This is a list of model organisms used in scientific research.
Viruses Phages (infecting prokaryotes): Escherichia virus Lambda (Phage lambda) Phi X 174, the first DNA genome ever to be sequenced (circular, 5386 base pairs in length), shortly after the RNA genome of bacteriophage MS2 (in 1976). T4 phage
Animal viruses: SV40 Human alphaherpesvirus (Herpes simplex virus)
Plant viruses: Tobacco mosaic virus
Bacteria
Escherichia coli (E. coli), common Gram-negative gut bacterium widely used in molecular genetics. Main lab strain is 'K-12'. Bacillus subtilis, endospore forming Gram-positive bacterium. Main lab strain is '168'. Caulobacter crescentus, bacterium that divides into two distinct cells used to study cellular differentiation. Mycoplasma genitalium, minimal organism and human STD pathogen. Aliivibrio fischeri, quorum sensing, bioluminescence and animal-bacterial symbiosis with Hawaiian bobtail squid. Bacteroides thetaiotaomicron, polysaccharide-degrading member of the human gut microbiota, used to study functional aspects of the gut microbiota. Synechocystis (specifically PCC 6803), photosynthetic cyanobacterium widely used in photosynthesis research. Pseudomonas fluorescens, soil bacterium that readily diversifies into different strains in the lab. Azotobacter vinelandii, obligate aerobe diazotroph used in nitrogen fixation research. Streptomyces coelicolor, soil-dwelling filamentous bacterium used to produce many clinically useful antibiotics.
Bacteria with minimal synthetic genomes Bacteria with synthetic, minimized genomes provide a near-"blank slate" for study. Foreign genes, natural or artificial, can be introduced into these minimal bacteria to study their function as well as what is needed for their function.
"Mycoplasma laboratorium", a series of minimized Mycoplasma mycoides strains. Syn3B has been used to research the interaction between Mycoplasma and mammal cells, specifically what genes are needed for intracellular parasitism. Escherichia coli Syn61, a minimized version of E. coli with three unused codons. Has been used to research expanded genetic code. Escherichia coli Syn57, a further minimization with seven unused codons.
Archaea Methanococcus and Methanosarcina, model methanogens, representing the two metabolic types of hydrogenotrophism and methylotrophism. Methanogenesis remains a key area of metabolic research. Halobacterium salinarum and Haloferax volcanii, model Haloarchaea. The former has a reputation in the study of DNA repair. The latter is more suited to more traditional genetics due to a shorter generation time and more stable genome. This order is known for its easy updake of genetic tools as well as resistance to culture contamination. Thermococcus kodakarensis, Pyrococcus abyssi, and Pyrococcus furiosus are the Thermococcales models. This order is known for its unique metabolic pathways. Three members of Sulfolobus, S. solfataricus PBL2025, S. islandicus E322S, and S. acidocaldarius are the current Sulfolobales models. Proteins from these thermophilic bacteria are easy to crystalize, simplifying structural work.
Eukaryotes
Protists Stentor coeruleus, used in molecular biology (its genome has been sequenced), and is studied as a model of single-cell regeneration. Dictyostelium discoideum, used in molecular biology and genetics (its genome has been sequenced), and is studied as an example of cell communication, differentiation, and programmed cell death. Tetrahymena thermophila, free living freshwater ciliate protozoan. Naegleria gruberi, freshwater non-pathogenic amoeboflagellate sometimes used in eukaryotic cell biology experiments. Emiliania huxleyi, unicellular marine coccolithophore alga, extensively studied as a model phytoplankton species. Thalassiosira pseudonana, unicellular marine diatom alga, extensively studied as a model marine diatom since its genome was published in 2004.
Fungi Ashbya gossypii, cotton pathogen, subject of genetics studies (polarity, cell cycle). Aspergillus nidulans, mold subject of genetics studies. Coprinus cinereus, mushroom (genetic studies of mushroom development, genetic studies of meiosis). Cryptococcus neoformans, opportunistic human pathogen Neurospora crassa, orange bread mold (genetic studies of meiosis, metabolic regulation, and circadian rhythm). Pichia pastoris (Komagataella phaffii), widely used in biochemical research and industry as an expression system for protein production, as well as genetic study Rhizophagus irregularis, used for studying arbuscular mycorrhizal symbiosis. Saccharomyces cerevisiae (baker's yeast or budding yeast), used in brewing and baking. Schizophyllum commune, model for mushroom formation. Schizosaccharomyces pombe, fission yeast, (cell cycle, cell polarity, RNAi, centromere structure and function, transcription). Ustilago maydis, dimorphic yeast and plant pathogen of maize (dimorphism, plant pathogen, transcription).
Plants
Vascular plants
Arabidopsis thaliana, currently the most popular model plant. This herbaceous dicot of the family Brassicaceae is closely related to the mustard plant. Its small stature and short generation time facilitates rapid genetic studies,About Arabidopsis on The Arabidopsis Information Resource page (TAIR) and many phenotypic and biochemical mutants have been mapped. Arabidopsis was the first plant to have its genome sequenced. Its genome sequence, along with a wide range of information concerning Arabidopsis, is maintained by the TAIR database.(Plant physiology, Developmental biology, Molecular genetics, Population genetics, Cytology, Molecular biology) Boechera genus, combines some of the experimental tractability and genetic tools developed for its close relative Arabidopsis with a largely undisturbed natural history, making it a promising model system for research at the intersection of genetics, genomics, ecology, and evolution. The genus includes species with the rare trait of apomixis at the diploid level.(Evolutionary ecology, Population genetics, Molecular ecology, Evolutionary biology, Ecological genetics) Selaginella moellendorffii, remnant of an ancient lineage of vascular plants that is key to understanding the evolution of land plants. It has a small genome size (~110Mb) and its sequence was released by the Joint Genome Institute in early 2008. (Evolutionary biology, Molecular biology) Brachypodium distachyon, emerging experimental model grass that has many attributes that make it an excellent model for temperate cereals. (Agronomy, Molecular biology, Genetics) Setaria viridis, emerging model grass for C4 photosynthesis and related bioenergy grasses. Lotus japonicus, model legume used to study the symbiosis responsible for nitrogen fixation. (Agronomy, Molecular biology)
Lemna gibba, rapidly growing aquatic monocot, one of the smallest flowering plants. Lemna growth assays are used to evaluate the toxicity of chemicals to plants in ecotoxicology. Because it can be grown in pure culture, microbial action can be excluded. Lemna is being used as a recombinant expression system for economical production of complex biopharmaceuticals. It is also used in education to demonstrate population growth curves. Zea mays L. (Maize/corn), cereal grain. It is a diploid monocot with 10 large chromosome pairs, easily studied with the microscope. Its genetic features, including many known and mapped phenotypic mutants and a large number of progeny per cross (typically 100–200) facilitated the discovery of transposons ("jumping genes"). Many DNA markers have been mapped and the genome has been sequenced. (Genetics, Molecular biology, Agronomy) Medicago truncatula, model legume, closely related to the common alfalfa. Its rather small genome is currently being sequenced. It is used to study the symbiosis responsible for nitrogen fixation. (Agronomy, Molecular biology) Mimulus guttatus, model organism used in evolutionary and functional genomes studies. The genus Mimulus contains c. 120 species and is in the family Phrymaceae. Several genetic resources have been designed for the study of this genus and some are free access (https://www.mimulusevolution.org) Nicotiana benthamiana, model organism for plant-pathogen studies. Nicotiana tabacum cv. BY-2 (Tobacco BY-2 cells), suspension cell line from tobacco (Nicotiana tabacum) that is useful for general plant physiology studies at the cell level. The genome of this particular cultivar will not be sequenced in the near future, but sequencing of its wild species Nicotiana tabacum is presently in progress. (Cytology, Plant physiology, Biotechnology) Oryza sativa (Rice) is used as a model for cereal biology. It has one of the smallest genomes of any cereal species, and sequencing of its genome is finished. (Agronomy, Molecular biology)
Populus, genus used as a model in forest genetics and woody plant studies. It has a small genome size, grows very rapidly, and is easily transformed. The genome sequence of black cottonwood (Populus trichocarpa) is publicly available.
Other Archaeplastida Chlamydomonas reinhardtii, unicellular green alga used to study photosynthesis, flagella and motility, regulation of metabolism, cell–cell recognition and adhesion, response to nutrient deprivation and many other topics. Chlamydomonas reinhardtii has well-studied genetics, with many known and mapped mutants and expressed sequence tags, and there are advanced methods for genetic transformation and selection of genes. Sequencing of the Chlamydomonas reinhardtii genome was reported in October 2007.Chlamydomonas genome sequenced published in Science, 12 October 2007 A Chlamydomonas genetic stock center exists at Duke University, and an international Chlamydomonas research interest group meets on a regular basis to discuss research results. Chlamydomonas is easy to grow on an inexpensive defined medium. Physcomitrella patens, moss increasingly used for studies on development and molecular evolution of plants. It is so far the only non-vascular plant(and so the only "primitive" plant) with its genome completely sequenced. Moreover, it is currently the only land plant with efficient gene targeting that enables gene knockout. The resulting knockout mosses are stored and distributed by the International Moss Stock Center. (Plant physiology, Evolutionary biology, Molecular genetics, Molecular biology) Marchantia polymorpha, liverwort that is also emerging as a model for plant biology and development.
Animals
Invertebrates
Amphimedon queenslandica, a demosponge from the phylum Porifera used as a model for evolutionary developmental biology and comparative genomics Arbacia punctulata, the purple-spined sea urchin, classical subject of embryological studies Aplysia, a sea slug, whose ink release response serves as a model in neurobiology and whose growth cones serve as a model of cytoskeletal rearrangements Branchiostoma floridae, a species commonly known as amphioxus or lancelet from the subphylum Cephalochordata of the phylum Chordata used as a model for understanding the evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates Caenorhabditis elegans, a nematode, usually called C. elegans - an excellent model for understanding the genetic control of development and physiology. C.elegans has a fixed number of 1031 cells. C. elegans was the first multicellular organism whose genome was completely sequenced Callosobruchus maculatus, the bruchid beetle, used to study sexual selection and sexual conflict Chorthippus parallelus (the meadow grasshopper), used to study sexual selection and sexual conflict Ciona intestinalis, a sea squirt Daphnia spp., small planktonic crustaceans, highly sensitive to pollution, used for evaluating environmental toxicity of chemicals on aquatic invertebrates. Coelopidae, seaweed flies, used to study sexual selection and sexual conflict