Methanococcus and Methanosarcina, model
methanogens, representing the two metabolic types of hydrogenotrophism and methylotrophism. Methanogenesis remains a key area of metabolic research.[4]
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.[4]
Some of the divisions given below are paraphyletic. This is, for now, considered acceptable, considering that some groups of organisms receive more attention than others.
Pichia pastoris (Komagataella phaffii), widely used in biochemical research and industry as an expression system for protein production, as well as genetic study
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)
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)
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
speciesNicotiana 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.[16](
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.[17]
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.[18] Sequencing of the Chlamydomonas reinhardtii genome was reported in October 2007.[19] 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.
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[23]
Caenorhabditis elegans, a
nematode, usually called C. elegans[24] - 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
Daphnia spp., small planktonic
crustaceans, highly sensitive to pollution, used for evaluating environmental toxicity of chemicals on aquatic invertebrates.[25]
Coelopidae, seaweed flies, used to study sexual selection and sexual conflict
Diopsidae, stalk-eyed flies, used to study sexual selection and sexual conflict
Galleria mellonella (the greater wax moth), the larvae of which are an excellent model organism for in vivo toxicology and pathogenicity testing, replacing the use of small mammals in such experiments.
Gryllus bimaculatus (the field cricket), used to study sexual selection and sexual conflict
Loligo pealei, a
squid is the subject of studies of nerve function because of its giant
axon (nearly 1 mm diameter, roughly a thousand times larger than typical mammalian axons)
Lymnaea stagnalis (great pond snail), a widely used model mollusc, for the study of biomineralization, neurobiology, eco-toxicology, sexual selection and body asymmetry[28]
Macrostomum lignano, a free-living, marine flatworm, a model organism for the study of stem cells, regeneration, ageing, gene function, and the evolution of sex. Easily raised in the lab, short generation time, indetermined growth, complex behaviour[29]
Parhyale hawaiensis an amphipod crustacean, used in evolutionary developmental (
evo-devo) studies, with an extensive toolbox for genetic manipulation.
Platynereis dumerilii a marine polychaetous annelid, which evolved very slowly and therefore retained many ancestral features.[40]
Podisma spp., in the Alps, used to study sexual selection and sexual conflict
Pristionchus pacificus, a roundworm used in evolutionary developmental biology in comparative analyses with C. elegans
Gallus gallus domesticus (Chicken), used for developmental studies, as it is an
amniote and excellent for micromanipulation (e.g. tissue grafting) and over-expression of gene products.
Cavia porcellus (Guinea pig), used by
Robert Koch and other early bacteriologists as a host for bacterial infections, hence a byword for "laboratory animal" even though less commonly used today.
Myotis lucifugus (Little brown bat), used to prove echolocation exists in bats in 1930s and also used in experiments predicting microbat behavior as it is a reliable species that has typical features of a temperate bat species.
Oryzias latipes (Medaka, or Japanese ricefish), important model in developmental biology, and has the advantage of being much sturdier than the traditional zebrafish.
Heterocephalus glaber (Naked mole-rat), studied for their characteristic pain insensitivity, thermoregulation, cancer resistance, eusociality, and longevity.
Nothobranchius furzeri, is studied because of their extreme short-lifespan in research on aging, disease and evolution.
Columba livia domestica (Pigeon), studied extensively for cognitive science and animal intelligence
Poecilia reticulata (Guppy), used to study sexual selection and sexual conflict
Rattus norvegicus (Rat), particularly useful as a toxicology model; also particularly useful as a neurological model and source of primary cell cultures, owing to the larger size of organs and suborganellar structures relative to the mouse. (
Molecular evolution,
Genomics)
Gasterosteus aculeatus (Three-spined stickleback), fish used to study ethology and behavioral ecology.
Xenopus tropicalis and Xenopus laevis (African clawed frog), the eggs and embryos from these frogs are used in developmental biology, cell biology, toxicology, and neuroscience[45][46]
Danio rerio (Zebrafish), freshwater fish with a transparent body during early development, which provides unique visual access to the animal's internal anatomy. Zebrafish are used to study development, toxicology and toxicopathology,[47] specific gene function and roles of signaling pathways.
^Ohm, R.; De Jong, J.; Lugones, L.; Aerts, A.; Kothe, E.; Stajich, J.; De Vries, R.; Record, E.; Levasseur, A.; Baker, S. E.; Bartholomew, K. A.; Coutinho, P. M.; Erdmann, S.; Fowler, T. J.; Gathman, A. C.; Lombard, V.; Henrissat, B.; Knabe, N.; Kües, U.; Lilly, W. W.; Lindquist, E.; Lucas, S.; Magnuson, J. K.; Piumi, F. O.; Raudaskoski, M.; Salamov, A.; Schmutz, J.; Schwarze, F. W. M. R.; Vankuyk, P. A.; Horton, J. S. (2010).
"Genome sequence of the model mushroom Schizophyllum commune". Nature Biotechnology. 28 (9): 957–963.
doi:10.1038/nbt.1643.
PMID20622885.
^Müller HG (1982). "Sensitivity of Daphnia magna straus against eight chemotherapeutic agents and two dyes". Bull. Environ. Contam. Toxicol. 28 (1): 1–2.
doi:
10.1007/BF01608403.
PMID7066538.
S2CID38046915.
^Manev H, Dimitrijevic N, Dzitoyeva S (2003). "Techniques: fruit flies as models for neuropharmacological research". Trends Pharmacol. Sci. 24 (1): 41–3.
doi:
10.1016/S0165-6147(02)00004-4.
PMID12498730.
^Chapman, J. A.; Kirkness, E. F.; Simakov, O.; Hampson, S. E.; Mitros, T.; Weinmaier, T.; Rattei, T.; Balasubramanian, P. G.; Borman, J.; Busam, D.; Disbennett, K.; Pfannkoch, C.; Sumin, N.; Sutton, G. G.; Viswanathan, L. D.; Walenz, B.; Goodstein, D. M.; Hellsten, U.; Kawashima, T.; Prochnik, S. E.; Putnam, N. H.; Shu, S.; Blumberg, B.; Dana, C. E.; Gee, L.; Kibler, D. F.; Law, L.; Lindgens, D.; Martinez, D. E.; et al. (2010).
"The dynamic genome of Hydra". Nature. 464 (7288): 592–596.
Bibcode:
2010Natur.464..592C.
doi:
10.1038/nature08830.
PMC4479502.
PMID20228792.
^Darling, J. A.; Reitzel, A. R.; Burton, P. M.; Mazza, M. E.; Ryan, J. F.; Sullivan, J. C.; Finnerty, J. R. (2005). "Rising starlet: the starlet sea anemone, Nematostella vectensis". BioEssays. 27 (2): 211–221.
doi:
10.1002/bies.20181.
PMID15666346.
^Tessmar-Raible, K.; Arendt, D. (2003). "Emerging systems: Between vertebrates and arthropods, the Lophotrochozoa". Current Opinion in Genetics & Development. 13 (4): 331–340.
doi:
10.1016/s0959-437x(03)00086-8.
PMID12888005.
^Srivastava, M.; Begovic, E.; Chapman, J.; Putnam, N. H.; Hellsten, U.; Kawashima, T.; Kuo, A.; Mitros, T.; Salamov, A.; Carpenter, M. L.; Signorovitch, A. Y.; Moreno, M. A.; Kamm, K.; Grimwood, J.; Schmutz, J.; Shapiro, H.; Grigoriev, I. V.; Buss, L. W.; Schierwater, B.; Dellaporta, S. L.; Rokhsar, D. S. (2008).
"The Trichoplax genome and the nature of placozoans"(PDF). Nature. 454 (7207): 955–960.
Bibcode:
2008Natur.454..955S.
doi:10.1038/nature07191.
PMID18719581.
^Reynoldson TB, Thompson SP, Bamsey JL (1991). "A sediment bioassay using the tubificid oligochaete worm Tubifex tubifex". Environ. Toxicol. Chem. 10 (8): 1061–72.
doi:
10.1002/etc.5620100811.
Methanococcus and Methanosarcina, model
methanogens, representing the two metabolic types of hydrogenotrophism and methylotrophism. Methanogenesis remains a key area of metabolic research.[4]
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.[4]
Some of the divisions given below are paraphyletic. This is, for now, considered acceptable, considering that some groups of organisms receive more attention than others.
Pichia pastoris (Komagataella phaffii), widely used in biochemical research and industry as an expression system for protein production, as well as genetic study
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)
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)
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
speciesNicotiana 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.[16](
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.[17]
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.[18] Sequencing of the Chlamydomonas reinhardtii genome was reported in October 2007.[19] 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.
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[23]
Caenorhabditis elegans, a
nematode, usually called C. elegans[24] - 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
Daphnia spp., small planktonic
crustaceans, highly sensitive to pollution, used for evaluating environmental toxicity of chemicals on aquatic invertebrates.[25]
Coelopidae, seaweed flies, used to study sexual selection and sexual conflict
Diopsidae, stalk-eyed flies, used to study sexual selection and sexual conflict
Galleria mellonella (the greater wax moth), the larvae of which are an excellent model organism for in vivo toxicology and pathogenicity testing, replacing the use of small mammals in such experiments.
Gryllus bimaculatus (the field cricket), used to study sexual selection and sexual conflict
Loligo pealei, a
squid is the subject of studies of nerve function because of its giant
axon (nearly 1 mm diameter, roughly a thousand times larger than typical mammalian axons)
Lymnaea stagnalis (great pond snail), a widely used model mollusc, for the study of biomineralization, neurobiology, eco-toxicology, sexual selection and body asymmetry[28]
Macrostomum lignano, a free-living, marine flatworm, a model organism for the study of stem cells, regeneration, ageing, gene function, and the evolution of sex. Easily raised in the lab, short generation time, indetermined growth, complex behaviour[29]
Parhyale hawaiensis an amphipod crustacean, used in evolutionary developmental (
evo-devo) studies, with an extensive toolbox for genetic manipulation.
Platynereis dumerilii a marine polychaetous annelid, which evolved very slowly and therefore retained many ancestral features.[40]
Podisma spp., in the Alps, used to study sexual selection and sexual conflict
Pristionchus pacificus, a roundworm used in evolutionary developmental biology in comparative analyses with C. elegans
Gallus gallus domesticus (Chicken), used for developmental studies, as it is an
amniote and excellent for micromanipulation (e.g. tissue grafting) and over-expression of gene products.
Cavia porcellus (Guinea pig), used by
Robert Koch and other early bacteriologists as a host for bacterial infections, hence a byword for "laboratory animal" even though less commonly used today.
Myotis lucifugus (Little brown bat), used to prove echolocation exists in bats in 1930s and also used in experiments predicting microbat behavior as it is a reliable species that has typical features of a temperate bat species.
Oryzias latipes (Medaka, or Japanese ricefish), important model in developmental biology, and has the advantage of being much sturdier than the traditional zebrafish.
Heterocephalus glaber (Naked mole-rat), studied for their characteristic pain insensitivity, thermoregulation, cancer resistance, eusociality, and longevity.
Nothobranchius furzeri, is studied because of their extreme short-lifespan in research on aging, disease and evolution.
Columba livia domestica (Pigeon), studied extensively for cognitive science and animal intelligence
Poecilia reticulata (Guppy), used to study sexual selection and sexual conflict
Rattus norvegicus (Rat), particularly useful as a toxicology model; also particularly useful as a neurological model and source of primary cell cultures, owing to the larger size of organs and suborganellar structures relative to the mouse. (
Molecular evolution,
Genomics)
Gasterosteus aculeatus (Three-spined stickleback), fish used to study ethology and behavioral ecology.
Xenopus tropicalis and Xenopus laevis (African clawed frog), the eggs and embryos from these frogs are used in developmental biology, cell biology, toxicology, and neuroscience[45][46]
Danio rerio (Zebrafish), freshwater fish with a transparent body during early development, which provides unique visual access to the animal's internal anatomy. Zebrafish are used to study development, toxicology and toxicopathology,[47] specific gene function and roles of signaling pathways.
^Ohm, R.; De Jong, J.; Lugones, L.; Aerts, A.; Kothe, E.; Stajich, J.; De Vries, R.; Record, E.; Levasseur, A.; Baker, S. E.; Bartholomew, K. A.; Coutinho, P. M.; Erdmann, S.; Fowler, T. J.; Gathman, A. C.; Lombard, V.; Henrissat, B.; Knabe, N.; Kües, U.; Lilly, W. W.; Lindquist, E.; Lucas, S.; Magnuson, J. K.; Piumi, F. O.; Raudaskoski, M.; Salamov, A.; Schmutz, J.; Schwarze, F. W. M. R.; Vankuyk, P. A.; Horton, J. S. (2010).
"Genome sequence of the model mushroom Schizophyllum commune". Nature Biotechnology. 28 (9): 957–963.
doi:10.1038/nbt.1643.
PMID20622885.
^Müller HG (1982). "Sensitivity of Daphnia magna straus against eight chemotherapeutic agents and two dyes". Bull. Environ. Contam. Toxicol. 28 (1): 1–2.
doi:
10.1007/BF01608403.
PMID7066538.
S2CID38046915.
^Manev H, Dimitrijevic N, Dzitoyeva S (2003). "Techniques: fruit flies as models for neuropharmacological research". Trends Pharmacol. Sci. 24 (1): 41–3.
doi:
10.1016/S0165-6147(02)00004-4.
PMID12498730.
^Chapman, J. A.; Kirkness, E. F.; Simakov, O.; Hampson, S. E.; Mitros, T.; Weinmaier, T.; Rattei, T.; Balasubramanian, P. G.; Borman, J.; Busam, D.; Disbennett, K.; Pfannkoch, C.; Sumin, N.; Sutton, G. G.; Viswanathan, L. D.; Walenz, B.; Goodstein, D. M.; Hellsten, U.; Kawashima, T.; Prochnik, S. E.; Putnam, N. H.; Shu, S.; Blumberg, B.; Dana, C. E.; Gee, L.; Kibler, D. F.; Law, L.; Lindgens, D.; Martinez, D. E.; et al. (2010).
"The dynamic genome of Hydra". Nature. 464 (7288): 592–596.
Bibcode:
2010Natur.464..592C.
doi:
10.1038/nature08830.
PMC4479502.
PMID20228792.
^Darling, J. A.; Reitzel, A. R.; Burton, P. M.; Mazza, M. E.; Ryan, J. F.; Sullivan, J. C.; Finnerty, J. R. (2005). "Rising starlet: the starlet sea anemone, Nematostella vectensis". BioEssays. 27 (2): 211–221.
doi:
10.1002/bies.20181.
PMID15666346.
^Tessmar-Raible, K.; Arendt, D. (2003). "Emerging systems: Between vertebrates and arthropods, the Lophotrochozoa". Current Opinion in Genetics & Development. 13 (4): 331–340.
doi:
10.1016/s0959-437x(03)00086-8.
PMID12888005.
^Srivastava, M.; Begovic, E.; Chapman, J.; Putnam, N. H.; Hellsten, U.; Kawashima, T.; Kuo, A.; Mitros, T.; Salamov, A.; Carpenter, M. L.; Signorovitch, A. Y.; Moreno, M. A.; Kamm, K.; Grimwood, J.; Schmutz, J.; Shapiro, H.; Grigoriev, I. V.; Buss, L. W.; Schierwater, B.; Dellaporta, S. L.; Rokhsar, D. S. (2008).
"The Trichoplax genome and the nature of placozoans"(PDF). Nature. 454 (7207): 955–960.
Bibcode:
2008Natur.454..955S.
doi:10.1038/nature07191.
PMID18719581.
^Reynoldson TB, Thompson SP, Bamsey JL (1991). "A sediment bioassay using the tubificid oligochaete worm Tubifex tubifex". Environ. Toxicol. Chem. 10 (8): 1061–72.
doi:
10.1002/etc.5620100811.