Protist Sequence Space: What’s Out There?

 In the following Table, Eukaryote taxa are listed with emphasis on protists. The numbers in parentheses after the Genbank taxa are the number of entries in Genbank. The PR-#s refer to the phyla of the Protoctista according to Margulis and Schwartz. (Margulis, L. and Schwartz, K.V. Five Kingdoms an illustrated guide to the phyla of life on earth. Freeman, New York 1998) Baldauf and Doolittle refers to their recent paper on phylogeny of eukaryotes (Baldauf SL, Roger AJ, Wenk-Siefert I, Doolittle WF. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science. 2000 Nov 3;290(5493):972-7.) Note that some lower eukaryote taxa have significant sequence sampling. Last modified May 22, 2001 David Nelson

Baldauf and Doolittle Taxa

GenBank Taxa

Margulis and Schwartz Taxa
Opisthokonta
  1. Fungi
  2. Metazoa
  3. Microsporidia
Fungi/Metazoa Group
  • Fungi (209,722)
  • Metazoa (9,363,304)
Microsporidia (327)		 Kingdom Fungi
  • 3 Phyla
PR-2 Microspora
now considered part of Fungi
PR-29 Chytridiomycota
considered as Fungi in GenBank

Kingdom Animalia
  • 37 Phyla
PR-24 Myxospora
considered as Metazoa in GenBank
Amoebozoa
  1. Mycetozoa



  2. Lobosa
Mycetozoa (20553,
20360 = Dictyostelium)
Cercozoa (72)
Entamoebidae (50196
all = Entamoeba, an anaerobic parasite)
Acanthamoebidae (615
all = Acanthamoeba)
Lobosea (20) 		PR-3 Rhizopoda

PR-6 Myxomycota
Plantae
  1. Viridiplantae
  2. Rhodophyta
  3. Glaucophyta
Viridiplantae (1,483,933)
Rhodophyta (12278,
10540 = Porphyra)
Glaucocystophyceae (76)
Cryptophyta (554) 		Kingdom Plantae

PR-25 Rhodophyta
PR-26 Gamophyta
treated as a plant in GenBank
PR-28 Chlorophyta
treated as a plant in GenBank
PR-11 Cryptomonada
Heterokonta Stramenopiles (7662)
  • Phytophthora (4548)
    pathogen of the Irish potato famine
  • Laminaria (995)
Plasmodiophorida (37) 		PR-13 Chrysomonada
PR-14 Xanthophyta
PR-15 Eustigmatophyta
PR-16 Diatoms
PR-17 Phaeophyta brown algae
PR-18 Labyrinthulata
PR-19 Plasmodiophora
PR-20 Oomycota
PR-21 Hypochytridiomycota
Alveolata
  1. Ciliophora

  2. Apicomplexa
Alveolata (80031)
  • Toxoplasma (16436)
    human parasite
  • Plasmodium (32763)
    malaria
  • Cryptosporidium (8287)
    human parasite
  • Eimeria (10456)
    chicken parasite
  • Paramecium (3322)
  • Sarcocystis (2021)
    animal parasite
  • Neospora (3193)
    cattle parasite
Granuloreticulosea (681) 		PR-4 Granuloreticulosa Foraminifera
PR-7 Dinomastigota
PR-8 Ciliophora
PR-9 Apicomplexa
PR-22 Haplospora
Discicristata
  1. Euglenozoa

  2. Heterolobosea
Euglenozoa (137677)
  • Trypanosoma (121074)
    human parasite
  • Leishmania (15407)
    human parasite
Heterolobosea (168) 		PR-12 Discomitochondria
Diplomonadida Diplomonadida (56513,
56476 = Giardia) 		PR-1 Archeaprotista
Parabasala Parabasalidea (372)
Oxymonadida (10,
alpha tubulin and EF1 alpha) 		PR-1 Archeaprotista
- Haptophyceae (163) PR-10 Haptomonada
- Paramyxea (2 rRNAs) PR-23 Paramyxa
- Polycystinea (12 all rRNAs) Acantharea (7 all rRNAs) PR-27 Actinopoda (radiolarians)
- Core Jakobids
(12 mito genome tubulins) Malawimonadidae
(5 mito genome tubulins)
 PR-30 Zoomastigota
- Not in Genbank PR-5 Xenyphyophora