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Table 2 Conserved regulators of gene expression evaluated for divergence time analysis

From: A multilocus timescale for oomycete evolution estimated under three distinct molecular clock models

Gene

Domainsa

Referenceb

Chromatin modification

  

Anti-silencing factor Asf1

asf1

PITG_17091

Brahma-like

HAS, SNF2 N-terminal, Helicase conserved C-terminal, Bromodomain

PITG_19037

Chromodomain-containing protein (A)

2x Chromo, SNF2 N-terminal, Helicase conserved C-terminal

PITG_15837

Chromodomain-containing protein (B)

[PDZ, QLQ], 2x Chromo, SNF2 N-terminal, Helicase conserved C-terminal, PHD-finger, PHD-like (zf-HC5HC2H_2)

PITG_10083

Chromodomain-containing protein (C)

PHD-finger, 2x Chromo, SNF2 N-terminal, Helicase conserved C-terminal

PITG_00140

Chromodomain-containing protein (D)

[Chromo], Bromodomain, PHD, Chromo, [PDZ], SNF2 N-terminal, Helicase conserved C-terminal, PHD, [PHD], PHD-like (zf-HC5HC2H), PHD

PITG_03401

CXXC zinc finger containing protein

[SNF2 N-terminal], 2x CXXC zinc finger, [FHA]

PITG_03547

DNA methyltransferase 1-associated protein

[DNA methyltransferase 1-associated protein]

PITG_15785

ESA1-like histone acetyltransferase

Tudor-knot RNA binding, MOZ/SAS

PITG_01456

GCN5-like histone acetyltransferase

GNAT Acetyltransferase, Bromodomain

PITG_20197

HAT1-like histone acetyltransferase

HAT1 N-terminus, [GNAT Acetyltransferase]

PITG_00186

KAT11 domain histone acetyltransferase (A)

TAZ zinc finger, Bromodomain, [PHD], KAT11, ZZ zinc finger, TAZ zinc finger

PITG_07302

KAT11 domain histone acetyltransferase (B)

[TAZ, TAZ], Bromodomain, [DUF902], [PHD], KAT11, [ZZ, TAZ]

PITG_06533

KAT11 domain histone acetyltransferase (C)

Bromodomain, [PHD], KAT11

PITG_18027

KAT11 domain histone acetyltransferase (D)

Bromodomain, KAT11

PITG_08587

Histone deacetylase HDA1

histone deacetylase

PITG_01897

Histone deacetylase HDA2

[ankyrin repeats], histone deacetylase

PITG_08237

Histone deacetylase HDA4

histone deacetylase

PITG_05176

Histone deacetylase HDA5

histone deacetylase

PITG_15415

Histone deacetylase HDA6

histone deacetylase

PITG_21309

Histone deacetylase HDA7

histone deacetylase

PITG_12962

Histone deacetylase HDA8

histone deacetylase

PITG_01911

Histone deacetylase HDA9

histone deacetylase

PITG_04499

DOT1-like histone methyltransferase

DOT1

PITG_00145

Histone-lysine N-methyltransferase

Bromodomain, PHD-like zinc-binding (zf-HC5HC2H), F/Y-rich N-terminus, SET

PITG_20502, PITG_04185

Protein methyltransferase w/bicoid

Methyltransferase, bicoid-interacting protein 3

PITG_14915

SLIDE domain-containing protein (A)

DUF1898, SNF2 N-terminal, Helicase conserved C-terminal, SLIDE, [myb-like DNA-binding], HMG box

PITG_02286

SLIDE domain-containing protein (B)

SNF2 N-terminal, Helicase conserved C-terminal, [HAND], SLIDE

PITG_17273

SSRP1 subunit, FACT complex

Structure-specific recognition protein, Histone chaperone Rttp106-like

PITG_14260

RNA Methylation

  

FtsJ-like rRNA Methyltransferase (A)

FtsJ-like methyltransferase

PITG_09405

FtsJ-like rRNA Methyltransferase (B)

FtsJ-like methyltransferase

PITG_06848

FtsJ-like rRNA Methyltransferase (C)

FtsJ-like methyltransferase

PITG_16337

Spb1-like rRNA Methyltransferase

FtsJ-like methyltransferase, DUF3381, Spb1 C-terminal domain

PITG_00663

Guanosine 2'O tRNA methyltransferase

CCCH zinc finger, U11-48 K CHHC zinc finger, TRM13 methyltransferase

PITG_04858

N2,N2-dimethylguanosine tRNA methyltransferase

N2,N2-dimethylguanosine tRNA methyltransferase (TRM)

PITG_10166

MnmA-like tRNA 2'-thiouridylase

tRNA methyltransferase

PITG_08823

RNA Silencing

  

Argonaute (A)

DUF1785, PAZ, Piwi

PITG_04470, PITG_04471

Argonaute (B)

DUF1785, PAZ, Piwi

PITG_01400, PITG_01443, PITG_01444

Dicer-like

[DEAD/H box helicase], dsRNA binding, 2x Rnase III domains

PITG_09292

Drosha-like

2x Rnase III domains, [dsRNA binding]

Psojae_300435

dsRNA-binding protein

dsRNA binding

PITG_12183

dsRNA-binding protein w/ Bin3

[methyltransferase], dsRNA binding, Bicoid-interacting 3

PITG_03262

RnaseIII domain protein

Rnase III domain, [dsRNA binding]

PITG_08831

RNA-dependant RNA polymerase

DEAD/H box helicase, Helicase conserved C-terminal, RdRP domain, [NTP transferase]

PITG_10457

Transcription factors

  

Histone-like CBF/NF-Y

CBF/NF-Y [CENP-S associated centromere protein X]

PITG_00914

Histone-like CBF/NF-Y w/HMG

HMG, CBF/NF-Y

PITG_19530

Med17 subunit of Mediator complex

Med17

PITG_03899

p15 transcriptional coactivator

2x PC4

PITG_07058

TFIIB

TFIIB zinc-binding, 2x TFIIB

PITG_14596

TFIID, TATA-binding protein (A)

2x TBP

PITG_07312

TFIID, TATA-binding protein (B)

2x TBP, [DUF3378]

PITG_12304

TFIID, TATA-binding protein (C)

TBP, [2x DUF3378], TBP

PITG_06201

TFIID, TAF1 subunit

DUF3591, Bromodomain

PITG_02547

TFIID, TAF2 subunit

Peptidase M1, [HEAT repeat]

PITG_18882, PITG_14044

TFIID, TAF5 subunit

TFIID 90 kDa, 5x WD domain

PITG_16023

TFIID, TAF6 subunit

TAF, DUF1546, [HEAT repeat]

PITG_03978

TFIID, TAF8 subunit

Bromodomain (histone-like fold), TAF8 C-terminal

PITG_18355

TFIID, TAF9 subunit

TFIID 31 kDa

PITG_04860

TFIID, TAF10 subunit

TFIID 23–30 kDa

PITG_07637, PITG_14668

TFIID, TAF12 subunit

TFIID 20 kDa

PITG_00683

TFIID, TAF14 subunit

YEATS

PITG_01229

TFIIE, alpha subunit

TFIIEalpha

PITG_08403

TFIIF, alpha subunit

TFIIFalpha

PITG_02327

TFIIF, beta subunit

TFIIFbeta

PITG_10081

TFIIH, Rad3 subunit

DEAD 2, DUF1227, Helicase C-terminal

PITG_15696

TFIIH, Ssl1 subunit

Ssl1-like, TFIIH c1-like

Psojae_345458

TFIIH, Tfb1 subunit

[TFIIH p62 N-terminal], BSD

PITG_03523

TFIIH, Tfb2 subunit

Tfb2

PITG_15486

TFIIH, Tfb4 subunit

Tfb4

PITG_00220

TFIIIB, Brf1-like subunit

TFIIB zinc-binding, 2x TFIIB, Brf1-like TBP-binding

PITG_16669

  1. aDomains in brackets indicate missing or non-significant matches in some species.
  2. bReference sequences from P. infestans T30-4 (PITG) or P. sojae P6497 v3.0.