2R | Nucleotide metabolism | 5/20 | Thymidine kinase | Most likely polyphyletic NCLDV although monophyly could not be statistically rejected |
NCVOG0320 | A48R | Nucleotide metabolism | 4/21 | Thymidylate kinase | Most likely polyphyletic NCLDV although monophyly could not be statistically rejected |
NCVOG1068 | F2L | Nucleotide metabolism | 4/30 | dUTPase (cl00493) | Polyphyletic NCLDV, monophyly rejected |
NCVOG0022 | D13L | Virion structure and morphogenesis | 6/45 | NCLDV major capsid protein | No homologs outside NCLDV – monophyletic NCLDV by default |
NCVOG0249 | A32L | Virion structure and morphogenesis | 6/45 | A32-like packaging ATPase | Only distant homologs outside NCLDV – monophyletic NCLDV by default |
NCVOG0211 | F9L, L1R | Virion structure and morphogenesis | 4/34 | myristylated envelope protein | No homologs outside NCLDV – monophyletic NCLDV by default |
NCVOG1122 | G9R, J5L, A16L | Virion structure and morphogenesis | 3/31 | Myristylated protein; pfam03003, DUF230 | No homologs outside NCLDV – monophyletic NCLDV by default |
NCVOG0052 | E10R | Virion structure and morphogenesis | 6/44 | disulfide (thiol) oxidoreductase/isomerase; Erv1 / Alr family (pfam04777) | Monophyletic NCLDV |
NCVOG0256 | H3L | Virion structure and morphogenesis | 2/22 | envelope protein, glycosyltransferase | Apparent monophyletic NCLDV but represented only in poxviruses and mimiviruses; independent acquisition cannot be ruled out |
NCVOG0040 | H1L | Signal transduction, regulation | 4/30 | cd00127, DSPc, Dual specificity phosphatases (DSP); Ser/Thr and Tyr protein phosphatases | Most likely independent acquisitions by different NCLDV |
NCVOG0330 | VACWR012, VACWR207 | Signal transduction, regulation | 5/26 | RING-finger-containing E3 ubiquitin ligase (COG5432: RAD18) | Most likely independent acquisition by different groups of the NCLDV; probably not an ancestral gene |
NCVOG0329 | Â | Signal transduction, regulation | 2/3 | UBCc, Ubiquitin-conjugating enzyme E2 (cd00195) | Present only in mimivirus and ASFV; independent acquisitions from eukaryotes, NCLDV monophyly rejected; not an ancestral gene |
NCVOG0246 | Â | Signal transduction, regulation | 3/4 | Ulp1-like protease/ deubiquitinating enzyme | Uncertain, highly diverged NCLDV sequences |
NCVOG0009 | Â | Virus-host interactions | 3/4 | pfam00653: BIR (Baculovirus Inhibitor of apoptosis protein Repeat) domain | Most likely independent acquisition by different groups of the NCLDV; probably not an ancestral gene |
NCVOG0012 | A33R, A44R, A40R | Virus-host interactions | 3/20 | C-type lectin: smart00034, cd03594, cd03593, pfam00059, cd00037, pfam05966 | Poorly conserved sequence, most likely independent acquisitions by different groups of NCLDV; probably not an ancestral gene |
NCVOG1361 | Â | Uncharacterized | 6/11 | T5orf172 domain (pfam10544) | Different domain architectures; most likely independent acquisition by different groups of the NCLDV; probably not an ancestral gene |
NCVOG1360 | VACWR011, VACWR208 | Uncharacterized | 3/18 | KilA domain (pfam04383); always present at protein N-termini except for mimiviruses. In some proteins fused to the a RING-finger domain. | Different domain architectures; most likely independent acquisition by different groups of the NCLDV; probably not an ancestral gene |
NCVOG1424 | Â | Uncharacterized | 3/6 | Uncharacterized domain; found downstream of KilA, BRO, and MSV199 domains. Also found in some baculoviruses. | Different domain architectures; most likely independent acquisition by different groups of the NCLDV; probably not an ancestral gene |
NCVOG0010 | Â | Uncharacterized | 4/11 | pfam02498: Bro-N; BRO family, N-terminal domain: This family includes the N-terminus of baculovirus BRO and ALI motif proteins. | Different domain architectures; most likely independent acquisition by different groups of the NCLDV; probably not an ancestral gene |
NCVOG0059 | Â | Uncharacterized | 2/3 | FtsJ-like methyltransferase family proteins (pfam01728) | Present only in mimivirus and ASFV; monophyly cannot be ruled out |