List of sequenced protist genomes

Last updated

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 are not included, nor are organelle only sequences.

Contents

Alveolata

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.

OrganismTypeRelevanceGenome sizeNumber of genes predictedOrganizationYear of completionAssembly statusLinks
Babesia bovis Apicomplexan Cattle pathogen8.2 Mb3,6712007 [1]
Breviolum minutim (Symbiodinium minutum; clade B1) Dinoflagellate Coral symbiont1.5 Gb47,014Okinawa Institute of Science and Technology2013 [2] DraftOIST Marine Genomics [3]
Cladocopium goreaui (Symbiodinium goreaui; Clade C1) Dinoflagellate Coral symbiont1.19 Gb35,913Reef Future Genomics (ReFuGe) 2020/ University of Queensland 2018 [4] DraftReFuGe 2020 [5]
Cladocopium C92 strain Y103 ( Symbiodinium sp. clade C; putative type C92) Dinoflagellate Foraminiferan symbiontUnknown (assembly size 0.70 Gb)65,832 Okinawa Institute of Science and Technology 2018 [6] DraftOIST Marine Genomics [3]
Cryptosporidium hominis
Strain:TU502
Apicomplexan Human pathogen10.4 Mb3,994 [7] Virginia Commonwealth University 2004 [7]
Cryptosporidium parvum
C- or genotype 2 isolate
Apicomplexan Human pathogen16.5 Mb3,807 [8] UCSF and University of Minnesota2004 [8]
Eimeria tenella
Houghton strain
Apicomplexan Intestinal parasite of domestic fowl55-60 Mb [9] The Wellcome Trust Sanger Institute [10] Available for download; [10] 2007 for Chr 1 [11]
Fugacium kawagutii CS156=CCMP2468 ( Symbiodinium kawagutii; clade F1) Dinoflagellate Coral symbiont?1.07 Gb26,609Reef Future Genomics (ReFuGe) 2020 / University of Queensland 2018 [4] DraftReFuGe 2020 [5]
Fugacium kawagutii CCMP2468 ( Symbiodinium kawagutii; clade F1) Dinoflagellate Coral symbiont?1.18 Gb36,850 University of Connecticut / Xiamen University 2015 [12] DraftS. kawagutii genome project [13]
Neospora caninum Apicomplexan Pathogen for cattle and dogs62 Mb [14] The Wellcome Trust Sanger Institute [15] Available for download [15]
Paramecium tetraurelia Ciliate Model organism72 Mb39,642 [16] Genoscope 2006 [16]
Polarella glacialis CCMP1383 Dinoflagellate Psychrophile, Antarctic3.02 Gb (diploid), 1.48 Gbp (haploid)58,232 University of Queensland 2020 [17] DraftUQ eSpace [18]
Polarella glacialis CCMP2088 Dinoflagellate Psychrophile, Arctic2.65 Gb (diploid), 1.30 Gbp (haploid)51,713 University of Queensland 2020 [17] DraftUQ eSpace [18]
Plasmodium berghei ANKA Apicomplexan Rabbit malaria18.5 Mb [19] 4,900; [19] 11,654 (UniProt)
Plasmodium chabaudi Apicomplexan Rodent malaria19.8 Mb [20] 5,000 [20]
Plasmodium falciparum
Clone:3D7
Apicomplexan Human pathogen (malaria)22.9 Mb5,268 [21] Malaria Genome Project Consortium2002 [21]
Plasmodium knowlesi Apicomplexan Primate pathogen (malaria)23.5 Mb5,188 [22] 2008 [22]
Plasmodium vivax Apicomplexan Human pathogen (malaria)26.8 Mb5,433 [23] 2008 [23]
Plasmodium yoelii yoelii
Strain:17XNL
Apicomplexan Rodent pathogen (malaria)23.1 Mb5,878 [24] TIGR and NMRC2002 [24]
Symbiodinium microadriaticum (clade A) Dinoflagellate Coral symbiont1.1 Gb49,109 King Abdullah University of Science and Technology 2016 [25] DraftReef Genomics [26]
Symbiodinium A3 strain Y106 ( Symbiodinium sp. clade A3) Dinoflagellate symbiontUnknown (assembly size 0.77 Gb)69,018 Okinawa Institute of Science and Technology 2018 [6] DraftOIST Marine Genomics [3]
Tetrahymena thermophila Ciliate Model organism104 Mb27,000 [27] 2006 [27]
Theileria annulata
Ankara clone C9
Apicomplexan Cattle pathogen8.3 Mb3,792Sanger2005 [28]
Theileria parva
Strain:Muguga
Apicomplexan Cattle pathogen (African east coast fever)8.3 Mb4,035 [29] TIGR and the International Livestock Research Institute2005 [29]
Toxoplasma gondii
GT1, ME49, VEG strains
Apicomplexan Mammal pathogen63 Mb (RefSeq)8,100 (UniProt) - 9,000 (EuPathDB)J. Craig Venter Inst., TIGR, UPenn.2008 [30]

Amoebozoa

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 Flabellinia. Some Amoeboza cause disease.

OrganismTypeRelevanceGenome sizeNumber of genes predictedOrganizationYear of completion
Dictyostelium discoideum
Strain:AX4
Slime mold Model organism34 Mb12,500 [31] Consortium from University of Cologne, Baylor College of Medicine and the Sanger Centre2005 [31]
Entamoeba histolytica
HM1:IMSS
Parasitic protozoanHuman pathogen (amoebic dysentery)23.8 Mb9,938 [32] TIGR, Sanger Institute and the London School of Hygiene and Tropical Medicine2005 [32]
Polysphondylium pallidum
Strain:PN500
Slime mold Model organism12,939, [33] 12,350 (UniProt)Leibniz Institute for Age Research2009 [33]

Chromista

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.

OrganismTypeRelevanceGenome sizeNumber of genes predictedOrganizationYear of completion
Albugo laibachii Oomycete Arabidopsis parasite, biotroph37 Mb [34] 13,032 [34] 2011 [34]
Aureococcus anophagefferens
Strain:CCMP1984
Pelagophyte DOE Joint Genome Institute2011 [35]
Bigelowiella natans Chlorarachniophyte Model organism nucleomorph: 0.331 Mb
nuclear: 95 Mb
nucleomorph: 373 [36]
nuclear: >21,000 [37]
nucleomorph: Hall Institute Australia, Univ. Melbourne, Univ. BC
nuclear: Dalhousie University, Halifax, Nova Scotia, Canada
2006, [36] 2012 [37]
Chroomonas mesostigmaticaCCMP1168 Cryptophyta 2012 [38]
Cryptomonas paramecium Cryptophyta 2010 [39]
Emiliania huxleyi
CCMP1516
Coccolithophore (phytoplankton)141.7 Mb [40] 30,569 [40] Joint Genome Institute 2013 [40]
Emiliania huxleyi
RCC1217
Coccolithophore (phytoplankton)Available for download [41]
Fragilariopsis cylindrus Diatom 61.1 Mb [42] 21,066 [42] Joint Genome Institute 2017 [42]
Guillardia theta Cryptomonad Model organism0.551 Mb (nucleomorph genome only)
87 Mb (nuclear genome)
nucleomorph: 465 [43] 513, 598 (UniProt)
nuclear: >21,000 [37]
nucleomorph: Canadian Institute of Advanced Research, Philipps-University Marburg and the University of British Columbia
nuclear: Dalhousie University, Halifax, Nova Scotia, Canada
2001, [43] 2012 [37]
Hemiselmis andersenii
CCMP7644
Cryptomonad Model organism0.572 Mb
(nucleomorph genome only)
472, [44] 502 (UniProt)Canadian Institute of Advanced Research2007 [44]
Hyaloperonospora arabidopsidis Oomycete obligate biotroph, Arabidopsis pathogenWUGSC2010 [45]
Nannochloropis gaditana
Strain: CCMP526
Eustigmatophyte Lipid-producing, biotechnology applicationsVirginia Bioinformatics Institute2012 [46]
Phaeodactylum tricornutum
Strain: CCAP1055/1
Diatom 27.4 Mb10,402 Joint Genome Institute 2008 [47]
Phytophthora infestans
Strain:T30-4
Oomycete Great Famine of Ireland pathogenBroad Institute2009 [48]
Phytophthora ramorum Oomycete Sudden oak death pathogen65 Mb (7x)15,743 Joint Genome Institute et al.2006 [49]
Phytophthora sojae Oomycete Soybean pathogen95 Mb (9x)19,027 Joint Genome Institute et al.2006 [49]
Pseudo-nitzschia multiseries Diatom Joint Genome Institute
Plasmodiophora brassicae Plasmodiophorid Clubroot disease pathogen25.5 Mb9,730 SLU Uppsala et al.2015 [50]
Pythium ultimum Oomycete ubiquitous plant pathogen42.8 Mb15,290 Michigan State University et al.2010 [51]
Thalassiosira pseudonana
Strain:CCMP 1335
Diatom 34.5 Mb11,242 [52] Joint Genome Institute and the University of Washington 2004 [52]

Excavata

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.

OrganismTypeRelevanceGenome sizeNumber of genes predictedOrganizationYear of completion
Giardia enterica (G. duodenalis assemblage B)Parasitic protozoanHuman pathogen (Giardiasis)11.7 Mb4,470 [53] multicenter collaboration2009 [53]
Giardia duodenalis
ATCC 50803
(Giardia duodenalis assemblage A)
Parasitic protozoanHuman pathogen (Giardiasis)11.7 Mb6,470, [54] 7,153 (UniProt)Karolinska Institutet, Marine Biological Laboratory2007 [54]
Leishmania braziliensis
MHOM/BR/75M2904
Parasitic protozoanHuman pathogen (Leishmaniasis)33 Mb8,314 [55] Sanger Institute, Universidade de São Paulo, Imperial College2007 [55]
Leishmania infantum
JPCM5
Parasitic protozoanHuman pathogen (Visceral leishmaniasis)33 Mb8,195 [55] Sanger Institute, Imperial College and University of Glasgow2007 [55]
Leishmania major
Strain:Friedlin
Parasitic protozoanHuman pathogen (Cutaneous leishmaniasis)32.8 Mb8,272 [56] Sanger Institute and Seattle Biomedical Research Institute 2005 [56]
Naegleria gruberi amoeboflagellate Diverged from other eukaryotes over 1 billion years ago41 Mb [57] 15,727 [57] 2010 [57]
Trichomonas vaginalis Parasitic protozoanHuman pathogen (Trichomoniasis)160 Mb59,681 [58] TIGR2007 [58]
Trypanosoma brucei
Strain:TREU927/4 GUTat10.1
Parasitic protozoanHuman pathogen (Sleeping sickness)26 Mb9,068 [59] Sanger Institute and TIGR2005 [59]
Trypanosoma cruzi
Strain:CL Brener TC3
Parasitic protozoanHuman pathogen (Chagas disease)34 Mb22,570 [60] TIGR, Seattle Biomedical Research Institute and Uppsala University2005 [60]

Opisthokonts, basal

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 the sister or near-sister group of animals.

OrganismTypeRelevanceGenome sizeNumber of genes predictedOrganizationYear of completion
Monosiga brevicollis Choanoflagellate close relative of metazoans41.6 Mb9,200 [61] Joint Genome Institute2007 [61]

See also

Related Research Articles

<span class="mw-page-title-main">Genome</span> All genetic material of an organism

In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA. The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as regulatory sequences, and often a substantial fraction of 'junk' DNA with no evident function. Almost all eukaryotes have mitochondria and a small mitochondrial genome. Algae and plants also contain chloroplasts with a chloroplast genome.

<span class="mw-page-title-main">Alveolate</span> Superphylum of protists

The alveolates are a group of protists, considered a major clade and superphylum within Eukarya. They are currently grouped with the stramenopiles and Rhizaria among the protists with tubulocristate mitochondria, the group being referred to as SAR.

<span class="mw-page-title-main">Genome size</span> Amount of DNA contained in a genome

Genome size is the total amount of DNA contained within one copy of a single complete genome. It is typically measured in terms of mass in picograms or less frequently in daltons, or as the total number of nucleotide base pairs, usually in megabases. One picogram is equal to 978 megabases. In diploid organisms, genome size is often used interchangeably with the term C-value.

<span class="mw-page-title-main">Ancient DNA</span> Method of archaeological study

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<span class="mw-page-title-main">Reticulon 4 receptor</span> Protein-coding gene in the species Homo sapiens

Reticulon 4 receptor (RTN4R) also known as Nogo-66 Receptor (NgR) or Nogo receptor 1 is a protein which in humans is encoded by the RTN4R gene. This gene encodes the receptor for reticulon 4, oligodendrocytemyelin glycoprotein and myelin-associated glycoprotein. This receptor mediates axonal growth inhibition and may play a role in regulating axonal regeneration and plasticity in the adult central nervous system.

<span class="mw-page-title-main">GNG11</span>

Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-11 is a protein that in humans is encoded by the GNG11 gene.

<span class="mw-page-title-main">RBM33</span>

RNA-binding protein 33 is a protein that in humans is encoded by the RBM33 gene.

<span class="mw-page-title-main">Neoaves</span> Clade of birds

Neoaves is a clade that consists of all modern birds with the exception of Paleognathae and Galloanserae. Almost 95% of the roughly 10,000 known species of extant birds belong to the Neoaves.

Guillardia is a genus of flagellate cryptomonad algae belonging to the family Geminigeraceae, containing a secondary plastid within a reduced cytoplasmic compartment that contains a vestigial nucleomorph. There is only one characterised member of this genus, Guillardia theta.

<span class="mw-page-title-main">Denisovan</span> Asian archaic human

The Denisovans or Denisova hominins(di-NEE-sə-və) are an extinct species or subspecies of archaic human that ranged across Asia during the Lower and Middle Paleolithic. Denisovans are known from few physical remains and consequently, most of what is known about them comes from DNA evidence. No formal species name has been established pending more complete fossil material.

Single-cell sequencing examines the sequence information from individual cells with optimized next-generation sequencing technologies, providing a higher resolution of cellular differences and a better understanding of the function of an individual cell in the context of its microenvironment. For example, in cancer, sequencing the DNA of individual cells can give information about mutations carried by small populations of cells. In development, sequencing the RNAs expressed by individual cells can give insight into the existence and behavior of different cell types. In microbial systems, a population of the same species can appear genetically clonal. Still, single-cell sequencing of RNA or epigenetic modifications can reveal cell-to-cell variability that may help populations rapidly adapt to survive in changing environments.

<span class="mw-page-title-main">Aequorlitornithes</span> Taxon of birds

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<span class="mw-page-title-main">Marine protists</span> Protists that live in saltwater or brackish water

Marine protists are defined by their habitat as protists that live in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. Life originated as marine single-celled prokaryotes and later evolved into more complex eukaryotes. Eukaryotes are the more developed life forms known as plants, animals, fungi and protists. Protists are the eukaryotes that cannot be classified as plants, fungi or animals. They are mostly single-celled and microscopic. The term protist came into use historically as a term of convenience for eukaryotes that cannot be strictly classified as plants, animals or fungi. They are not a part of modern cladistics because they are paraphyletic.

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