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Table 1 Evolutionary scenarios for the ancestral NCLDV genes

From: Hidden evolutionary complexity of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes

NCVOG[3, 4]

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

 

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

 

Uncharacterized

2/3

FtsJ-like methyltransferase family proteins (pfam01728)

Present only in mimivirus and ASFV; monophyly cannot be ruled out

  1. 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.