The art of medaka genetics and genomics: What makes them so unique?

Annual Review of Genetics

Volumn 44, Issue , 2010, Pages 217-241

  Takeda, Hiroyuki ^a   Shimada, Atsuko ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

cilia; disease; pigmentation; QTL; transposon; Zebrafish

Indexed keywords

ALBINISM; ANIMAL GENETICS; CELL STRUCTURE; CHROMATIN; DNA TRANSFER; GENE ISOLATION; GENE MUTATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC VARIABILITY; GENOMICS; MUTAGENESIS; NONHUMAN; ORYZIAS; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; RETROPOSON; REVIEW; ZYGOTE;

ANIMALS; DISEASE MODELS, ANIMAL; GENETIC TECHNIQUES; GENOME; HUMANS; JAPAN; ORYZIAS;

DANIO RERIO; ORYZIAS LATIPES; ORYZIINAE; VERTEBRATA;

EID: 78149443392     PISSN: 00664197     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev-genet-051710-151001     Document Type: Review

References (94)

1. Aida T. 1921. On the inheritance of color in a fresh-water fish, Aplocheilus latipes Temmick and Schlegel, with special reference to sex-linked inheritance. Genetics 6:554-73
2. Albertson RC, Streelman JT, Kocher TD. 2003. Directional selection has shaped the oral jaws of Lake Malawi cichlid fishes. Proc. Natl. Acad. Sci. USA 100:5252-57
3. Asakawa K, SusterML, Mizusawa K, Nagayoshi S, Kotani T, et al. 2008. Genetic dissection of neural circuits by Tol2 transposon-mediated Gal4 gene and enhancer trapping in zebrafish. Proc. Natl. Acad. Sci. USA 105:1255-60
4. Ciruna B, Weidinger G, Knaut H, Thisse B, Thisse C, et al. 2002. Production of maternal-zygotic mutant zebrafish by germ-line replacement. Proc. Natl. Acad. Sci. USA 99:14919-24
5. Dohmoto A, Shimizu K, Asada Y, Maeda T. 2002. Quantitative trait loci on chromosomes 10 and 11 influencing mandible size of SMXA RI mouse strains. J. Dent. Res. 81:501-4
6. Dosch R, Wagner DS, Mintzer KA, Runke G, Wiemelt AP, Mullins MC. 2004. Maternal control of vertebrate development before the midblastula transition: mutants from the zebrafish I. Dev. Cell 6:771-80
7. Edmunds JS, McCarthy RA, Ramsdell JS. 2000. Permanent and functional male-to-female sex reversal in d-rR strain medaka (Oryzias latipes) following egg microinjection of o,p'-DDT. Environ. Health Perspect. 108:219-24
8. Essner JJ, Amack JD, Nyholm MK, Harris EB, Yost HJ. 2005. Kupffer's vesicle is a ciliated organ of asymmetry in the zebrafish embryo that initiates left-right development of the brain, heart and gut. Development 132:1247-60
9. Fraser MJ, Ciszczon T, Elick T, Bauser C. 1996. Precise excision of TTAA-specific lepidopteran trans-posons piggyBac (IFP2) and tagalong (TFP3) from the baculovirus genome in cell lines from two species of Lepidoptera. Insect Mol. Biol. 5:141-51
10. Fukamachi S, Asakawa S, Wakamatsu Y, Shimizu N, Mitani H, Shima A. 2004. Conserved function of medaka pink-eyeddilution in melanin synthesis and its divergent transcriptional regulation in gonads among vertebrates. Genetics 168:1519-27
11. Fukamachi S, Shimada A, Shima A. 2001. Mutations in the gene encoding B, a novel transporter protein, reduce melanin content in medaka. Nat. Genet. 28:381-85
12. Fukamachi S, Sugimoto M, Mitani H, Shima A. 2004. Somatolactin selectively regulates proliferation and morphogenesis of neural-crest derived pigment cells in medaka. Proc. Natl. Acad. Sci. USA 101:10661-66
13. Fukamachi S, Yada T, Meyer A, Kinoshita M. 2009. Effects of constitutive expression of somatolactin alpha on skin pigmentation in medaka. Gene 442:81-87
14. Furutani-Seiki M, Sasado T, Morinaga C, Suwa H, Niwa K, et al. 2004. A systematic genome-wide screen for mutations affecting organogenesis in Medaka, Oryzias latipes. Mech. Dev. 121:647-58
15. Halpern M, ed. 2004. Mechanisms of Development: Special Issue on Medaka. 121(7-8):597-1008
16. Hamaguchi S, Sakaizumi M. 1992. Sexually differentiated mechanisms of sterility in interspecific hybrids between Oryzias latipes and O. curvinotus. J. Exp. Zool. 263:323-29
17. Hashimoto H, Miyamoto R, Watanabe N, Shiba D, Ozato K, et al. 2009. Polycystic kidney disease in the medaka (Oryzias latipes) pc mutant caused by a mutation in the Gli-Similar3 (glis3) gene. PLoS One 4:e6299
18. Hayashida Y, Kawamura T, Hori-e R, Yamashita I. 2004. Retionic acid and its receptors are required for expression of aryl hydrocarbon receptor mRNA and embryonic development of blood vessel and bone in the medaka fish, Oryzias latipes. Zool. Sci. 21:541-51
19. Hojo M, Takashima S, Kobayashi D, Sumeragi A, Shimada A, et al. 2007. Right-elevated expression of charon is regulated by fluid flow in medaka Kupffer's vesicle. Dev. Growth Differ. 49:395-405
20. Huang B, Piperno G, Luck DJ. 1979. Paralyzed flagella mutants of Chlamydomonas reinhardtii. Defective for axonemal doublet microtubule arms. J. Biol. Chem. 254:3091-99
21. Hyodo-Taguchi Y. 1980. Establishment of inbred strains of the teleost, Oryzias latipes. Zool. Mag. 89:283-301
22. Hyodo-Taguchi Y. 1990. Inbred strains of the medaka and their characteristics. In Biology of the Medaka, ed. N Egami, K Yamagami, A Shima, pp. 129-42. Tokyo: Tokyo Univ. Press
23. Iida A, Inagaki H, Suzuki M, Wakamatsu Y, Hori H, Koga A. 2004. The tyrosinase gene of the i(b) albino mutant of the medaka fish carries a transposable element insertion in the promoter region. Pigment Cell Res. 17:158-64
24. Ishikawa Y. 2000. Medakafish as a model system for vertebrate developmental genetics. Bioessays 22:487-95.
25. Ishikawa Y, Yoshimoto M, Yamamoto N, Ito H. 1999. Different brain morphologies from different genotypes in a single teleost species, the medaka (Oryzias latipes). Brain Behav. Evol. 53:2-9
26. Ivics Z, Hackett PB, Plasterk RH, Izsvak Z. 1997. Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells. Cell 91:501-10
27. Johannsdottir B, Thorarinsson F, Thordarson A, Magnusson TE. 2005. Heritability of craniofacial characteristics between parents and offspring estimated from lateral cephalograms. Am. J. Orthod. Dentofacial Orthop. 127:200-7; quiz 260-61
28. Kasahara M, Naruse K, Sasaki S, Nakatani Y, Qu W, et al. 2007. The medaka draft genome and insights into vertebrate genome evolution. Nature 447:714-19
29. Kawakami K. 2007. Tol2: a versatile gene transfer vector in vertebrates. Genome Biol. 8(Suppl 1):S7
30. Kimura T, Shimada A, Sakai N, Mitani H, Naruse K, et al. 2007. Genetic analysis of craniofacial traits in the medaka. Genetics 177:2379-88
31. Klingenberg CP, Leamy LJ, Cheverud JM. 2004. Integration and modularity of quantitative trait locus effects on geometric shape in the mouse mandible. Genetics 166:1909-21
32. Klingenberg CP, Leamy LJ, Routman EJ, Cheverud JM. 2001. Genetic architecture of mandible shape in mice: effects of quantitative trait loci analyzed by geometric morphometrics. Genetics 157:785-802
33. Kobayashi D, Takeda H. 2008. Medaka genome project. Brief. Funct. Genomics Proteomics 7:415-26
34. Koga A, Cheah FS, Hamaguchi S, Yeo GH, Chong SS. 2008. Germline transgenesis of zebrafish using the medaka Tol1 transposon system. Dev. Dyn. 237:2466-74
35. Koga A, Higashide I, Hori H, Wakamatsu Y, Kyono-Hamaguchi Y, Hamaguchi S. 2007. The Tol1 element of medaka fish is transposed with only terminal regions and can deliver large DNA fragments into the chromosomes. J. Hum. Genet. 52:1026-30
36. Koga A, Hori H. 2001. The Tol2 transposable element of the medaka fish: an active DNA-based element naturally occurring in a vertebrate genome. Genes Genet. Syst. 76:1-8
37. Koga A, Inagaki H, Bessho Y, Hori H. 1995. Insertion of a novel transposable element in the tyrosinase gene is responsible for an albino mutation in the medaka fish, Oryzias latipes. Mol. Gen. Genet. 249:400-5
38. Koga A, Sakaizumi M, Hori H. 2002. Transposable elements in medaka fish. Zool. Sci. 19:1-6
39. Koga A, Shimada A, Shima A, Sakaizumi M, Tachida H, Hori H. 2000. Evidence for recent invasion of the medaka fish genome by the Tol2 transposable element. Genetics 155:273-81
40. Koga A, Suzuki M, Inagaki H, Bessho Y, Hori H. 1996. Transposable element in fish. Nature 383:30
41. Koga A, Wakamatsu Y, Sakaizumi M, Hamaguchi S, Shimada A. 2009. Distribution of complete and defective copies of the Tol1 transposable element in natural populations of the medaka fish Oryzias latipes. Genes Genet. Syst. 84:345-52
42. Kondo M, Nanda I, Hornung U, Schmid M, Schartl M. 2004. Evolutionary origin of the medaka Y chromosome. Curr. Biol. 14:1664-69
43. Korzh V. 2007. Transposons as tools for enhancer trap screens in vertebrates. Genome Biol. 8(Suppl 1):S8
44. Kramer-Zucker AG, Olale F, Haycraft CJ, Yoder BK, Schier AF, Drummond IA. 2005. Cilia-driven fluid flow in the zebrafish pronephros, brain and Kupffer's vesicle is required for normal organogenesis. Development 132:1907-21
45. Kurokawa H, Saito D, Nakamura S, Katoh-Fukui Y, Ohta K, et al. 2007. Germ cells are essential for sexual dimorphism in the medaka gonad. Proc. Natl. Acad. Sci. USA 104:16958-63
46. Kwan KM, Fujimoto E, Grabher C, Mangum BD, Hardy ME, et al. 2007. The Tol2kit: a multisite gateway-based construction kit for Tol2 transposon transgenesis constructs. Dev. Dyn. 236:3088-99
47. Lang DH, Sharkey NA, Mack HA, Vogler GP, Vandenbergh DJ, et al. 2005. Quantitative trait loci analysis of structural and material skeletal phenotypes in C57BL/6J and DBA/2 second-generation and recombinant inbred mice. J. Bone Miner. Res. 20:88-99
48. Levin M. 2005. Left-right asymmetry in embryonic development: a comprehensive review. Mech. Dev. 122:3-25
49. Loosli F, Koster RW, Carl M, Kuhnlein R, Henrich T, et al. 2000. A genetic screen for mutations affecting embryonic development in medaka fish (Oryzias latipes). Mech. Dev. 97:133-39
50. Loosli F, Winkler S, Burgtorf C, Wurmbach E, Ansorge W, et al. 2001. Medaka eyeless is the key factor linking retinal determination and eye growth. Development 128:4035-44
51. Matsuda M, Nagahama Y, Shinomiya A, Sato T, Matsuda C, et al. 2002. DMY is a Y-specific DM-domain gene required for male development in the medaka fish. Nature 417:559-63
52. Morinaga C, Saito D, Nakamura S, Sasaki T, Asakawa S, et al. 2007. The hotei mutation of medaka in the anti-Mullerian hormone receptor causes the dysregulation of germ cell and sexual development. Proc. Natl. Acad. Sci. USA 104:9691-96
53. Nakamura S, Kobayashi K, Nishimura T, Higashijima S, Tanaka M. 2010. Identification of germline stem cells in the ovary of the teleost medaka. Science 328:1561-63
54. NakamuraS, Saito D, Tanaka M. 2008. Generationoftransgenic medaka using modified bacterial artificial chromosome. Dev. Growth Differ. 50:415-19
55. Nishimura I, Drake TA, Lusis AJ, Lyons KM, Nadeau JH, Zernik J. 2003. ENU large-scale mutagen-esis and quantitative trait linkage (QTL) analysis in mice: novel technologies for searching polygenetic determinants of craniofacial abnormalities. Crit. Rev. Oral. Biol. Med. 14:320-30
56. Ohtsuka M, Kikuchi N, Yokoi H, Kinoshita M, Wakamatsu Y, et al. 2004. Possible roles of zic1 and zic4, identified within the medaka double anal fin (Da) locus, in dorsoventral patterning of the trunk-tail region (related to phenotypes of the Da mutant). Mech. Dev. 121:873-82
57. Okada Y, Takeda S, Tanaka Y, Belmonte J-CI, Hirokawa N. 2005. Mechanism of nodal flow: a conserved symmetry breaking event in left-right axis determination. Cell 121:633
58. Omran H, Kobayashi D, Olbrich H, Tsukahara T, Loges NT, et al. 2008. Ktu/PF13 is required for cytoplasmic pre-assembly of axonemal dyneins. Nature 456:611-16
59. Ozato K, Wakamatsu Y. 1994. Developmental genetics of medaka. Dev. Growth Differentiation 36:437-43
60. Pace JK 2nd, Gilbert C, Clark MS, Feschotte C. 2008. Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods. Proc. Natl. Acad. Sci. USA 105:17023-28
61. Patyna PJ, Davi RA, Parkerton TF, Brown RP, Cooper KR. 1999. A proposed multigeneration protocol for Japanese medaka (Oryzias latipes) to evaluate effects of endocrine disruptors. Sci. Total Environ. 233:211-20
62. Raya A, Izpisua Belmonte JC. 2006.Left-right asymmetry in the vertebrate embryo: from early information to higher-level integration. Nat. Rev. Genet. 7:283-93
63. Rohner N, Bercsenyi M, Orban L, Kolanczyk ME, Linke D, et al. 2009. Duplication of fgfr1 permits Fgf signaling to serve as a target for selection during domestication. Curr. Biol. 19:1642-47
64. Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, et al. 2007. Genome-wide detection and characterization of positive selection in human populations. Nature 449:913-18
65. SakaguchiS, Nakatani Y, Takamatsu N, Hori H, KawakamiA, etal. 2006. Medaka unextended-fin mutants suggest a role for Hoxb8a in cell migration and osteoblast differentiation during appendage formation. Dev. Biol. 293:426-38
66. Sasaki S, Mello CC, Shimada A, Nakatani Y, Hashimoto S, et al. 2009. Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites. Science 323:401-4
67. Savoye I, Loos R, Carels C, Derom C, Vlietinck R. 1998. A genetic study of anteroposterior and vertical facial proportions using model-fitting. Angle Orthod. 68:467-70
68. Setiamarga DH, Miya M, Yamanoue Y, Azuma Y, Inoue JG, et al. 2009. Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates. Biol. Lett. 5:812-16
69. Shima A, Mitani H. 2004. Medaka as a research organism: past, present and future. Mech. Dev. 121:599-604
70. Shimada A, Takeda H. 2008. Production of a maternal-zygotic medaka mutant using hybrid sterility. Dev. Growth Differ. 50:421-26
71. Shimada A, Yabusaki M, Niwa H, Yokoi H, Hatta K, et al. 2008. Maternal-zygotic medaka mutants for fgfr1 reveal its essential role in the migration of the axial mesoderm but not the lateral mesoderm. Development 135:281-90
72. Shimizu M, Shibata N, Yamashita M. 1997. Spermiogenesis without preceding meiosis in the hybrid medaka between Oryzias latipes and O. curvinotus. J. Exp. Zool. 279:102-12
73. Spritz RA, Chiang PW, Oiso N, Alkhateeb A. 2003. Human and mouse disorders of pigmentation. Curr. Opin. Genet. Dev. 13:284-89
74. Sullivan-Brown J, Schottenfeld J, Okabe N, Hostetter CL, Serluca FC, et al. 2007. Zebrafish mutations affecting cilia motility share similar cystic phenotypes and suggest a mechanism of cyst formation that differs from pkd2 morphants. Dev. Biol. 314(2):261-75
75. Takeda H. 2008. Draft genome of the medaka fish: a comprehensive resource for medaka developmental genetics and vertebrate evolutionary biology. Dev. Growth Differ. 50(Suppl 1):S157-66
76. Takehana Y, Nagai N, Matsuda M, Tsuchiya K, Sakaizumi M. 2003. Geographic variation and diversity of the cytochrome b gene in Japanese wild populations of medaka, Oryzias latipes. Zool. Sci. 20:1279-91
77. Takehana Y, Naruse K, Sakaizumi M. 2005. Molecular phylogeny of the medaka fishes genus Oryzias (Beloniformes: Adrianichthyidae) based on nuclear and mitochondrial DNA sequences. Mol. Phylogenet. Evol. 36:417-28
78. Tanaka M, Kinoshita M, Kobayashi D, Nagahama Y. 2001. Establishment of medaka (Oryzias latipes) transgenic lines with the expression of green fluorescent protein fluorescence exclusively in germ cells: a useful model to monitor germ cells in a live vertebrate. Proc. Natl. Acad. Sci. USA 98:2544-49
79. Tanaka M, Saito D, Morinaga C, Kurokawa H. 2008. Cross talk between germ cells and gonadal somatic cells is critical for sex differentiation of the gonads in the teleost fish, medaka (Oryzias latipes). Dev. Growth Differ. 50:273-78
80. Tao Q, Yokota C, Puck H, Kofron M, Birsoy B, et al. 2005. Maternal wnt11 activates the canonical wnt signaling pathway required for axis formation in Xenopus embryos. Cell 120:857-71
81. Taylor MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, Semple CA. 2006. Heterotachy in mammalian promoter evolution. PLoS Genet. 2:e30
82. Temminck CJ, Schlegel H. 1845. Pisces, Part VIII, ed. Lugduni, Batavorum, pp. 134-35.
83. Urasaki A, Asakawa K, Kawakami K. 2008. Efficient transposition of the Tol2 transposable element from a single-copy donor in zebrafish. Proc. Natl. Acad. Sci. USA 105:19827-32
84. Villefranc JA, Amigo J, Lawson ND. 2007. Gateway compatible vectors for analysis of gene function in the zebrafish. Dev. Dyn. 236:3077-87
85. Wakamatsu Y, Pristyazhnyuk S, Kinoshita M, Tanaka M, Ozato K. 2001. The see-through medaka: a fish model that is transparent throughout life. Proc. Natl. Acad. Sci. USA 98:10046-50
86. Warnecke T, Batada NN, Hurst LD. 2008. The impact of the nucleosome code on protein-coding sequence evolution in yeast. PLoS Genet. 4:e1000250
87. Washietl S, Machne R, Goldman N. 2008. Evolutionary footprints of nucleosome positions in yeast. Trends Genet. 24:583-87
88. Wilson PD. 2004. Polycystic kidney disease. N. Engl. J. Med. 350:151-64
89. Wu CI, Ting CT. 2004. Genes and speciation. Nat. Rev. Genet. 5:114-22
90. Yamamoto T. 1953. Artificial induction of functional sex-reversal in genotypic females of the medaka (Oryzias latipes). J. Exp. Zool. 123:571-94
91. Yasutake J, Inohaya K, Kudo A. 2004. Twist functions in vertebral column formation in medaka, Oryzias latipes. Mech. Dev. 121:883-94
92. Yokoi H, Shimada A, Carl M, Takashima S, Kobayashi D, et al. 2007. Mutant analyses reveal different functions of fgfr1 in medaka and zebrafish despite conserved ligand-receptor relationships. Dev. Biol. 304:326-37
93. Yu JF, Fukamachi S, Mitani H, Hori H, Kanamori A. 2006. Reduced expression of vps11 causes less pigmentation in medaka, Oryzias latipes. Pigment Cell Res. 19:628-34
94. Zariwala MA, Knowles MR, Omran H. 2007. Genetic defects in ciliary structure and function. Annu. Rev. Physiol. 69:423-50