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. 2003 Apr;4(2):182–193. doi: 10.1002/cfg.259

Genomics and Mapping of Teleostei (Bony Fish)

Melody S Clark 1,✉
PMCID: PMC2447409  PMID: 18629122

Abstract

Until recently, the Human Genome Project held centre stage in the press releases concerning sequencing programmes. However, in October 2001, it was announced that the Japanese puffer fish (Takifugu rubripes, Fugu) was the second vertebrate organism to be sequenced to draft quality. Briefly, the spotlight was on fish genomes. There are currently two other fish species undergoing intensive sequencing, the green spotted puffer fish (Tetraodon nigroviridis) and the zebrafish (Danio rerio). But this trio are, in many ways, atypical representations of the current state of fish genomic research. The aim of this brief review is to demonstrate the complexity of fish as a group of vertebrates and to publicize the ‘lesser-known’ species, all of which have something to offer.

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Selected References

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  1. Amores A., Force A., Yan Y. L., Joly L., Amemiya C., Fritz A., Ho R. K., Langeland J., Prince V., Wang Y. L. Zebrafish hox clusters and vertebrate genome evolution. Science. 1998 Nov 27;282(5394):1711–1714. doi: 10.1126/science.282.5394.1711. [DOI] [PubMed] [Google Scholar]
  2. Bailey G. S., Poulter R. T., Stockwell P. A. Gene duplication in tetraploid fish: model for gene silencing at unlinked duplicated loci. Proc Natl Acad Sci U S A. 1978 Nov;75(11):5575–5579. doi: 10.1073/pnas.75.11.5575. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bailey G. S., Williams D. E., Hendricks J. D. Fish models for environmental carcinogenesis: the rainbow trout. Environ Health Perspect. 1996 Mar;104 (Suppl 1):5–21. doi: 10.1289/ehp.96104s15. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Ballatori Nazzareno, Villalobos Alice R. Defining the molecular and cellular basis of toxicity using comparative models. Toxicol Appl Pharmacol. 2002 Sep 15;183(3):207–220. doi: 10.1006/taap.2002.9488. [DOI] [PubMed] [Google Scholar]
  5. Barbazuk W. B., Korf I., Kadavi C., Heyen J., Tate S., Wun E., Bedell J. A., McPherson J. D., Johnson S. L. The syntenic relationship of the zebrafish and human genomes. Genome Res. 2000 Sep;10(9):1351–1358. doi: 10.1101/gr.144700. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bolis C. L., Piccolella M., Dalla Valle A. Z., Rankin J. C. Fish as model in pharmacological and biological research. Pharmacol Res. 2001 Oct;44(4):265–280. doi: 10.1006/phrs.2001.0845. [DOI] [PubMed] [Google Scholar]
  7. Bonaventura C. NIEHS workshop: unique marine/freshwater models for environmental health research. Environ Health Perspect. 1999 Jan;107(1):89–92. doi: 10.1289/ehp.9910789. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Cao D., Kocabas A., Ju Z., Karsi A., Li P., Patterson A., Liu Z. Transcriptome of channel catfish (Ictalurus punctatus): initial analysis of genes and expression profiles of the head kidney. Anim Genet. 2001 Aug;32(4):169–188. doi: 10.1046/j.1365-2052.2001.00753.x. [DOI] [PubMed] [Google Scholar]
  9. Davey G. C., Caplice N. C., Martin S. A., Powell R. A survey of genes in the Atlantic salmon (Salmo salar) as identified by expressed sequence tags. Gene. 2001 Jan 24;263(1-2):121–130. doi: 10.1016/s0378-1119(00)00587-4. [DOI] [PubMed] [Google Scholar]
  10. Dodd A., Curtis P. M., Williams L. C., Love D. R. Zebrafish: bridging the gap between development and disease. Hum Mol Genet. 2000 Oct;9(16):2443–2449. doi: 10.1093/hmg/9.16.2443. [DOI] [PubMed] [Google Scholar]
  11. Douglas SE, Gallant JW, Bullerwell CE, Wolff C, Munholland J, Reith ME. Winter Flounder Expressed Sequence Tags: Establishment of an EST Database and Identification of Novel Fish Genes. Mar Biotechnol (NY) 1999 Sep;1(5):458–0464. doi: 10.1007/pl00011802. [DOI] [PubMed] [Google Scholar]
  12. Driever W., Solnica-Krezel L., Schier A. F., Neuhauss S. C., Malicki J., Stemple D. L., Stainier D. Y., Zwartkruis F., Abdelilah S., Rangini Z. A genetic screen for mutations affecting embryogenesis in zebrafish. Development. 1996 Dec;123:37–46. doi: 10.1242/dev.123.1.37. [DOI] [PubMed] [Google Scholar]
  13. Fent K. Fish cell lines as versatile tools in ecotoxicology: assessment of cytotoxicity, cytochrome P4501A induction potential and estrogenic activity of chemicals and environmental samples. Toxicol In Vitro. 2001 Aug-Oct;15(4-5):477–488. doi: 10.1016/s0887-2333(01)00053-4. [DOI] [PubMed] [Google Scholar]
  14. Gates M. A., Kim L., Egan E. S., Cardozo T., Sirotkin H. I., Dougan S. T., Lashkari D., Abagyan R., Schier A. F., Talbot W. S. A genetic linkage map for zebrafish: comparative analysis and localization of genes and expressed sequences. Genome Res. 1999 Apr;9(4):334–347. [PubMed] [Google Scholar]
  15. Grunwald David Jonah, Eisen Judith S. Headwaters of the zebrafish -- emergence of a new model vertebrate. Nat Rev Genet. 2002 Sep;3(9):717–724. doi: 10.1038/nrg892. [DOI] [PubMed] [Google Scholar]
  16. Haffter P., Granato M., Brand M., Mullins M. C., Hammerschmidt M., Kane D. A., Odenthal J., van Eeden F. J., Jiang Y. J., Heisenberg C. P. The identification of genes with unique and essential functions in the development of the zebrafish, Danio rerio. Development. 1996 Dec;123:1–36. doi: 10.1242/dev.123.1.1. [DOI] [PubMed] [Google Scholar]
  17. Hahn M. E. Dioxin toxicology and the aryl hydrocarbon receptor: insights from fish and other non-traditional models. Mar Biotechnol (NY) 2001 Jun;3(Suppl 1):S224–S238. doi: 10.1007/s10126-001-0045-y. [DOI] [PubMed] [Google Scholar]
  18. Harshbarger J. C., Slatick M. S. Lesser known aquarium fish tumor models. Mar Biotechnol (NY) 2001 Jun;3(Suppl 1):S115–S129. doi: 10.1007/s10126-001-0033-2. [DOI] [PubMed] [Google Scholar]
  19. Hinegardner R. The cellular DNA content of sharks, rays and some other fishes. Comp Biochem Physiol B. 1976;55(3B):367–370. doi: 10.1016/0305-0491(76)90305-9. [DOI] [PubMed] [Google Scholar]
  20. Hughes A. L., da Silva J., Friedman R. Ancient genome duplications did not structure the human Hox-bearing chromosomes. Genome Res. 2001 May;11(5):771–780. doi: 10.1101/gr.160001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Ju Z., Dunham R. A., Liu Z. Differential gene expression in the brain of channel catfish ( Ictalurus punctatus) in response to cold acclimation. Mol Genet Genomics. 2002 Jul 20;268(1):87–95. doi: 10.1007/s00438-002-0727-9. [DOI] [PubMed] [Google Scholar]
  22. Ju Z., Karsi A., Kocabas A., Patterson A., Li P., Cao D., Dunham R., Liu Z. Transcriptome analysis of channel catfish (Ictalurus punctatus): genes and expression profile from the brain. Gene. 2000 Dec 31;261(2):373–382. doi: 10.1016/s0378-1119(00)00491-1. [DOI] [PubMed] [Google Scholar]
  23. Karsi Attila, Cao Dongfeng, Li Ping, Patterson Andrea, Kocabas Arif, Feng Jinian, Ju Zhenlin, Mickett Kathryn D., Liu Zhanjiang. Transcriptome analysis of channel catfish (Ictalurus punctatus): initial analysis of gene expression and microsatellite-containing cDNAs in the skin. Gene. 2002 Feb 20;285(1-2):157–168. doi: 10.1016/s0378-1119(02)00414-6. [DOI] [PubMed] [Google Scholar]
  24. Katagiri T., Asakawa S., Minagawa S., Shimizu N., Hirono I., Aoki T. Construction and characterization of BAC libraries for three fish species; rainbow trout, carp and tilapia. Anim Genet. 2001 Aug;32(4):200–204. doi: 10.1046/j.1365-2052.2001.00764.x. [DOI] [PubMed] [Google Scholar]
  25. Katsiadaki I., Scott A. P., Mayer I. The potential of the three-spined stickleback (Gasterosteus aculeatus L.) as a combined biomarker for oestrogens and androgens in European waters. Mar Environ Res. 2002 Sep-Dec;54(3-5):725–728. doi: 10.1016/s0141-1136(02)00110-1. [DOI] [PubMed] [Google Scholar]
  26. Kazianis S., Morizot D. C., McEntire B. B., Nairn R. S., Borowsky R. L. Genetic mapping in Xiphophorus hybrid fish: assignment of 43 AP-PCR/RAPD and isozyme markers to multipoint linkage groups. Genome Res. 1996 Apr;6(4):280–289. doi: 10.1101/gr.6.4.280. [DOI] [PubMed] [Google Scholar]
  27. Kocher T. D., Lee W. J., Sobolewska H., Penman D., McAndrew B. A genetic linkage map of a cichlid fish, the tilapia (Oreochromis niloticus). Genetics. 1998 Mar;148(3):1225–1232. doi: 10.1093/genetics/148.3.1225. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Korpi Esa R., Gründer Gerhard, Lüddens Hartmut. Drug interactions at GABA(A) receptors. Prog Neurobiol. 2002 Jun;67(2):113–159. doi: 10.1016/s0301-0082(02)00013-8. [DOI] [PubMed] [Google Scholar]
  29. Larkin Patrick, Folmar Leroy C., Hemmer Michael J., Poston Arianna J., Lee H. Stephen, Denslow Nancy D. Array technology as a tool to monitor exposure of fish to xenoestrogens. Mar Environ Res. 2002 Sep-Dec;54(3-5):395–399. doi: 10.1016/s0141-1136(02)00172-1. [DOI] [PubMed] [Google Scholar]
  30. Lindner K. R., Seeb J. E., Habicht C., Knudsen K. L., Kretschmer E., Reedy D. J., Spruell P., Allendorf F. W. Gene-centromere mapping of 312 loci in pink salmon by half-tetrad analysis. Genome. 2000 Jun;43(3):538–549. [PubMed] [Google Scholar]
  31. Liu Z, Karsi A, Dunham RA. Development of Polymorphic EST Markers Suitable for Genetic Linkage Mapping of Catfish. Mar Biotechnol (NY) 1999 Sep;1(5):437–0447. doi: 10.1007/pl00011800. [DOI] [PubMed] [Google Scholar]
  32. Masahito P., Ishikawa T., Okamoto N., Sugano H. Nephroblastomas in the Japanese eel, Anguilla japonica Temminck and Schlegel. Cancer Res. 1992 May 1;52(9):2575–2579. [PubMed] [Google Scholar]
  33. Matsuda M., Kawato N., Asakawa S., Shimizu N., Nagahama Y., Hamaguchi S., Sakaizumi M., Hori H. Construction of a BAC library derived from the inbred Hd-rR strain of the teleost fish, Oryzias latipes. Genes Genet Syst. 2001 Feb;76(1):61–63. doi: 10.1266/ggs.76.61. [DOI] [PubMed] [Google Scholar]
  34. McConnell S. K., Beynon C., Leamon J., Skibinski D. O. Microsatellite marker based genetic linkage maps of Oreochromis aureus and O. niloticus (Cichlidae): extensive linkage group segment homologies revealed. Anim Genet. 2000 Jun;31(3):214–218. doi: 10.1046/j.1365-2052.2000.00631.x. [DOI] [PubMed] [Google Scholar]
  35. Metcalfe C. D., Metcalfe T. L., Kiparissis Y., Koenig B. G., Khan C., Hughes R. J., Croley T. R., March R. E., Potter T. Estrogenic potency of chemicals detected in sewage treatment plant effluents as determined by in vivo assays with Japanese medaka (Oryzias latipes). Environ Toxicol Chem. 2001 Feb;20(2):297–308. [PubMed] [Google Scholar]
  36. Nakamura Mashio, Okada Osamu, Sakuma Masahito, Nakanishi Norifumi, Miyahara Yoshiyuki, Yamada Norikazu, Fujioka Hirofumi, Kuriyama Takayuki, Kunieda Takeyoshi, Sugimoto Tsuneaki. Incidence and clinical characteristics of chronic pulmonary thromboembolism in Japan compared with acute pulmonary thromboembolism: results of a multicenter registry of the Japanese Society of Pulmonary Embolism Research. Circ J. 2002 Mar;66(3):257–260. doi: 10.1253/circj.66.257. [DOI] [PubMed] [Google Scholar]
  37. Naruse K., Fukamachi S., Mitani H., Kondo M., Matsuoka T., Kondo S., Hanamura N., Morita Y., Hasegawa K., Nishigaki R. A detailed linkage map of medaka, Oryzias latipes: comparative genomics and genome evolution. Genetics. 2000 Apr;154(4):1773–1784. doi: 10.1093/genetics/154.4.1773. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Nüsslein-Volhard C. Of flies and fishes. Science. 1994 Oct 28;266(5185):572–574. doi: 10.1126/science.7939708. [DOI] [PubMed] [Google Scholar]
  39. Postlethwait J. H., Woods I. G., Ngo-Hazelett P., Yan Y. L., Kelly P. D., Chu F., Huang H., Hill-Force A., Talbot W. S. Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Res. 2000 Dec;10(12):1890–1902. doi: 10.1101/gr.164800. [DOI] [PubMed] [Google Scholar]
  40. Robinson-Rechavi M., Laudet V. Evolutionary rates of duplicate genes in fish and mammals. Mol Biol Evol. 2001 Apr;18(4):681–683. doi: 10.1093/oxfordjournals.molbev.a003849. [DOI] [PubMed] [Google Scholar]
  41. Robinson-Rechavi M., Marchand O., Escriva H., Bardet P. L., Zelus D., Hughes S., Laudet V. Euteleost fish genomes are characterized by expansion of gene families. Genome Res. 2001 May;11(5):781–788. doi: 10.1101/gr.165601. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Roest Crollius H., Jaillon O., Bernot A., Dasilva C., Bouneau L., Fischer C., Fizames C., Wincker P., Brottier P., Quétier F. Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence. Nat Genet. 2000 Jun;25(2):235–238. doi: 10.1038/76118. [DOI] [PubMed] [Google Scholar]
  43. Rotchell J. M., Ulnal E., Van Beneden R. J., Ostrander G. K. Retinoblastoma gene mutations in chemically induced liver tumor samples of Japanese medaka (Oryzias latipes). Mar Biotechnol (NY) 2001 Jun;3(Suppl 1):S44–S49. doi: 10.1007/s10126-001-0026-1. [DOI] [PubMed] [Google Scholar]
  44. Rothenberg E. V. Mapping of complex regulatory elements by pufferfish/zebrafish transgenesis. Proc Natl Acad Sci U S A. 2001 Jun 5;98(12):6540–6542. doi: 10.1073/pnas.131199098. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Sakamoto T., Danzmann R. G., Gharbi K., Howard P., Ozaki A., Khoo S. K., Woram R. A., Okamoto N., Ferguson M. M., Holm L. E. A microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) characterized by large sex-specific differences in recombination rates. Genetics. 2000 Jul;155(3):1331–1345. doi: 10.1093/genetics/155.3.1331. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Setlow R. B., Woodhead A. D. Three unique experimental fish stories: Poecilia (the Past), Xiphophorus (the Present), and Medaka (the Future). Mar Biotechnol (NY) 2001 Jun;3(Suppl 1):S17–S23. doi: 10.1007/s1012601-0023-4. [DOI] [PubMed] [Google Scholar]
  47. Shima A., Shimada A. The medaka as a model for studying germ-cell mutagenesis and genomic instability. Mar Biotechnol (NY) 2001 Jun;3(Suppl 1):S162–S167. doi: 10.1007/s10126-001-0038-x. [DOI] [PubMed] [Google Scholar]
  48. Solnica-Krezel L., Schier A. F., Driever W. Efficient recovery of ENU-induced mutations from the zebrafish germline. Genetics. 1994 Apr;136(4):1401–1420. doi: 10.1093/genetics/136.4.1401. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Taylor J. S., Van de Peer Y., Braasch I., Meyer A. Comparative genomics provides evidence for an ancient genome duplication event in fish. Philos Trans R Soc Lond B Biol Sci. 2001 Oct 29;356(1414):1661–1679. doi: 10.1098/rstb.2001.0975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Taylor J. S., Van de Peer Y., Meyer A. Genome duplication, divergent resolution and speciation. Trends Genet. 2001 Jun;17(6):299–301. doi: 10.1016/s0168-9525(01)02318-6. [DOI] [PubMed] [Google Scholar]
  51. Tiersch T. R., Chandler R. W., Wachtel S. S., Elias S. Reference standards for flow cytometry and application in comparative studies of nuclear DNA content. Cytometry. 1989 Nov;10(6):706–710. doi: 10.1002/cyto.990100606. [DOI] [PubMed] [Google Scholar]
  52. Todorov Julia R., Elskus Adria A., Schlenk Daniel, Ferguson P. Lee, Brownawell Bruce J., McElroy Anne E. Estrogenic responses of larval sunshine bass (Morone saxatilis x M. Chrysops) exposed to New York City sewage effluent. Mar Environ Res. 2002 Sep-Dec;54(3-5):691–695. doi: 10.1016/s0141-1136(02)00197-6. [DOI] [PubMed] [Google Scholar]
  53. Wisneski L. A. Salmon calcitonin in the acute management of hypercalcemia. Calcif Tissue Int. 1990;46 (Suppl):S26–S30. doi: 10.1007/BF02553290. [DOI] [PubMed] [Google Scholar]
  54. Woods I. G., Kelly P. D., Chu F., Ngo-Hazelett P., Yan Y. L., Huang H., Postlethwait J. H., Talbot W. S. A comparative map of the zebrafish genome. Genome Res. 2000 Dec;10(12):1903–1914. doi: 10.1101/gr.10.12.1903. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Wright J. E., Jr, Johnson K., Hollister A., May B. Meiotic models to explain classical linkage, pseudolinkage, and chromosome pairing in tetraploid derivative salmonid genomes. Isozymes Curr Top Biol Med Res. 1983;10:239–260. [PubMed] [Google Scholar]
  56. Young W. P., Wheeler P. A., Coryell V. H., Keim P., Thorgaard G. H. A detailed linkage map of rainbow trout produced using doubled haploids. Genetics. 1998 Feb;148(2):839–850. doi: 10.1093/genetics/148.2.839. [DOI] [PMC free article] [PubMed] [Google Scholar]

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