Model organisms

Organisms become models that have already accumulated a lot of scientific data. Usually, several laboratories or research groups are specially engaged in the model organism, and from the results of its study, from several hundred to many thousands of articles have been published.

Organisms that are easy to maintain and breed under laboratory conditions ( Escherichia coli , Tetrahymena thermophila , Arabidopsis thaliana , Caenorhabditis elegans , Drosophila melanogaster , Mus musculus ) are usually chosen as model organisms. Additional advantages are a short generation time (quick change of generations), the possibility of genetic manipulation (the presence of inbred lines , in the case of multicellular cells, the possibility of obtaining stem cells, developed methods of genetic transformation ).

Additional reasons for choosing this object as a model can be its position on the phylogenetic tree : for example, rhesus macaque is an important model organism for medical research because of its relatively close relationship with humans (for the same reason, the chimpanzee gene was chosen for complete decoding )

Finally, for some areas of research, the choice of an object as a model is determined primarily by the features of its structure. Thus, in the study of “simple nervous systems” , such organisms are used as models in which neurons are identifiable, relatively few and (preferably) large - for example, aplizia .

Historically, model organisms (E. coli, yeast, Drosophila) were the first among the corresponding groups of organisms whose genome was completely sequenced. In the future, the presence of a fully sequenced and decrypted genome became an important requirement for using the body as a model in biochemistry, genetics, molecular biology, and most other areas. For this reason, sometimes the choice of an organism was determined by the peculiarities of its genome: for example, Fugu rubripes puffer fish was chosen as a model for studying the genome due to its small size (low percentage of non-coding sequences).

Another criterion for choosing a model organism is its economic importance. Therefore, for example, in addition to Arabidópsis thaliána , rice Oryza sativa L., alfalfa Medicago truncatula , etc. are used as model plant species.

Viruses

• Phage lambda - molecular genetics
• Phi X 174 - molecular genetics; the first fully sequenced genome (circular DNA containing 11 genes , length 5386 np.

Prokaryotes

• Escherichia coli ( E. coli ) - gram-negative bacterium, molecular genetics (one of the main objects).
• Bacillus subtilis - gram-positive bacterium, molecular genetics, the study of sporulation , the work of flagella .
• Mycoplasma genitalium - “minimal organism”, has one of the smallest genomes among all cellular organisms; in 2007, a close species was used by Craig Venter for genomic transplantation, as a result of which one species of bacteria was transformed into another [1] .
• Salmonella typhimurium , a gram-negative bacterium pathogenic for mice and other small rodents, conditionally pathogenic for humans, is used to study the mutagenic and carcinogenic effects of various chemicals in the Ames test .

Protists

• Dictyostelium discoideum - molecular biology and genetics (its genome is sequenced), embryology ( intercellular communication , cell differentiation , apoptosis ).
• Tetrahymena thermophila - freshwater ciliates ; molecular genetics (genome sequenced).

Mushrooms

• Thick neurospore Neurospora crassa - mold , study of the genetic regulation of metabolism , meiosis and circadian rhythms ^[1]
• Saccharomyces cerevisiae yeast , genetics ( cell cycle regulation, etc.), use in bakery and brewing
• Schizosaccharomyces pombe fissile yeast ( cell cycle , cell polarity , RNA interference , centrosome structure and function)

Plants

• Chlamydomonas Chlamydomonas reinhardtii - unicellular green algae, the study of photosynthesis , eukaryotic flagellum , cell motility, regulation of metabolism , cell adhesion (“gluing” of gametes during sexual reproduction), etc. Well studied genetically ^{[2] The} genome was sequenced in 2007 ^[3]
• Fiskomitrella green moss ( Physcomitrella patens ) - is increasingly used in research on the development and evolutionary biology of plants ^[4] So far this is the only representative of bryophytes whose genome is fully sequenced; a genetic transformation technique for this species has been developed
• Plaunok species Selaginella moellendorffii - plant evolution, molecular biology; the genome (one of the shortest among higher plants, about 100 megabytes) was sequenced in 2007 ^[5] .
• Talus rezovidka ( Arabidopsis thaliana ), the most popular model plant used in many areas; annual cruciferous ephemer having an extremely short life cycle and small genome size (the first of the plants whose genome is sequenced) ^[6] Many morphological and biochemical mutations have been mapped and studied ^[6] Genetic database containing a large amount of other information about this species - TAIR ^[6]
  
• Species of the genus Poplar ( Populus ) - model species for the study of genetics and cultivation of woody plants. They have a small genome size and rapid growth, a transformation technique has been developed. Fully sequenced by the genome of the North American species Populus trichocarpa
• Alfalfa truncatula ( Medicago truncatula ) - model bean, a close relative of sowing alfalfa ( Medicago sativa ) (molecular biology, agronomy)
• Sweet corn ( Zea mays ) - one of the main crops and a classic genetic model organism; this diploid monocotyledonous plant has 10 pairs of large chromosomes, which are easy to study under a microscope, which facilitates cytogenetic studies; A large number of phenotypically expressed mutations are known whose genes are mapped (which is why transposons were discovered during the study of maize), and a large number of offspring from each cross (genetics, molecular biology, agronomy) revealed the phenomenon of male cytoplasmic sterility in maize for the first time. The genome of the maize has been sequenced almost completely; there is a special database ^[7] devoted to the genetic and molecular biological studies of the maize genome.
• Sowing rice ( Oryza sativa ) - one of the most important crops; has one of the smallest genomes among cereals, which is completely sequenced (agronomy, molecular biology)
• Onion ( Allium cepa ) is a model organism in genotoxicological studies. It has a well-studied genome (2n = 16) and is therefore suitable for anaphase analysis . Test results with Allium cepa correlate with other tests on animals, plants and microorganisms, and can also be extrapolated to humans.

Animals

Stalking

• Nematostella vectensis , nematostella is an littoral burrowing sea anemone from the family Edwardsiidae, which in recent years has become the main model object for studying molecular biology and biology of the development of cnidaria . In 2007, the nematostella genome was completely sequenced ^[8]

Xenaceomorphs

• Symsagittifera roscoffensis (syn. Convoluta roscoffensis ), representative of the primitive group of “intestinal turbellaria” (now a subtype of Acoelomorpha ) - study of the evolution of the plan of the structure of bilaterally symmetric animals

Worms

• Triclade Schmidtea mediterranea - developmental biology, regeneration [2] ; genome partially sequenced [3]
• Nematode Caenorhabditis elegans ( C. elegans ) ^[9] - genetic control of development and physiological processes (the first multicellular organism whose genome was completely sequenced; it is currently sequenced by a gene of the second species from this genus, C. briggsae )

Arthropods

• Drosophila (genus Drosophila ), in particular, the species Drosophila melanogaster - fruit fly, a famous object of genetic research. It is easily kept and bred in the laboratory, has a quick change of generations and many mutations with different phenotypic expressions. In the second half of the XX century, one of the main objects of developmental biology. The genome is fully sequenced. Recently it has been used for neuropharmacological studies ^[10] .

Mollusks

• Aplizia Aplysia californica , posterior gill mollusk (neurobiology, molecular mechanisms of memory, cytoskeleton rearrangement)
• Squid Loligo pealei , a classic object for studying the work of nerve cells and their cytoskeleton (has giant axons with a diameter of up to 1 mm)

Echinoderms

• Sea urchins Arbacia punctulata and Strongylocentrotus purpuratus , classic objects of embryology

Chordates

• Ascidia Ciona intestinalis - embryology, evolution of the chordate genome
• Fugu ( Takifugu rubripes ) - a fish from the Tetraodontidae family - has a compact genome with a small number of non-coding sequences. The genome is sequenced.
• Striped zebrafish ( Danio rerio ), almost transparent in the early stages of development, freshwater fish; an important object of developmental biology, aquatic toxicology and toxicopathology ^[11] . The genome is sequenced.
• African Spur frog ( Xenopus laevis ) - one of the main objects of developmental biology; oocytes are also used to study gene expression. The genome is sequenced.
• Chicken ( Gallus gallus domesticus ) - a model object of amniotic embryology, has been used from ancient times to the present day, the mechanisms of memory and learning are studied on chickens.
• Zebra amadina ( Taeniopygia guttata ) - a variety of weavers, an object of study of behavior genetics, learning mechanisms.
• The house mouse ( Mus musculus ) is the main model object among mammals. A lot of inbred pure lines were obtained , including those selected according to characteristics of interest to medicine. ethology, etc. (a tendency to obesity. increased and decreased intelligence, a tendency to consume alcohol, various life expectancy, etc.). The genome is fully sequenced. Developed methods for producing transgenic mice using stem cells. Of additional interest is an object for studying population genetics and speciation processes, since it has a complex intraspecific structure (many subspecies that differ in karyotype chromosomal races ).
• Gray rat ( Rattus norvegicus ) - an important model for toxicology, neurobiology and physiology; It is also used, along with the mouse, in molecular genetics and genomics. The genome is fully sequenced.
• Domestic cat ( Felis domesticus ) - used in studies of the physiology of the brain, cheaper to maintain compared to monkeys .
• Rhesus macaque ( Macaca mulatta ) - medical research (including the study of infectious diseases), ethology, neurobiology
• Chimpanzees (two species, common chimpanzee ( Pan troglodytes ) and pygmy chimpanzee ( Pan paniscus ) are the closest relatives of humans among living species. Now it is mainly used to study complex forms of behavior and cognitive activity of animals. Pan troglodytes genome is sequenced.
• Various corvids ( Corvidae ) - ethology, complex forms of behavior. The genome of Corvus brachyrhynchus is sequenced.
• Homo sapiens ( Homo sapiens ) - the genome is completely sequenced. In a broad sense, it is not a model organism. For humans, the most complete list of hereditary diseases is known. The importance for neurophysiological studies is determined by the ability to communicate their feelings and follow the instructions of the experimenter.

It is clear that in the above list, organisms are unequal in importance, and the list itself can easily be expanded primarily due to organisms that are used as models in narrower areas of research. For example, the land snail Cepaea nemoralis is a classic object for studying population ecology and genetics, including the action of natural selection on populations; the medical leech Hirudo medicinalis is one of the model objects for studying locomotion in neurobiology, etc.

In addition to organisms, biological systems of other levels of organization can also serve as model objects — molecules, cells and their parts (for example, the giant squid axon), cell lines (for example, the human cell line HeLa), organs (for example, the dentogastric ganglion of the decapods mentioned in the invertebrates crayfish), populations and ecosystems.

• [4] GMOD, Genetic Model Organism Database - Databases on model objects of genetics.