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">Genomics</span> Discipline in genetics

Genomics is an interdisciplinary field of molecular biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dimensional structural configuration. In contrast to genetics, which refers to the study of individual genes and their roles in inheritance, genomics aims at the collective characterization and quantification of all of an organism's genes, their interrelations and influence on the organism. Genes may direct the production of proteins with the assistance of enzymes and messenger molecules. In turn, proteins make up body structures such as organs and tissues as well as control chemical reactions and carry signals between cells. Genomics also involves the sequencing and analysis of genomes through uses of high throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes. Advances in genomics have triggered a revolution in discovery-based research and systems biology to facilitate understanding of even the most complex biological systems such as the brain.

<span class="mw-page-title-main">Dinoflagellate</span> Unicellular algae with two flagella

The dinoflagellates are a monophyletic group of single-celled eukaryotes constituting the phylum Dinoflagellata and are usually considered protists. Dinoflagellates are mostly marine plankton, but they also are common in freshwater habitats. Their populations vary with sea surface temperature, salinity, and depth. Many dinoflagellates are photosynthetic, but a large fraction of these are in fact mixotrophic, combining photosynthesis with ingestion of prey.

<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 into the SAR supergroup.

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

Nucleomorphs are small, vestigial eukaryotic nuclei found between the inner and outer pairs of membranes in certain plastids. They are thought to be vestiges of primitive red and green algal nuclei that were engulfed by a larger eukaryote. Because the nucleomorph lies between two sets of membranes, nucleomorphs support the endosymbiotic theory and are evidence that the plastids containing them are complex plastids. Having two sets of membranes indicate that the plastid, a prokaryote, was engulfed by a eukaryote, an alga, which was then engulfed by another eukaryote, the host cell, making the plastid an example of secondary endosymbiosis.

<span class="mw-page-title-main">Comparative genomics</span> Field of biological research

Comparative genomics is a branch of biological research that examines genome sequences across a spectrum of species, spanning from humans and mice to a diverse array of organisms from bacteria to chimpanzees. This large-scale holistic approach compares two or more genomes to discover the similarities and differences between the genomes and to study the biology of the individual genomes. Comparison of whole genome sequences provides a highly detailed view of how organisms are related to each other at the gene level. By comparing whole genome sequences, researchers gain insights into genetic relationships between organisms and study evolutionary changes. The major principle of comparative genomics is that common features of two organisms will often be encoded within the DNA that is evolutionarily conserved between them. Therefore, Comparative genomics provides a powerful tool for studying evolutionary changes among organisms, helping to identify genes that are conserved or common among species, as well as genes that give unique characteristics of each organism. Moreover, these studies can be performed at different levels of the genomes to obtain multiple perspectives about the organisms.

<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">Chromosome conformation capture</span>

Chromosome conformation capture techniques are a set of molecular biology methods used to analyze the spatial organization of chromatin in a cell. These methods quantify the number of interactions between genomic loci that are nearby in 3-D space, but may be separated by many nucleotides in the linear genome. Such interactions may result from biological functions, such as promoter-enhancer interactions, or from random polymer looping, where undirected physical motion of chromatin causes loci to collide. Interaction frequencies may be analyzed directly, or they may be converted to distances and used to reconstruct 3-D structures.

<span class="mw-page-title-main">GNG11</span> Protein-coding gene in the species Homo sapiens

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">Holozoa</span> Clade containing animals and some protists

Holozoa is a clade of organisms that includes animals and their closest single-celled relatives, but excludes fungi and all other organisms. Together they amount to more than 1.5 million species of purely heterotrophic organisms, including around 300 unicellular species. It consists of various subgroups, namely Metazoa and the protists Choanoflagellata, Filasterea, Pluriformea and Ichthyosporea. Along with fungi and some other groups, Holozoa is part of the Opisthokonta, a supergroup of eukaryotes. Choanofila was previously used as the name for a group similar in composition to Holozoa, but its usage is discouraged now because it excludes animals and is therefore paraphyletic.

<i>Amphidinium</i> Genus of dinoflagellates

Amphidinium is a genus of dinoflagellates. The type for the genus is Amphidinium operculatum Claparède & Lachmann. The genus includes the species Amphidinium carterae which is used as a model organism.

Single-cell sequencing examines the nucleic acid 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.

A plant genome assembly represents the complete genomic sequence of a plant species, which is assembled into chromosomes and other organelles by using DNA fragments that are obtained from different types of sequencing technology.

References

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