List of model organisms

Last updated

Escherichia coli is a gram-negative prokaryotic model organism E coli at 10000x, original.jpg
Escherichia coli is a gram-negative prokaryotic model organism
Drosophila melanogaster, one of the most famous subjects for experiments Drosophila melanogaster - side (aka).jpg
Drosophila melanogaster , one of the most famous subjects for experiments

This is a list of model organisms used in scientific research.

Contents

Viruses

Phages (infecting prokaryotes):

Animal viruses:

Plant viruses:

Bacteria

Sporulating Bacillus subtilis Bacillus subtilis Spore.jpg
Sporulating Bacillus subtilis

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.

Archaea

Eukaryotes

Protists

Fungi

Plants

Vascular plants

Arabidopsis thaliana Arabidopsis thaliana.jpg
Arabidopsis thaliana
Lemna gibba L gibba2.jpg
Lemna gibba
Physcomitrella patens Physcomitrella Sporophyt.JPG
Physcomitrella patens
  • 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. [20]

Other Archaeplastida

Animals

Invertebrates

Caenorhabditis elegans Caenorhabditis elegans.jpg
Caenorhabditis elegans

Vertebrates

Laboratory mice Lightmatter lab mice.jpg
Laboratory mice

References

  1. Daniel Ryan; Laura Jenniches; Sarah Reichardt; Lars Barquist; Alexander Westermann (16 July 2020). "A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron". Nature Communications. 11 (1): 3557. Bibcode:2020NatCo..11.3557R. doi: 10.1038/s41467-020-17348-5 . PMC   7366714 . PMID   32678091.
  2. "Streptomyces coelicolor". John Innes Center. Archived from the original on 11 October 2018. Retrieved 13 April 2018.
  3. Zhou, Zhan; Li, Qi; Tudyk, Julie; Li, Yong-Quan; Wang, Yufeng (4–6 December 2011). ECF sigma factor-associated regulatory networks in Streptomyces colicolor A3(2). 2011 IEEE International Workshop on Genomic Signal Processing and Statistics. San Antonio, Texas, USA: IEEE.
  4. Bittencourt, Daniela Matias de C.; Brown, David M.; Assad-Garcia, Nacyra; Romero, Michaela R.; Sun, Lijie; Palhares de Melo, Luis Alberto M.; Freire, Marcelo; Glass, John I. (19 April 2024). "Minimal Bacterial Cell JCVI-syn3B as a Chassis to Investigate Interactions between Bacteria and Mammalian Cells". ACS Synthetic Biology. 13 (4): 1128–1141. doi:10.1021/acssynbio.3c00513. PMC   11036491 .
  5. Fredens, Julius; Wang, Kaihang; de la Torre, Daniel; Funke, Louise F. H.; Robertson, Wesley E.; Christova, Yonka; Chia, Tiongsun; Schmied, Wolfgang H.; Dunkelmann, Daniel L.; Beránek, Václav; Uttamapinant, Chayasith; Llamazares, Andres Gonzalez; Elliott, Thomas S.; Chin, Jason W. (23 May 2019). "Total synthesis of Escherichia coli with a recoded genome". Nature. 569 (7757): 514–518. doi:10.1038/s41586-019-1192-5.
  6. Robertson, Wesley E.; Funke, Louise F. H.; de la Torre, Daniel; Fredens, Julius; Elliott, Thomas S.; Spinck, Martin; Christova, Yonka; Cervettini, Daniele; Böge, Franz L.; Liu, Kim C.; Buse, Salvador; Maslen, Sarah; Salmond, George P. C.; Chin, Jason W. (4 June 2021). "Sense codon reassignment enables viral resistance and encoded polymer synthesis". Science. 372 (6546): 1057–1062. Bibcode:2021Sci...372.1057R. doi:10.1126/science.abg3029. PMC   7611380 . PMID   34083482.
  7. 1 2 3 4 Leigh, John A.; Albers, Sonja-Verena; Atomi, Haruyuki; Allers, Thorsten (July 2011). "Model organisms for genetics in the domain Archaea: methanogens, halophiles, Thermococcales and Sulfolobales". FEMS Microbiology Reviews. 35 (4): 577–608. doi: 10.1111/j.1574-6976.2011.00265.x . PMID   21265868.
  8. Slabodnick, Mark M.; Ruby, J. Graham; Reiff, Sarah B.; Swart, Estienne C.; Gosai, Sager; Prabakaran, Sudhakaran; Witkowska, Ewa; Larue, Graham E.; Fisher, Susan; Freeman, Robert M.; Gunawardena, Jeremy; Chu, William; Stover, Naomi A.; Gregory, Brian D.; Nowacki, Mariusz; Derisi, Joseph; Roy, Scott W.; Marshall, Wallace F.; Sood, Pranidhi (2017). "The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell". Current Biology. 27 (4): 569–575. Bibcode:2017CBio...27..569S. doi:10.1016/j.cub.2016.12.057. PMC   5659724 . PMID   28190732.
  9. Kües U (June 2000). "Life history and developmental processes in the basidiomycete Coprinus cinereus". Microbiol. Mol. Biol. Rev. 64 (2): 316–53. doi:10.1128/MMBR.64.2.316-353.2000. PMC   98996 . PMID   10839819.
  10. Davis, Rowland H. (2000). Neurospora: contributions of a model organism. Oxford [Oxfordshire]: Oxford University Press. ISBN   978-0-19-512236-7.
  11. Cornell, Calvin; Kokkoris, Vasilis; Turcu, Bianca; Dettman, Jeremy; Stefani, Franck; Corradi, Nicolas (January 2022). "The arbuscular mycorrhizal fungus Rhizophagus irregularis harmonizes nuclear dynamics in the presence of distinct abiotic factors". Fungal Genetics and Biology. 158: 103639. doi:10.1016/j.fgb.2021.103639. PMID   34800644. S2CID   244421564.
  12. "Home - Rhizophagus irregularis DAOM 181602 v1.0". mycocosm.jgi.doe.gov. Retrieved 25 May 2023.
  13. 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 . PMID   20622885.
  14. 1 2 3 4 About Arabidopsis on The Arabidopsis Information Resource page (TAIR)
  15. Rushworth, C; et al. (2011). "Boechera, a model system for ecological genomics". Molecular Ecology. 20 (23): 4843–57. doi:10.1111/j.1365-294X.2011.05340.x. PMC   3222738 . PMID   22059452.
  16. Brutnell, T; et al. (2010). "Setaria viridis: a model for C4 photosynthesis". Plant Cell . 22 (8): 2537–44. doi:10.1105/tpc.110.075309. PMC   2947182 . PMID   20693355.
  17. Jiang, Hui; Barbier, Hugues; Brutnell, Thomas (2013). "Methods for Performing Crosses in Setaria viridis, a New Model System for the Grasses". Journal of Visualized Experiments (80): 50527. doi:10.3791/50527. ISSN   1940-087X. PMC   3938206 . PMID   24121645.
  18. Goodin, Michael; David Zaitlin; Rayapati Naidu; Steven Lommel (August 2008). "Nicotiana benthamiana: its history and future as a model for plant-pathogen interactions". Molecular Plant-Microbe Interactions. 21 (8): 1015–1026. doi: 10.1094/MPMI-21-8-1015 . PMID   18616398.
  19. Zhou, S.; Bechner, M. C.; Place, M.; Churas, C. P.; Pape, L.; Leong, S. A.; Runnheim, R.; Forrest, D. K.; Goldstein, S.; Livny, M.; Schwartz, D. C. (2007). "Validation of rice genome sequence by optical mapping". BMC Genomics. 8: 278. doi: 10.1186/1471-2164-8-278 . PMC   2048515 . PMID   17697381.
  20. "Populus trichocarpa (Western poplar)". Phytozome. Retrieved 22 July 2013.
  21. "Chlamydomonas reinhardtii resources at the Joint Genome Institute". Archived from the original on 23 July 2008. Retrieved 1 February 2015.
  22. Chlamydomonas genome sequenced published in Science, 12 October 2007
  23. 1 2 Rensing SA, Lang D, Zimmer AD, et al. (January 2008). "The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants". Science. 319 (5859): 64–9. Bibcode:2008Sci...319...64R. doi:10.1126/science.1150646. hdl: 11858/00-001M-0000-0012-3787-A . PMID   18079367. S2CID   11115152.
  24. Reski, Ralf (1998). "Physcomitrella and Arabidopsis: the David and Goliath of reverse genetics". Trends in Plant Science. 3 (6): 209–210. doi:10.1016/S1360-1385(98)01257-6.
  25. Srivastava, M.; Simakov, O.; Chapman, J.; Fahey, B.; Gauthier, M. E. A.; Mitros, T.; Richards, G. S.; Conaco, C.; Dacre, M.; Hellsten, U.; Larroux, C.; Putnam, N. H.; Stanke, M.; Adamska, M.; Darling, A.; Degnan, S. M.; Oakley, T. H.; Plachetzki, D. C.; Zhai, Y.; Adamski, M.; Calcino, A.; Cummins, S. F.; Goodstein, D. M.; Harris, C.; Jackson, D. J.; Leys, S. P.; Shu, S.; Woodcroft, B. J.; Vervoort, M.; Kosik, K. S. (2010). "The Amphimedon queenslandica genome and the evolution of animal complexity". Nature. 466 (7307): 720–726. Bibcode:2010Natur.466..720S. doi:10.1038/nature09201. PMC   3130542 . PMID   20686567.
  26. Holland, L. Z.; Albalat, R.; Azumi, K.; Benito-Gutiérrez, E.; Blow, M. J.; Bronner-Fraser, M.; Brunet, F.; Butts, T.; Candiani, S.; Dishaw, L. J.; Ferrier, D. E. K.; Garcia-Fernàndez, J.; Gibson-Brown, J. J.; Gissi, C.; Godzik, A.; Hallböök, F.; Hirose, D.; Hosomichi, K.; Ikuta, T.; Inoko, H.; Kasahara, M.; Kasamatsu, J.; Kawashima, T.; Kimura, A.; Kobayashi, M.; Kozmik, Z.; Kubokawa, K.; Laudet, V.; Litman, G. W.; McHardy, A. C. (2008). "The amphioxus genome illuminates vertebrate origins and cephalochordate biology". Genome Research. 18 (7): 1100–1111. doi:10.1101/gr.073676.107. PMC   2493399 . PMID   18562680.
  27. Riddle, Donald L. (1997). C. elegans II. Plainview, N.Y: Cold Spring Harbor Laboratory Press. ISBN   978-0-87969-532-3.
  28. 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. PMID   7066538. S2CID   38046915.
  29. 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. PMID   12498730.
  30. 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. PMC   4479502 . PMID   20228792.
  31. Fodor, István; Hussein, Ahmed AA; Benjamin, Paul R; Koene, Joris M; Pirger, Zsolt (16 June 2020). King, Stuart RF; Rodgers, Peter; Irisarri, Iker; Voronezhskaya, Elena E; Coutellec, Marie-Agnes (eds.). "The unlimited potential of the great pond snail, Lymnaea stagnalis". eLife. 9: e56962. doi: 10.7554/eLife.56962 . ISSN   2050-084X. PMC   7297532 . PMID   32539932.
  32. Ladurner, P; Schärer, L; Salvenmoser, W; Rieger, R (2005). "A new model organism among the lower Bilateria and the use of digital microscopy in taxonomy of meiobenthic Platyhelminthes: Macrostomum lignano, n. sp. (Rhabditophora, Macrostomorpha)". Journal of Zoological Systematics and Evolutionary Research. 43 (2): 114–126. doi:10.1111/j.1439-0469.2005.00299.x. Archived from the original on 5 January 2013.
  33. Koshkina, Olga; Rheinberger, Timo; Flocke, Vera; Windfelder, Anton; Bouvain, Pascal; Hamelmann, Naomi M.; Paulusse, Jos M. J.; Gojzewski, Hubert; Flögel, Ulrich; Wurm, Frederik R. (19 July 2023). "Biodegradable polyphosphoester micelles act as both background-free 31P magnetic resonance imaging agents and drug nanocarriers". Nature Communications. 14 (1): 4351. doi:10.1038/s41467-023-40089-0. ISSN   2041-1723. PMC   10356825 . PMID   37468502.
  34. Windfelder, Anton G.; Müller, Frank H. H.; Mc Larney, Benedict; Hentschel, Michael; Böhringer, Anna Christina; von Bredow, Christoph-Rüdiger; Leinberger, Florian H.; Kampschulte, Marian; Maier, Lorenz; von Bredow, Yvette M.; Flocke, Vera; Merzendorfer, Hans; Krombach, Gabriele A.; Vilcinskas, Andreas; Grimm, Jan (24 November 2022). "High-throughput screening of caterpillars as a platform to study host–microbe interactions and enteric immunity". Nature Communications. 13 (1): 7216. doi:10.1038/s41467-022-34865-7. ISSN   2041-1723. PMC   9700799 . PMID   36433960.
  35. Windfelder, Anton G.; Steinbart, Jessica; Flögel, Ulrich; Scherberich, Jan; Kampschulte, Marian; Krombach, Gabriele A.; Vilcinskas, Andreas (June 2023). "A quantitative micro-tomographic gut atlas of the lepidopteran model insect Manduca sexta". iScience. 26 (6): 106801. doi:10.1016/j.isci.2023.106801. ISSN   2589-0042. PMC   10291339 . PMID   37378344.
  36. Pang, K.; Martindale, M. Q. (2008). "Ctenophores". Current Biology. 18 (24): R1119 –R1120. doi: 10.1016/j.cub.2008.10.004 . PMID   19108762.
  37. Ryan, J. F.; Pang, K.; Comparative Sequencing Program; Mullikin, J. C.; Martindale, M. Q.; Baxevanis, A. D.; NISC Comparative Sequencing Program (2010). "The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa". EvoDevo. 1 (1): 9. doi: 10.1186/2041-9139-1-9 . PMC   2959044 . PMID   20920347.
  38. 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. PMID   15666346.
  39. Putnam, N. H.; Srivastava, M.; Hellsten, U.; Dirks, B.; Chapman, J.; Salamov, A.; Terry, A.; Shapiro, H.; Lindquist, E.; Kapitonov, V. V.; Jurka, J.; Genikhovich, G.; Grigoriev, I. V.; Lucas, S. M.; Steele, R. E.; Finnerty, J. R.; Technau, U.; Martindale, M. Q.; Rokhsar, D. S. (2007). "Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization". Science. 317 (5834): 86–94. Bibcode:2007Sci...317...86P. doi:10.1126/science.1139158. PMID   17615350. S2CID   9868191.
  40. The Appendicularia Facility at the Sars International Centre for Marine Molecular Biology
  41. Cade, W. (26 December 1975). "Acoustically Orienting Parasitoids: Fly Phonotaxis to Cricket Song". Science. 190 (4221): 1312–1313. Bibcode:1975Sci...190.1312C. doi:10.1126/science.190.4221.1312. ISSN   0036-8075. S2CID   85233362.
  42. Wang, X.; Lavrov, D. V. (2006). "Mitochondrial Genome of the Homoscleromorph Oscarella carmela (Porifera, Demospongiae) Reveals Unexpected Complexity in the Common Ancestor of Sponges and Other Animals". Molecular Biology and Evolution. 24 (2): 363–373. doi: 10.1093/molbev/msl167 . PMID   17090697.
  43. 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. PMID   12888005.
  44. Whiteman, Noah K.; Groen, Simon C.; Chevasco, Daniela; Bear, Ashley; Beckwith, Noor; Gregory, T. Ryan; Denoux, Carine; Mammarella, Nicole; Ausubel, Frederick M.; Pierce, Naomi E. (13 November 2010). "Mining the plant-herbivore interface with a leafmining Drosophila of Arabidopsis". Molecular Ecology. 20 (5): 995–1014. doi:10.1111/j.1365-294x.2010.04901.x. PMC   3062943 . PMID   21073583.
  45. Cheng, Daifeng; Zhang, Zhiling; He, Xiaofang; Liang, Guangwen (28 February 2013). "Validation of Reference Genes in Solenopsis invicta in Different Developmental Stages, Castes and Tissues". PLOS ONE. 8 (2): e57718. doi: 10.1371/journal.pone.0057718 . ISSN   1932-6203. PMC   3585193 . PMID   23469057.
  46. 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 . PMID   18719581.
  47. 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.
  48. Kolb, E. M.; Rezende, E. L.; Holness, L.; Radtke, A.; Lee, S. K.; Obenaus, A.; Garland Jr, T (2013). "Mice selectively bred for high voluntary wheel running have larger midbrains: support for the mosaic model of brain evolution". Journal of Experimental Biology . 216 (3): 515–523. doi: 10.1242/jeb.076000 . PMID   23325861.
  49. Wallingford, J.; Liu, K.; Zheng, Y. (2010). "Xenopus". Current Biology. 20 (6): R263–4. doi: 10.1016/j.cub.2010.01.012 . PMID   20334828.
  50. Harland, R.M.; Grainger, R.M. (2011). "Xenopus research: metamorphosed by genetics and genomics". Trends in Genetics. 27 (12): 507–15. doi:10.1016/j.tig.2011.08.003. PMC   3601910 . PMID   21963197.
  51. Spitsbergen JM, Kent ML (2003). "The state of the art of the zebrafish model for toxicology and toxicologic pathology research—advantages and current limitations". Toxicol Pathol. 31 (Suppl): 62–87. doi:10.1080/01926230390174959. PMC   1909756 . PMID   12597434.