List of sequenced protist genomes

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This list of sequenced protist genomes contains all the protist species known to have publicly available complete genome sequences that have been assembled, annotated and published; draft genomes aren't included, nor are organelle only sequences.

Alveolata[edit]

Alveolata are a group of protists which includes the Ciliophora, Apicomplexa and Dinoflagellata. Members of this group are of particular interest to science as the cause of serious human and livestock diseases.

Organism Type Relevance Genome size Number of genes predicted Organization Year of completion
Babesia bovis Apicomplexan Cattle pathogen 8.2 Mb 3,671 2007[1]
Cryptosporidium hominis
Strain:TU502
Apicomplexan Human pathogen 10.4 Mb 3,994[2] Virginia Commonwealth University 2004[2]
Cryptosporidium parvum
C- or genotype 2 isolate
Apicomplexan Human pathogen 16.5 Mb 3,807[3] UCSF and University of Minnesota 2004[3]
Eimeria tenella
Houghton strain
Apicomplexan Intestinal parasite of domestic fowl 55-60 Mb[4] The Wellcome Trust Sanger Institute[5] Available for download;[5] 2007 for Chr 1[6]
Neospora caninum Apicomplexan Pathogen for cattle and dogs 62 Mb[7] The Wellcome Trust Sanger Institute[8] Available for download[8]
Paramecium tetraurelia Ciliate Model organism 72 Mb 39,642[9] Genoscope 2006[9]
Plasmodium berghei
Strain:Anka
Apicomplexan Rabbit malaria 18.5 Mb[10] 4,900;[10] 11,654 (UniProt)
Plasmodium chabaudi Apicomplexan Rodent malaria 19.8 Mb[11] 5,000[11]
Plasmodium falciparum
Clone:3D7
Apicomplexan Human pathogen (malaria) 22.9 Mb 5,268[12] Malaria Genome Project Consortium 2002[12]
Plasmodium knowlesi Apicomplexan Primate pathogen (malaria) 23.5 Mb 5,188[13] 2008[13]
Plasmodium vivax Apicomplexan Human pathogen (malaria) 26.8 Mb 5,433[14] 2008[14]
Plasmodium yoelii yoelii
Strain:17XNL
Apicomplexan Rodent pathogen (malaria) 23.1 Mb 5,878[15] TIGR and NMRC 2002[15]
Tetrahymena thermophila Ciliate Model organism 104 Mb 27,000[16] 2006[16]
Theileria annulata
Ankara clone C9
Apicomplexan Cattle pathogen 8.3 Mb 3,792 Sanger 2005[17]
Theileria parva
Strain:Muguga
Apicomplexan Cattle pathogen (African east coast fever) 8.3 Mb 4,035[18] TIGR and the International Livestock Research Institute 2005[18]
Toxoplasma gondii
GT1, ME49, VEG strains
Apicomplexan Mammal pathogen 63 Mb (RefSeq) 8,100 (UniProt) - 9,000 (EuPathDB) J. Craig Venter Inst., TIGR, UPenn. 2008[19]

Amoebozoa[edit]

Amoebozoa are a group of motile amoeboid protists, members of this group move or feed by means of temporary projections, called pseudopods. The best known member of this group is the slime mold which has been studied for centuries; other members include the Archamoebae, Tubulinea and Flabellinea. Some Amoeboza cause disease.

Organism Type Relevance Genome size Number of genes predicted Organization Year of completion
Dictyostelium discoideum
Strain:AX4
Slime mold Model organism 34 Mb 12,500[20] Consortium from University of Cologne, Baylor College of Medicine and the Sanger Centre 2005[20]
Entamoeba histolytica
HM1:IMSS
Parasitic protozoan Human pathogen (amoebic dysentery) 23.8 Mb 9,938[21] TIGR, Sanger Institute and the London School of Hygiene and Tropical Medicine 2005[21]
Polysphondylium pallidum
Strain:PN500
Slime mold Model organism 12,939,[22] 12,350 (UniProt) Leibniz Institute for Age Research 2009[22]

Chromista[edit]

The Chromista are a group of protists that contains the algal phyla Heterokontophyta (stramenopiles), Haptophyta and Cryptophyta. Members of this group are mostly studied for evolutionary interest.

Organism Type Relevance Genome size Number of genes predicted Organization Year of completion
Albugo laibachii Oomycete Arabidopsis parasite, biotroph 37 Mb[23] 13,032[23] 2011[23]
Aureococcus anophagefferens
Strain:CCMP1984
Pelagophyte DOE Joint Genome Institute 2011[24]
Bigelowiella natans Chlorarachniophyte Model organism nucleomorph: 0.331 Mb
nuclear: 95 Mb
nucleomorph: 373[25]
nuclear: >21,000[26]
nucleomorph: Hall Institute Australia, Univ. Melbourne, Univ. BC
nuclear: Dalhousie University, Halifax, Nova Scotia, Canada
2006,[25] 2012[26]
Chroomonas mesostigmatica CCMP1168 Cryptophyta 2012[27]
Cryptomonas paramecium Cryptophyta 2010[28]
Emiliania huxleyi
CCMP1516
Coccolithophore (phytoplankton) Joint Genome Institute Available for download[29]
Emiliania huxleyi
RCC1217
Coccolithophore (phytoplankton) Available for download[30]
Fragilariopsis cylindrus Diatom Joint Genome Institute Available for download[31]
Guillardia theta Cryptomonad Model organism 0.551 Mb (nucleomorph genome only)
87 Mb (nuclear genome)
nucleomorph: 465[32] 513, 598 (UniProt)
nuclear: >21,000[26]
nucleomorph: Canadian Institute of Advanced Research, Philipps-University Marburg and the University of British Columbia
nuclear: Dalhousie University, Halifax, Nova Scotia, Canada
2001,[32] 2012[26]
Hemiselmis andersenii
CCMP7644
Cryptomonad Model organism 0.572 Mb
(nucleomorph genome only)
472,[33] 502 (UniProt) Canadian Institute of Advanced Research 2007[33]
Hyaloperonospora arabidopsidis Oomycete obligate biotroph, Arabidopsis pathogen WUGSC 2010[34]
Nannochloropis gaditana
Strain: CCMP526
Eustigmatophyte Lipid-producing, biotechnology applications Virginia Bioinformatics Institute 2012[35]
Phaeodactylum tricornutum
Strain: CCAP1055/1
Diatom 27.4 Mb 10,402 Joint Genome Institute 2008[36]
Phytophthora infestans
Strain:T30-4
Oomycete Irish potato famine pathogen Broad Institute 2009[37]
Phytophthora ramorum Oomycete Sudden oak death pathogen 65 Mb (7x) 15,743 Joint Genome Institute et al. 2006[38]
Phytophthora sojae Oomycete Soybean pathogen 95 Mb (9x) 19,027 Joint Genome Institute et al. 2006[38]
Pseudo-nitzschia multiseries Diatom Joint Genome Institute
Pythium ultimum Oomycete ubiquitous plant pathogen 42.8 Mb 15,290 Michigan State University et al. 2010[39]
Thalassiosira pseudonana
Strain:CCMP 1335
Diatom 34.5 Mb 11,242[40] Joint Genome Institute and the University of Washington 2004[40]

Excavata[edit]

Excavata is a group of related free living and symbiotic protists; it includes the Metamonada, Loukozoa, Euglenozoa and Percolozoa. They are researched for their role in human disease.

Organism Type Relevance Genome size Number of genes predicted Organization Year of completion
Giardia enterica (G. duodenalis assemblage B) Parasitic protozoan Human pathogen (Giardiasis) 11.7 Mb 4,470[41] multicenter collaboration 2009[41]
Giardia duodenalis
ATCC 50803
(Giardia duodenalis assemblage A)
Parasitic protozoan Human pathogen (Giardiasis) 11.7 Mb 6,470,[42] 7,153 (UniProt) Karolinska Institutet, Marine Biological Laboratory 2007[42]
Leishmania braziliensis
MHOM/BR/75M2904
Parasitic protozoan Human pathogen (Leishmaniasis) 33 Mb 8,314[43] Sanger Institute, Universidade de São Paulo, Imperial College 2007[43]
Leishmania infantum
JPCM5
Parasitic protozoan Human pathogen (Visceral leishmaniasis) 33 Mb 8,195[43] Sanger Institute, Imperial College and University of Glasgow 2007[43]
Leishmania major
Strain:Friedlin
Parasitic protozoan Human pathogen (Cutaneous leishmaniasis) 32.8 Mb 8,272[44] Sanger Institute and Seattle Biomedical Research Institute 2005[44]
Naegleria gruberi amoeboflagellate Diverged from other eukaryotes over 1 billion years ago 41 Mb[45] 15,727[45] 2010[45]
Trichomonas vaginalis Parasitic protozoan Human pathogen (Trichomoniasis) 160 Mb 59,681[46] TIGR 2007[46]
Trypanosoma brucei
Strain:TREU927/4 GUTat10.1
Parasitic protozoan Human pathogen (Sleeping sickness) 26 Mb 9,068[47] Sanger Institute and TIGR 2005[47]
Trypanosoma cruzi
Strain:CL Brener TC3
Parasitic protozoan Human pathogen (Chagas disease) 34 Mb 22,570[48] TIGR, Seattle Biomedical Research Institute and Uppsala University 2005[48]

Opisthokonts, basal[edit]

Opisthokonts are a group of eukaryotes that include both animals and fungi as well as basal groups that are not classified in these groups. These basal opisthokonts are reasonably categorized as protists and include choanoflagellates, which are distantly related to sponges that are considered animals.

Organism Type Relevance Genome size Number of genes predicted Organization Year of completion
Monosiga brevicollis Choanoflagellate close relative of metazoans 41.6 Mb 9,200[49] Joint Genome Institute 2007[49]

See also[edit]

References[edit]

  1. ^ Brayton KA, Lau AOT, Herndon DR, et al. (2007). "Genome Sequence of Babesia bovis and Comparative Analysis of Apicomplexan Hemoprotozoa". PLoS Pathogens. 3 (10): 1401–13. doi:10.1371/journal.ppat.0030148. PMC 2034396Freely accessible. PMID 17953480. 
  2. ^ a b Xu P, Widmer G, Wang Y, et al. (October 2004). "The genome of Cryptosporidium hominis". Nature. 431 (7012): 1107–12. Bibcode:2004Natur.431.1107X. doi:10.1038/nature02977. PMID 15510150. 
  3. ^ a b Abrahamsen MS, Templeton TJ, Enomoto S, et al. (April 2004). "Complete genome sequence of the apicomplexan, Cryptosporidium parvum". Science. 304 (5669): 441–5. Bibcode:2004Sci...304..441A. doi:10.1126/science.1094786. PMID 15044751. 
  4. ^ genedb
  5. ^ a b Sanger
  6. ^ Ling K-H, Rajandream M-A, Rivailler P, et al. (2007). "Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization". Genome Research. 17 (3): 311–319. doi:10.1101/gr.5823007. PMC 1800922Freely accessible. PMID 17284678. 
  7. ^ genedb
  8. ^ a b Sanger
  9. ^ a b Aury JM, Jaillon O, Duret L, et al. (November 2006). "Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia". Nature. 444 (7116): 171–8. Bibcode:2006Natur.444..171A. doi:10.1038/nature05230. PMID 17086204. 
  10. ^ a b Ensembl entry
  11. ^ a b Ensembl entry
  12. ^ a b Gardner MJ, Hall N, Fung E, et al. (October 2002). "Genome sequence of the human malaria parasite Plasmodium falciparum". Nature. 419 (6906): 498–511. Bibcode:2002Natur.419..498G. doi:10.1038/nature01097. PMID 12368864. 
  13. ^ a b A. Pain, U. Böhme, A. E. Berry, K. Mungall, R. D. Finn, A. P. Jackson, T. Mourier, J. Mistry, E. M. Pasini, M. A. Aslet, S. Balasubrammaniam, K. Borgwardt, K. Brooks, C. Carret, T. J. Carver, I. Cherevach, T. Chillingworth, T. G. Clark, M. R. Galinski, N. Hall, D. Harper, D. Harris, H. Hauser, A. Ivens, C. S. Janssen, T. Keane, N. Larke, S. Lapp, M. Marti, S. Moule, I. M. Meyer, D. Ormond, N. Peters, M. Sanders, S. Sanders, T. J. Sargeant, M. Simmonds, F. Smith, R. Squares, S. Thurston, A. R. Tivey, D. Walker, B. White, E. Zuiderwijk, C. Churcher, M. A. Quail, A. F. Cowman, C. M. R. Turner, M. A. Rajandream, C. H. M. Kocken, A. W. Thomas, C. I. Newbold, B. G. Barrell & M. Berriman; Böhme; Berry; Mungall; Finn; Jackson; Mourier; Mistry; Pasini; Aslett; Balasubrammaniam; Borgwardt; Brooks; Carret; Carver; Cherevach; Chillingworth; Clark; Galinski; Hall; Harper; Harris; Hauser; Ivens; Janssen; Keane; Larke; Lapp; Marti; et al. (9 October 2008). "The genome of the simian and human malaria parasite Plasmodium knowlesi". Nature. 455 (7214): 799–803. Bibcode:2008Natur.455..799P. doi:10.1038/nature07306. PMC 2656934Freely accessible. PMID 18843368. 
  14. ^ a b JM Carlton, JH Adams, JC Silva, et al. (9 October 2008). "Comparative genomics of the neglected human malaria parasite Plasmodium vivax". Nature. 455 (7214): 757–763. Bibcode:2008Natur.455..757C. doi:10.1038/nature07327. PMC 2651158Freely accessible. PMID 18843361. 
  15. ^ a b Carlton JM, Angiuoli SV, Suh BB, et al. (October 2002). "Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii". Nature. 419 (6906): 512–9. Bibcode:2002Natur.419..512C. doi:10.1038/nature01099. PMID 12368865. 
  16. ^ a b Eisen JA, Coyne RS, Wu M, et al. (September 2006). "Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote". PLoS Biology. 4 (9): e286. doi:10.1371/journal.pbio.0040286. PMC 1557398Freely accessible. PMID 16933976. 
  17. ^ Pain A, Renauld H, Berriman M, et al. (July 2005). "Genome of the host-cell transforming parasite Theileria annulata compared with T. parva". Science. 309 (5731): 131–3. Bibcode:2005Sci...309..131P. doi:10.1126/science.1110418. PMID 15994557. 
  18. ^ a b Gardner MJ, Bishop R, Shah T, et al. (July 2005). "Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes". Science. 309 (5731): 134–7. Bibcode:2005Sci...309..134G. doi:10.1126/science.1110439. PMID 15994558. 
  19. ^ NCBI Genome T. gondii ME49
  20. ^ a b Eichinger L, Pachebat JA, Glöckner G, et al. (May 2005). "The genome of the social amoeba Dictyostelium discoideum". Nature. 435 (7038): 43–57. Bibcode:2005Natur.435...43E. doi:10.1038/nature03481. PMC 1352341Freely accessible. PMID 15875012. 
  21. ^ a b Loftus B, Anderson I, Davies R, et al. (February 2005). "The genome of the protist parasite Entamoeba histolytica". Nature. 433 (7028): 865–8. Bibcode:2005Natur.433..865L. doi:10.1038/nature03291. PMID 15729342. 
  22. ^ a b NCBI accession
  23. ^ a b c Kemen E, Gardiner A, Schultz-Larsen T, et al. (July 2011). Ausubel FM, ed. "Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thaliana". PLoS Biology. 9 (7): e1001094. doi:10.1371/journal.pbio.1001094. PMC 3130010Freely accessible. PMID 21750662. 
  24. ^ Gobler CJ, Berry DL, Dyhrman ST, et al. (15 March 2011). "Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics". PNAS. 108 (11): 4352–4357. Bibcode:2011PNAS..108.4352G. doi:10.1073/pnas.1016106108. PMC 3060233Freely accessible. PMID 21368207. 
  25. ^ a b Gilson PR, Su V, Slamovits CH, Reith ME, Keeling PJ, McFadden GI; Su; Slamovits; Reith; Keeling; McFadden (June 2006). "Complete nucleotide sequence of the chlorarachniophyte nucleomorph: Nature's smallest nucleus". PNAS. 103 (25): 9566–71. Bibcode:2006PNAS..103.9566G. doi:10.1073/pnas.0600707103. PMC 1480447Freely accessible. PMID 16760254. 
  26. ^ a b c d Curtis BA, Tanifuji G, Burki F; Tanifuji; Burki; Gruber; Irimia; Maruyama; Arias; Ball; Gile; Hirakawa; Hopkins; Kuo; Rensing; Schmutz; Symeonidi; Elias; Eveleigh; Herman; Klute; Nakayama; Oborník; Reyes-Prieto; Armbrust; Aves; Beiko; Coutinho; Dacks; Durnford; Fast; et al. (2012). "Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs". Nature. 492 (7427): 59–65. Bibcode:2012Natur.492...59C. doi:10.1038/nature11681. PMID 23201678. 
  27. ^ Moore CE, Curtis B, Mills T, et al. (2012). "Nucleomorph genome sequence of the cryptophyte alga Chroomonas mesostigmatica CCMP1168 reveals lineage-specific gene loss and genome complexity". Genome Biol Evolution. 4 (11): 1162–75. doi:10.1093/gbe/evs090. PMC 3514955Freely accessible. PMID 23042551. 
  28. ^ Tanifuji G, Onodera NT, Wheeler TJ; Onodera; Wheeler; Dlutek; Donaher; Archibald; et al. (2012). "Complete nucleomorph genome sequence of the nonphotosynthetic alga Cryptomonas paramecium reveals a core nucleomorph gene set". Genome Biology Evolution. 3: 44–54. doi:10.1093/gbe/evq082. PMC 3017389Freely accessible. PMID 21147880. 
  29. ^ JGI Entry
  30. ^ Entry
  31. ^ JGI-PSF Entry
  32. ^ a b Douglas S, Zauner S, Fraunholz M, et al. (April 2001). "The highly reduced genome of an enslaved algal nucleus". Nature. 410 (6832): 1091–6. doi:10.1038/35074092. PMID 11323671. 
  33. ^ a b Lane CE, van den Heuvel K, Kozera C, et al. (December 2007). "Nucleomorph genome of Hemiselmis andersenii reveals complete intron loss and compaction as a driver of protein structure and function". PNAS. 104 (50): 19908–13. Bibcode:2007PNAS..10419908L. doi:10.1073/pnas.0707419104. PMC 2148396Freely accessible. PMID 18077423. 
  34. ^ Baxter, L; Tripathy, S; Ishaque, N; Boot, N; Cabral, A; Kemen, E; Thines, M; Ah-Fong, A; et al. (2010). "Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome". Science. 330 (6010): 1549–51. Bibcode:2010Sci...330.1549B. doi:10.1126/science.1195203. PMID 21148394. 
  35. ^ Radakovits; Jinkerson; Fuerstenberg; Tae; Settlage; Boore; Posewitz; et al. (2012). "Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropis gaditana". Nature Communications. 3 (2): 686. Bibcode:2012NatCo...3E.686R. doi:10.1038/ncomms1688. PMC 3293424Freely accessible. PMID 22353717. 
  36. ^ Bowler C, Allen AE, Badger JH, et al. (November 2008). "The Phaeodactylum genome reveals the evolutionary history of diatom genomes". Nature. 456 (7219): 239–244. Bibcode:2008Natur.456..239B. doi:10.1038/nature07410. PMID 18923393. 
  37. ^ Haas BJ, Kamoun S, Zody MC, et al. (September 17, 2009). "Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans". Nature. 461 (7262): 393–398. Bibcode:2009Natur.461..393H. doi:10.1038/nature08358. PMID 19741609. 
  38. ^ a b Tyler, BM; Tripathy, S; Zhang, X; Dehal, P; Jiang, RH; Aerts, A; Arredondo, FD; Baxter, L; et al. (2006). "Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis". Science. 313 (5791): 1261–6. Bibcode:2006Sci...313.1261T. doi:10.1126/science.1128796. PMID 16946064. 
  39. ^ Carbone, A; Siu, A; Patel, R (2010). "Pediatric atopic dermatitis: A review of the medical management". The Annals of pharmacotherapy. 44 (9): 1448–58. doi:10.1345/aph.1P098. PMID 20628042. 
  40. ^ a b Armbrust EV, Berges JA, Bowler C, et al. (October 2004). "The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism". Science. 306 (5693): 79–86. Bibcode:2004Sci...306...79A. doi:10.1126/science.1101156. PMID 15459382. 
  41. ^ a b Franzen O, Jerlstrom-Hultqvist J, Castro E, et al. (2009). Petri W, ed. "Draft genome sequencing of Giardia intestinalis assemblage B isolate GS: Is human giardiasis caused by two different species?". PLoS Pathogens. 5 (8): e1000560. doi:10.1371/journal.ppat.1000560. PMC 2723961Freely accessible. PMID 19696920. 
  42. ^ a b HG Morrison, AG McArthur, FD Gillin, et al. (September 2007). "Genomic Minimalism in the Early Diverging Intestinal Parasite Giardia lamblia". Science. 317 (5846): 1921–26. Bibcode:2007Sci...317.1921M. doi:10.1126/science.1143837. PMID 17901334. 
  43. ^ a b c d Peacock CS, Seeger K, Harris D, et al. (July 2007). "Comparative genomic analysis of three Leishmania species that cause diverse human disease". Nature Genetics. 39 (7): 839–47. doi:10.1038/ng2053. PMC 2592530Freely accessible. PMID 17572675. 
  44. ^ a b Ivens AC, Peacock CS, Worthey EA, et al. (July 2005). "The Genome of the Kinetoplastid Parasite, Leishmania major". Science. 309 (5733): 436–42. Bibcode:2005Sci...309..436I. doi:10.1126/science.1112680. PMC 1470643Freely accessible. PMID 16020728. 
  45. ^ a b c Fritz-Laylin LK, Prochnik SE, Ginger ML, et al. (2010). "The genome of Naegleria gruberi illuminates early eukaryotic versatility". Cell. 140 (5): 631–642. doi:10.1016/j.cell.2010.01.032. PMID 20211133. 
  46. ^ a b Carlton JM, Hirt RP, Silva JC, et al. (January 2007). "Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis". Science. 315 (5809): 207–12. Bibcode:2007Sci...315..207C. doi:10.1126/science.1132894. PMC 2080659Freely accessible. PMID 17218520. 
  47. ^ a b Berriman M, Ghedin E, Hertz-Fowler C, et al. (July 2005). "The genome of the African trypanosome Trypanosoma brucei". Science. 309 (5733): 416–22. Bibcode:2005Sci...309..416B. doi:10.1126/science.1112642. PMID 16020726. 
  48. ^ a b El-Sayed NM, Myler PJ, Bartholomeu DC, et al. (July 2005). "The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease". Science. 309 (5733): 409–15. Bibcode:2005Sci...309..409E. doi:10.1126/science.1112631. PMID 16020725. 
  49. ^ a b King, Nicole; et al. (February 2008). "The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans". Nature. 451 (7180): 783–788. Bibcode:2008Natur.451..783K. doi:10.1038/nature06617. PMC 2562698Freely accessible. PMID 18273011.