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Logo of viroljBioMed CentralBiomed Central Web Sitesearchsubmit a manuscriptregisterthis articleVirology JournalJournal Front Page
 
From:
Published online 2012 August 14. doi: 10.1186/1743-422X-9-161

Table 1

Evolutionary scenarios for the ancestral NCLDV genes

NCVOG[3,4]Vaccinia virus gene numberaFunctional category# of viral families/ genomesNCVOG annotationEvolutionary 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
 
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
 
Signal transduction, regulation
3/4
Ulp1-like protease/
deubiquitinating enzyme
Uncertain, highly diverged NCLDV sequences
NCVOG0009
 
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
 
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
 
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
 
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 Uncharacterized2/3FtsJ-like methyltransferase family proteins (pfam01728)Present only in mimivirus and ASFV; monophyly cannot be ruled out

aThe systematic gene names are for the Copenhagen strain of Vaccinia virus except for the names starting with VACWR which are from the WR strain because the respective genes are missing/disrupted in the Copenhagen strain.