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Cited by 94Chromosomal and Genetic VariationsGenome Rearrangement AlgorithmsGenomics and Phylogenetic Studies

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Teleost fish with specific genome duplication as unique models of vertebrate evolution

Sato, Yukuto, Nishida, Mutsumi·2010·Environmental Biology of Fishes
DOI 10.1007/s10641-010-9628-7
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  • Certain ancestral features have been lost in teleosts, the most derived fish lineage to evolve after whole-genome duplication.

    “Although certain ancestral features have been lost in teleosts, the most derived fish lineage to evolve after whole-genome duplication (Sato & Nishida, 2010), they have been recreated in zebrafish by modifying their genetic makeup to reactivate the ancestral genetic network (Hawkins et al., 2021).”

    From Ancestral developmental potentials in early bony fish contributed to vertebrate water-to-land transition (2021) · cites this paper as Sato & Nishida, 2010

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  1. Abi-Rached L, Gilles A, Shiina T, Pontarotti P, Inoko H (2002) Evidence of en bloc duplication in vertebrate genomes. Nat Genet 31:100–105. doi: 10.1038/ng855 · DOI
  2. Allendorf FW, Thorgaard GH (1984) Tetraploidy and the evolution of salmonid fishes. In: Turner BJ (ed) The evolutionary genetics of fishes. Plenum Press, New York, pp 1–53 · DOI
  3. Amemiya CT, Prohaska SJ, Hill-Force A, Cook A, Wasserscheid J, Ferrier DE, Pascual-Anaya J, Garcia-Fernàndez J, Dewar K, Stadler PF (2008) The amphioxus Hox cluster: characterization, comparative genomics, and evolution. J Exp Zoolog B Mol Dev Evol 310:465–477. doi: 10.1002/jez.b.21213 · DOI
  4. Amores A, Force A, Yan YL, Joly L, Amemiya C, Fritz A, Ho RK, Langeland J, Prince V, Wang YL, Westerfield M, Ekker M, Postlethwait JH (1998) Zebrafish hox clusters and vertebrate genome evolution. Science 282:1711–1714. doi: 10.1126/science.282.5394.1711 · DOI
  5. Amores A, Suzuki T, Yan YL, Pomeroy J, Singer A, Amemiya C, Postlethwait JH (2004) Developmental roles of pufferfish Hox clusters and genome evolution in ray-fin fish. Genome Res 14:1–10. doi: 10.1101/gr.1717804 · DOI
  6. Aparicio S (2000) Vertebrate evolution: recent perspectives from fish. Trends Genet 16:54–56. doi: 10.1016/S0168-9525(99)01934-4 · DOI
  7. Aparicio S, Hawker K, Cottage A, Mikawa Y, Zuo L, Venkatesh B, Chen E, Krumlauf R, Brenner S (1997) Organization of the Fugu rubripes Hox clusters: evidence for continuing evolution of vertebrate Hox complexes. Nat Genet 16:79–83. doi: 10.1038/ng0597-79 · DOI
  8. Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, Gelpke MD, Roach J, Oh T, Ho IY, Wong M, Detter C, Verhoef F, Predki P, Tay A, Lucas S, Richardson P, Smith SF, Clark MS, Edwards YJ, Doggett N, Zharkikh A, Tavtigian SV, Pruss D, Barnstead M, Evans C, Baden H, Powell J, Glusman G, Rowen L, Hood L, Tan YH, Elgar G, Hawkins T, Venkatesh B, Rokhsar D, Brenner S (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297:1301–1310. doi: 10.1126/science.1072104 · DOI · Paper page
  9. Avise JC, Kitto GB (1973) Phosphoglucose isomerase gene duplication in the bony fishes: an evolutionary history. Biochem Genet 8:113–132. doi: 10.1007/BF00485540 · DOI
  10. Azuma Y, Kumazawa Y, Miya M, Mabuchi K, Nishida M (2008) Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences. BMC Evol Biol 8:215. doi: 10.1186/1471-2148-8-215 · DOI
  11. Benton MJ (1993) The fossil record volume 2. Chapman & Hall, London
  12. Braasch I, Salzburger W, Meyer A (2006) Asymmetric evolution in two fish-specifically duplicated receptor tyrosine kinase paralogons involved in teleost coloration. Mol Biol Evol 23:1192–1202. doi: 10.1093/molbev/msk003 · DOI
  13. Braasch I, Schartl M, Volff JN (2007) Evolution of pigment synthesis pathways by gene and genome duplication in fish. BMC Evol Biol 7:74. doi: 10.1186/1471-2148-7-74 · DOI
  14. Braasch I, Brunet F, Volff JN, Schartl M (2009) Pigmentation pathway evolution after whole genome duplication in fish. Genome Biol Evol, in press. doi: 10.1093/gbe/evp050 · DOI
  15. Chambers KE, McDaniell R, Raincrow JD, Deshmukh M, Stadler PF, Chiu CH (2009) Hox cluster duplication in the basal teleost Hiodon alosoides (Osteoglossomorpha). Theory Biosci 128:109–120. doi: 10.1007/s12064-009-0056-1 · DOI
  16. Cheng CH, Chen L (1999) Evolution of an antifreeze glycoprotein. Nature 401:443–444. doi: 10.1038/46721 · DOI
  17. Chiu CH, Amemiya C, Dewar K, Kim CB, Ruddle FH, Wagner GP (2002) Molecular evolution of the HoxA cluster in the three major gnathostome lineages. Proc Natl Acad Sci U S A 99:5492–5497. doi: 10.1073/pnas.052709899 · DOI
  18. Chiu CH, Dewar K, Wagner GP, Takahashi K, Ruddle F, Ledje C, Bartsch P, Scemama JL, Stellwag E, Fried C, Prohaska SJ, Stadler PF, Amemiya CT (2004) Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution. Genome Res 14:11–17. doi: 10.1101/gr.1712904 · DOI
  19. Christoffels A, Koh EG, Chia JM, Brenner S, Aparicio S, Venkatesh B (2004) Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes. Mol Biol Evol 21:1146–1151. doi: 10.1093/molbev/msh114 · DOI
  20. Christoffels A, Brenner S, Venkatesh B (2006) Tetraodon genome analysis provides further evidence for whole-genome duplication in the ray-finned fish. Comp Biochem Physiol Part D Genomics Proteomics 1:13–19. doi: 10.1016/j.cbd.2005.06.001 · DOI
  21. Crow KD, Wagner GP (2006) What is the role of genome duplication in the evolution of complexity and diversity? Mol Biol Evol 23:887–892. doi: 10.1093/molbev/msj083 · DOI
  22. Crow KD, Stadler PF, Lynch VJ, Amemiya C, Wagner GP (2006) The “fish-specific” Hox cluster duplication is coincident with the origin of teleosts. Mol Biol Evol 23:121–136. doi: 10.1093/molbev/msj020 · DOI
  23. de Boer JG, Yazawa R, Davidson WS, Koop BF (2007) Bursts and horizontal evolution of DNA transposons in the speciation of pseudotetraploid salmonids. BMC Genomics 8:422 · DOI
  24. Dehal P, Boore JL (2005) Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol 3:e314. doi: 10.1371/journal.pbio.0030314 · DOI · Paper page
  25. Donoghue PC, Purnell MA (2005) Genome duplication, extinction and vertebrate evolution. Trends Ecol Evol 20:312–319. doi: 10.1016/j.tree.2005.04.008 · DOI
  26. Douard V, Brunet F, Boussau B, Ahrens I, Vlaeminck-Guillem V, Haendler B, Laudet V, Guiguen Y (2008) The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event? BMC Evol Biol 8:336. doi: 10.1186/1471-2148-8-336 · DOI
  27. Ferris SD, Portnoy SL, Whitt GS (1979) The roles of speciation and divergence time in the loss of duplicate gene expression. Theor Popul Biol 15:114–139. doi: 10.1016/0040-5809(79)90030-3 · DOI
  28. Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Eyre T, Fitzgerald S, Fernandez-Banet J, Gräf S, Haider S, Hammond M, Holland R, Howe KL, Howe K, Johnson N, Jenkinson A, Kähäri A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Slater G, Smedley D, Spudich G, Trevanion S, Vilella AJ, Vogel J, White S, Wood M, Birney E, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Hubbard TJ, Kasprzyk A, Proctor G, Smith J, Ureta-Vidal A, Searle S (2008) Ensembl 2008. Nucleic Acids Res 36:D707–D714. doi: 10.1093/nar/gkm988 · DOI
  29. Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531–1545 · DOI · Paper page
  30. Furlong RF, Holland PW (2002) Were vertebrates octoploid? Philos Trans R Soc Lond B Biol Sci 357:531–544. doi: 10.1098/rstb.2001.1035 · DOI
  31. Gehring WJ (1998) The homeobox story. Yale University Press, New Haven
  32. Gibson TJ, Spring J (2000) Evidence in favour of ancient octaploidy in the vertebrate genome. Biochem Soc Trans 28:259–264 · DOI
  33. Gregory TR (2005) The evolution of the genome. Elsevier, San Diego
  34. Hashiguchi Y, Nishida M (2007) Evolution of trace amine associated receptor (TAAR) gene family in vertebrates: lineage-specific expansions and degradations of a second class of vertebrate chemosensory receptors expressed in the olfactory epithelium. Mol Biol Evol 24:2099–2107. doi: 10.1093/molbev/msm140 · DOI
  35. He X, Zhang J (2005) Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics 169:1157–1164. doi: 10.1534/genetics.104.037051 · DOI · Paper page
  36. Hedges SB, Kumar S (2003) Genomic clocks and evolutionary timescales. Trends Genet 19:200–206. doi: 10.1016/S0168-9525(03)00053-2 · DOI
  37. Hoegg S, Meyer A (2005) Hox clusters as models for vertebrate genome evolution. Trends Genet 21:421–424. doi: 10.1016/j.tig.2005.06.004 · DOI
  38. Hoegg S, Meyer A (2007) Phylogenomic analyses of KCNA clusters in vertebrates: why do some clusters stay intact? BMC Evol Biol 7:139. doi: 10.1186/1471-2148-7-139 · DOI
  39. Hoegg S, Brinkmann H, Taylor JS, Meyer A (2004) Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish. J Mol Evol 59:190–203. doi: 10.1007/s00239-004-2613-z · DOI
  40. Holland PW, Garcia-Fernàndez J, Williams NA, Sidow A (1994) Gene duplications and the origins of vertebrate development. Dev Suppl 1994:125–133
  41. Horton AC, Mahadevan NR, Ruvinsky I, Gibson-Brown JJ (2003) Phylogenetic analyses alone are insufficient to determine whether genome duplication(s) occurred during early vertebrate evolution. J Exp Zoolog B Mol Dev Evol 299:41–53. doi: 10.1002/jez.b.40 · DOI
  42. Hubbs CL (1955) Hybridization between fish species in nature. Syst Zool 4:1–20 · DOI
  43. Hufton AL, Groth D, Vingron M, Lehrach H, Poustka AJ, Panopoulou G (2008) Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement. Genome Res 18:1582–1591. doi: 10.1101/gr.080119.108 · DOI
  44. Hughes MK, Hughes AL (1993) Evolution of duplicate genes in a tetraploid animal, Xenopus laevis. Mol Biol Evol 10:1360–1369
  45. Hughes AL, da Silva J, Friedman R (2001) Ancient genome duplications did not structure the human Hox-bearing chromosomes. Genome Res 11:771–780. doi: 10.1101/gr.GR-1600R · DOI
  46. Imai S, Sasaki T, Shimizu A, Asakawa S, Hori H, Shimizu N (2007) The genome size evolution of medaka (Oryzias latipes) and fugu (Takifugu rubripes). Genes Genet Syst 82:135–144. doi: 10.1266/ggs.82.135 · DOI
  47. Inoue JG, Miya M, Tsukamoto K, Nishida M (2003) Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the “ancient fish”. Mol Phylogenet Evol 26:110–120. doi: 10.1016/S1055-7903(02)00331-7 · DOI
  48. Inoue JG, Miya M, Venkatesh B, Nishida M (2005) The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii: Coelacanthiformes) and divergence time estimation between the two coelacanths. Gene 349:227–235. doi: 10.1016/j.gene.2005.01.008 · DOI
  49. International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431:931–945. doi: 10.1038/nature03001 · DOI · Paper page
  50. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32(Database issue):D277-D280. doi: 10.1093/nar/gkh063 · DOI
  51. Kao HW, Lee SC (2002) Phosphoglucose isomerases of hagfish, zebrafish, gray mullet, toad, and snake, with reference to the evolution of the genes in vertebrates. Mol Biol Evol 19:367–374 · DOI
  52. Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, Ahrén D, Tsoka S, Darzentas N, Kunin V, López-Bigas N (2005) Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res 33:6083–6089. doi: 10.1093/nar/gki892 · DOI
  53. Kasahara M, Nakaya J, Satta Y, Takahata N (1997) Chromosomal duplication and the emergence of the adaptive immune system. Trends Genet 13:90–92. doi: 10.1016/S0168-9525(97)01065-2 · DOI
  54. Kasahara M, Naruse K, Sasaki S, Nakatani Y, Qu W, Ahsan B, Yamada T, Nagayasu Y, Doi K, Kasai Y, Jindo T, Kobayashi D, Shimada A, Toyoda A, Kuroki Y, Fujiyama A, Sasaki T, Shimizu A, Asakawa S, Shimizu N, Hashimoto S, Yang J, Lee Y, Matsushima K, Sugano S, Sakaizumi M, Narita T, Ohishi K, Haga S, Ohta F, Nomoto H, Nogata K, Morishita T, Endo T, Shin-I T, Takeda H, Morishita S, Kohara Y (2007) The medaka draft genome and insights into vertebrate genome evolution. Nature 447:714–719. doi: 10.1038/nature05846 · DOI · Paper page
  55. Kawahara R, Miya M, Mabuchi K, Lavoué S, Inoue JG, Satoh TP, Kawaguchi A, Nishida M (2008) Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): a new perspective based on whole mitogenome sequences from 75 higher teleosts. Mol Phylogenet Evol 46:224–236. doi: 10.1016/j.ympev.2007.07.009 · DOI
  56. Kawahara R, Miya M, Mabuchi K, Near TJ, Nishida M (2009) Stickleback phylogenies resolved: evidence from mitochondrial genomes and 11 nuclear genes. Mol Phylogenet Evol 50:401–404. doi: 10.1016/j.ympev.2008.10.014 · DOI
  57. Kellis M, Birren BW, Lander ES (2004) Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428:617–624. doi: 10.1038/nature02424 · DOI
  58. Kim CB, Amemiya C, Bailey W, Kawasaki K, Mezey J, Miller W, Minoshima S, Shimizu N, Wagner G, Ruddle F (2000) Hox cluster genomics in the horn shark, Heterodontus francisci. Proc Natl Acad Sci U S A 97:1655–1660. doi: 10.1073/pnas.030539697 · DOI
  59. Koh EG, Lam K, Christoffels A, Erdmann MV, Brenner S, Venkatesh B (2003) Hox gene clusters in the Indonesian coelacanth, Latimeria menadoensis. Proc Natl Acad Sci U S A 100:1084–1088. doi: 10.1073/pnas.0237317100 · DOI
  60. Kumar S, Hedges SB (1998) A molecular timescale for vertebrate evolution. Nature 392:917–920. doi: 10.1038/31927 · DOI · Paper page
  61. Kuraku S, Meyer A, Kuratani S (2009) Timing of genome duplications relative to the origin of the vertebrates: did cyclostomes diverge before or after? Mol Biol Evol 26:47–59. doi: 10.1093/molbev/msn222 · DOI
  62. Kurosawa G, Takamatsu N, Takahashi M, Sumitomo M, Sanaka E, Yamada K, Nishii K, Matsuda M, Asakawa S, Ishiguro H, Miura K, Kurosawa Y, Shimizu N, Kohara Y, Hori H (2006) Organization and structure of hox gene loci in medaka genome and comparison with those of pufferfish and zebrafish genomes. Gene 370:75–82. doi: 10.1016/j.gene.2005.11.015 · DOI
  63. Lander ES, International Human Genome Sequencing Consortium et al (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921 · DOI · Paper page
  64. Lavoué S, Miya M, Inoue JG, Saitoh K, Ishiguro NB, Nishida M (2005) Molecular systematics of the gonorynchiform fishes (Teleostei) based on whole mitogenome sequences: implications for higher-level relationships within the Otocephala. Mol Phylogenet Evol 37:165–177. doi: 10.1016/j.ympev.2005.03.024 · DOI
  65. Lavoué S, Miya M, Poulsen JY, Møller PR, Nishida M (2008) Monophyly, phylogenetic position and inter-familial relationships of the Alepocephaliformes (Teleostei) based on whole mitogenome sequences. Mol Phylogenet Evol 47:1111–1121. doi: 10.1016/j.ympev.2007.12.002 · DOI
  66. Ledje C, Kim CB, Ruddle FH (2002) Characterization of Hox genes in the bichir, Polypterus palmas. J Exp Zool 294:107–111. doi: 10.1002/jez.10152 · DOI
  67. Leggatt RA, Iwama GK (2003) Occurrence of polyploidy in the fishes. Rev Fish Biol Fish 13:237–246. doi: 10.1023/B:RFBF.0000033049.00668.fe · DOI
  68. Lemons D, McGinnis W (2006) Genomic evolution of Hox gene clusters. Science 313:1918–1922. doi: 10.1126/science.1132040 · DOI · Paper page
  69. Lister JA, Close J, Raible DW (2001) Duplicate mitf genes in zebrafish: complementary expression and conservation of melanogenic potential. Dev Biol 237:333–344. doi: 10.1006/dbio.2001.0379 · DOI
  70. Longhurst TJ, Joss JM (1999) Homeobox genes in the australian lungfish Neoceratodus forsteri. J Exp Zool 285:140–145. doi:10.1002/(SICI)1097-010X(19990815)285:2<140::AID-JEZ6>3.0.CO;2-V · DOI
  71. Lundin LG (1993) Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse. Genomics 16:1–19. doi: doi:10.1006/geno.1993.1133 · DOI
  72. Lundin LG, Larhammar D, Hallböök F (2003) Numerous groups of chromosomal regional paralogies strongly indicate two genome doublings at the root of the vertebrates. J Struct Funct Genomics 3:53–63. doi: 10.1023/A:1022600813840 · DOI
  73. Lynch M (2002) Gene duplication and evolution. Science 297:945–947. doi: 10.1126/science.1075472 · DOI
  74. Lynch M (2007) Genomic expansion by gene duplication. In: Lynch M (ed) The origins of genome architecture. Sinauer, Sunderland, pp 193–235
  75. Lynch M, Force AG (2000) The origin of interspecific genomic incompatibility via gene duplication. Am Nat 156:590–605. doi: 10.1086/316992 · DOI
  76. Mak HC, Daly M, Gruebel B, Ideker T (2007) CellCircuits: a database of protein network models. Nucleic Acids Res 35:D538–D545. doi: 10.1093/nar/gkl937 · DOI
  77. Mank JE, Avise JC (2006a) Phylogenetic conservation of chromosome numbers in Actinopterygiian fishes. Genetica 127:321–327. doi: 10.1007/s10709-005-5248-0 · DOI
  78. Mank JE, Avise JC (2006b) The evolution of reproductive and genomic diversity in ray-finned fishes: insights from phylogeny and comparative analysis. J Fish Biol 69:1–27. doi: 10.1111/j.1095-8649.2006.01132.x · DOI
  79. Martin A (2001) Is tetralogy true? Lack of support for the “one-to-four rule”. Mol Biol Evol 18:89–93 · DOI
  80. Mayden RL, Chen WJ, Bart HL, Doosey MH, Simons AM, Tang KL, Wood RM, Agnew MK, Yang L, Hirt MV, Clements MD, Saitoh K, Sado T, Miya M, Nishida M (2009) Reconstructing the phylogenetic relationships of the earth’s most diverse clade of freshwater fishes–order Cypriniformes (Actinopterygii: Ostariophysi): a case study using multiple nuclear loci and the mitochondrial genome. Mol Phylogenet Evol 51:500–514. doi: 10.1016/j.ympev.2008.12.015 · DOI
  81. Merritt TJS, Quattro JM (2001) Evidence for a period of directional selection following gene duplication in a neurally expressed locus of triosephosphate isomerase. Genetics 159:689–697 · DOI
  82. Meyer A, Málaga-Trillo E (1999) Vertebrate genomics: More fishy tales about Hox genes. Curr Biol 9:R210–R213. doi: 10.1016/S0960-9822(99)80131-6 · DOI
  83. Meyer A, Schartl M (1999) Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions. Curr Opin Cell Biol 11:699–704. doi: 10.1016/S0955-0674(99)00039-3 · DOI
  84. Miya M, Takeshima H, Endo H, Ishiguro NB, Inoue JG, Mukai T, Satoh TP, Yamaguchi M, Kawaguchi A, Mabuchi K, Shirai SM, Nishida M (2003) Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol Phylogenet Evol 26:121–138. doi: 10.1016/S1055-7903(02)00332-9 · DOI
  85. Miya M, Satoh TP, Nishida M (2005) The phylogenetic position of toadfishes (order Batrachoidiformes) in the higher ray-finned fish as inferred from partitioned Bayesian analysis of 102 whole mitochondrial genome sequences. Biol J Linn Soc Lond 85:289–306. doi: 10.1111/j.1095-8312.2005.00483.x · DOI
  86. Moghadam HK, Ferguson MM, Danzmann RG (2005) Evolution of Hox clusters in Salmonidae: a comparative analysis between Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss). J Mol Evol 61:636–649. doi: 10.1007/s00239-004-0338-7 · DOI
  87. Mouse Genome Sequencing Consortium (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420:520–562. doi: 10.1038/nature01262 · DOI · Paper page
  88. Mulley JF, Chiu CH, Holland PW (2006) Breakup of a homeobox cluster after genome duplication in teleosts. Proc Natl Acad Sci U S A 103:10369–10372. doi: 10.1073/pnas.0600341103 · DOI
  89. Murphy WJ, Pevzner PA, O’Brien SJ (2004) Mammalian phylogenomics comes of age. Trends Genet 20:631–639. doi: 10.1016/j.tig.2004.09.005 · DOI
  90. Nagasaki M, Doi A, Matsuno H, Miyano S (2003) Genomic object net: I. A platform for modelling and simulating biopathways. Appl Bioinformatics 2:181–184
  91. Nagasaki M, Saito A, Doi A, Matsuno H, Miyano S (2009) Foundations of systems biology: using Cell Illustrator and pathway databases. Springer-Verlag, New York · DOI
  92. Nakatani Y, Takeda H, Kohara Y, Morishita S (2007) Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates. Genome Res 17:1254–1265. doi: 10.1101/gr.6316407 · DOI · Paper page
  93. Naruse K, Fukamachi S, Mitani H, Kondo M, Matsuoka T, Kondo S, Hanamura N, Morita Y, Hasegawa K, Nishigaki R, Shimada A, Wada H, Kusakabe T, Suzuki N, Kinoshita M, Kanamori A, Terado T, Kimura H, Nonaka M, Shima A (2000) A detailed linkage map of medaka, Oryzias latipes: comparative genomics and genome evolution. Genetics 154:1773–1784 · DOI
  94. Naruse K, Tanaka M, Mita K, Shima A, Postlethwait J, Mitani H (2004) A medaka gene map: the trace of ancestral vertebrate proto-chromosomes revealed by comparative gene mapping. Genome Res 14:820–828. doi: 10.1101/gr.2004004 · DOI
  95. Nelson JS (2006) Fishes of the world, 4th edn. Wiley, New Jersey
  96. Ohno S (1970) Evolution by gene duplication. Springer-Verlag, New York · DOI · Paper page
  97. Ohno S (1999) Gene duplication and the uniqueness of vertebrate genomes circa 1970–1999. Semin Cell Dev Biol 10:517–522. doi: 10.1006/scdb.1999.0332 · DOI
  98. Pakchung AAH, Simpson PJL, Codd R (2006) Life on earth. Extremophiles continue to move the goal posts Environ Chem 3:77–93. doi: 10.1071/EN05093 · DOI
  99. Panopoulou G, Poustka AJ (2005) Timing and mechanism of ancient vertebrate genome duplications—the adventure of a hypothesis. Trends Genet 21:559–567. doi: 10.1016/j.tig.2005.08.004 · DOI
  100. Panopoulou G, Hennig S, Groth D, Krause A, Poustka AJ, Herwig R, Vingron M, Lehrach H (2003) New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes. Genome Res 13:1056–1066. doi: 10.1101/gr.874803 · DOI
  101. Postlethwait JH, Yan YL, Gates MA, Horne S, Amores A, Brownlie A, Donovan A, Egan ES, Force A, Gong Z, Goutel C, Fritz A, Kelsh R, Knapik E, Liao E, Paw B, Ransom D, Singer A, Thomson M, Abduljabbar TS, Yelick P, Beier D, Joly JS, Larhammar D, Rosa F, Westerfield M, Zon LI, Johnson SL, Talbot WS (1998) Vertebrate genome evolution and the zebrafish gene map. Nat Genet 18:345–349. doi: 10.1038/ng0498-345 · DOI
  102. Postlethwait JH, Woods IG, Ngo-Hazelett P, Yan YL, Kelly PD, Chu F, Huang H, Hill-Force A, Talbot WS (2000) Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Res 10:1890–1902 · DOI · Paper page
  103. Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Gutiérrez EL, Dubchak I, Garcia-Fernàndez J, Gibson-Brown JJ, Grigoriev IV, Horton AC, de Jong PJ, Jurka J, Kapitonov VV, Kohara Y, Kuroki Y, Lindquist E, Lucas S, Osoegawa K, Pennacchio LA, Salamov AA, Satou Y, Sauka-Spengler T, Schmutz J, Shin-I T, Toyoda A, Bronner-Fraser M, Fujiyama A, Holland LZ, Holland PW, Satoh N, Rokhsar DS (2008) The amphioxus genome and the evolution of the chordate karyotype. Nature 453:1064–1071. doi: 10.1038/nature06967 · DOI
  104. Rastogi S, Liberles DA (2005) Subfunctionalization of duplicated genes as a transition state to neofunctionalization. BMC Evol Biol 5:28. doi: 10.1186/1471-2148-5-28 · DOI
  105. Ravi V, Venkatesh B (2008) Rapidly evolving fish genomes and teleost diversity. Curr Opin Genet Dev 18:544–550. doi: 10.1016/j.gde.2008.11.001 · DOI
  106. Robinson-Rechavi M, Marchand O, Escriva H, Laudet V (2001a) An ancestral whole-genome duplication may not have been responsible for the abundance of duplicated fish genes. Curr Biol 11:R458–R459. doi: 10.1016/S0960-9822(01)00280-9 · DOI
  107. Robinson-Rechavi M, Marchand O, Escriva H, Bardet PL, Zelus D, Hughes S, Laudet V (2001b) Euteleost fish genomes are characterized by expansion of gene families. Genome Res 11:781–788 · DOI
  108. Robinson-Rechavi M, Boussau B, Laudet V (2004) Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference. Mol Biol Evol 21:580–586. doi: 10.1093/molbev/msh046 · DOI
  109. Robinson-Rechavi M, Alibés A, Godzik A (2006) Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima. J Mol Biol 356:547–557. doi: 10.1016/j.jmb.2005.11.065 · DOI
  110. Ruddle FH, Amemiya CT, Carr JL, Kim CB, Ledje C, Shashikant CS, Wagner GP (1999) Evolution of chordate hox gene clusters. Ann N Y Acad Sci 870:238–248 · DOI
  111. Salzburger W (2009) The interaction of sexually and naturally selected traits in the adaptive radiations of cichlid fishes. Mol Ecol 18:169–185. doi: 10.1111/j.1365-294X.2008.03981.x · DOI
  112. San Mauro D, Vences M, Alcobendas M, Zardoya R, Meyer A (2005) Initial diversification of living amphibians predated the breakup of Pangea. Am Nat 165:590–599. doi: 10.1086/429523 · DOI
  113. Sasaki T, Nishihara H, Hirakawa M, Fujimura K, Tanaka M, Kokubo N, Kimura-Yoshida C, Matsuo I, Sumiyama K, Saitou N, Shimogori T, Okada N (2008) Possible involvement of SINEs in mammalian-specific brain formation. Proc Natl Acad Sci U S A 105:4220–4225. doi: 10.1073/pnas.0709398105 · DOI
  114. Sato Y, Nishida M (2007) Post-duplication charge evolution of phosphoglucose isomerases in teleost fishes through weak selection on many amino acid sites. BMC Evol Biol 7:204. doi: 10.1186/1471-2148-7-204 · DOI
  115. Sato Y, Nishida M (2009) Electric charge divergence in proteins: insights into the evolution of their three-dimensional properties. Gene 441:3–11. doi: 10.1016/j.gene.2008.06.026 · DOI
  116. Sato Y, Hashiguchi Y, Nishida M (2009a) Temporal pattern of loss/persistence of duplicate genes involved in signal transduction and metabolic pathways after teleost-specific genome duplication. BMC Evol Biol 9:127. doi: 10.1186/1471-2148-9-127 · DOI
  117. Sato Y, Hashiguchi Y, Nishida M (2009b) Evolution of multiple phosphodiesterase isoforms in stickleback involved in cAMP signal transduction pathway. BMC Syst Biol 3:23. doi: 10.1186/1752-0509-3-23 · DOI
  118. Sauro HM, Hucka M, Finney A, Wellock C, Bolouri H, Doyle J, Kitano H (2003) Next generation simulation tools: the systems biology workbench and BioSPICE integration. OMICS 7:355–372. doi: 10.1089/153623103322637670 · DOI
  119. Seehausen O, Terai Y, Magalhaes IS, Carleton KL, Mrosso HD, Miyagi R, van der Sluijs I, Schneider MV, Maan ME, Tachida H, Imai H, Okada N (2008) Speciation through sensory drive in cichlid fish. Nature 455:620–626. doi: 10.1038/nature07285 · DOI
  120. Sémon M, Wolfe KH (2007a) Reciprocal gene loss between Tetraodon and zebrafish after whole genome duplication in their ancestor. Trends Genet 23:108–112. doi: 10.1016/j.tig.2007.01.003 · DOI
  121. Sémon M, Wolfe KH (2007b) Rearrangement rate following the whole-genome duplication in teleosts. Mol Biol Evol 24:860–867. doi: 10.1093/molbev/msm003 · DOI
  122. Setiamarga DH, Miya M, Yamanoue Y, Mabuchi K, Satoh TP, Inoue JG, Nishida M (2008) Interrelationships of Atherinomorpha (medakas, flyingfishes, killifishes, silversides, and their relatives): the first evidence based on whole mitogenome sequences. Mol Phylogenet Evol 49:598–605. doi: 10.1016/j.ympev.2008.08.008 · DOI
  123. Setiamarga DH, Miya M, Yamanoue Y, Azuma Y, Inoue JG, Ishiguro NB, Mabuchi K, Nishida M (2009) Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates. Biol Lett 5:812–816. doi: 10.1098/rsbl.2009.0419 · DOI
  124. Sidow A (1996) Gen(om)e duplications in the evolution of early vertebrates. Curr Opin Genet Dev 6:715–722. doi: 10.1016/S0959-437X(96)80026-8 · DOI
  125. Siegel N, Hoegg S, Salzburger W, Braasch I, Meyer A (2007) Comparative genomics of ParaHox clusters of teleost fishes: gene cluster breakup and the retention of gene sets following whole genome duplications. BMC Genomics 8:312. doi: 10.1186/1471-2164-8-312 · DOI
  126. Spring J (1997) Vertebrate evolution by interspecific hybridisation—are we polyploid? FEBS Lett 40:2–8. doi: 10.1016/S0014-5793(96)01351-8 · DOI
  127. Stadler PF, Fried C, Prohaska SJ, Bailey WJ, Misof BY, Ruddle FH, Wagner GP (2004) Evidence for independent Hox gene duplications in the hagfish lineage: a PCR-based gene inventory of Eptatretus stoutii. Mol Phylogenet Evol 32:686–694. doi: 10.1016/j.ympev.2004.03.015 · DOI
  128. Steinke D, Hoegg S, Brinkmann H, Meyer A (2006) Three rounds (1R/2R/3R) of genome duplications and the evolution of the glycolytic pathway in vertebrates. BMC Biol 4:16. doi: 10.1186/1741-7007-4-16 · DOI
  129. 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 20:1279–1291. doi: 10.2108/zsj.20.1279 · DOI
  130. Taylor JS, Van de Peer Y, Meyer A (2001a) Genome duplication, divergent resolution and speciation. Trends Genet 17:299–301. doi: 10.1016/S0168-9525(01)02318-6 · DOI
  131. Taylor JS, Van de Peer Y, Braasch I, Meyer A (2001b) Comparative genomics provides evidence for an ancient genome duplication event in fish. Philos Trans R Soc Lond B Biol Sci 356:1661–1679. doi: 10.1098/rstb.2001.0975 · DOI
  132. Taylor JS, Braasch I, Frickey T, Meyer A, Van de Peer Y (2003) Genome duplication, a trait shared by 22000 species of ray-finned fish. Genome Res 13:382–390. doi: 10.1101/gr.640303 · DOI
  133. Van der Hoeven F, Sordino P, Fraudeau N, Izpisúa-Belmonte JC, Duboule D (1996) Teleost HoxD and HoxA genes: comparison with tetrapods and functional evolution of the HoxD complex. Mech Dev 4:9–21. doi: 10.1016/0925-4773(95)00455-6 · DOI
  134. Van de Peer Y, Taylor JS, Braasch I, Meyer A (2001) The ghost of selection past: rates of evolution and functional divergence of anciently duplicated genes. J Mol Evol 53:436–446. doi: 10.1007/s002390010233 · DOI
  135. Van de Peer Y, Taylor JS, Meyer A (2003) Are all fishes ancient polyploids? J Struct Funct Genomics 3:65–73. doi: 10.1023/A:1022652814749 · DOI
  136. Vandepoele K, De Vos W, Taylor JS, Meyer A, Van de Peer Y (2004) Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates. Proc Natl Acad Sci U S A 101:1638–1643. doi: 10.1073/pnas.0307968100 · DOI
  137. Venkatesh B (2003) Evolution and diversity of fish genomes. Curr Opin Genet Dev 13:588–592. doi: 10.1016/j.gde.2003.09.001 · DOI
  138. Venkatesh B, Kirkness EF, Loh YH, Halpern AL, Lee AP, Johnson J, Dandona N, Viswanathan LD, Tay A, Venter JC, Strausberg RL, Brenner S (2007) Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome. PLoS Biol 5:e101. doi: 10.1371/journal.pbio.0050101 · DOI
  139. Vogel G (1998) Doubled genes may explain fish diversity. Science 281:1119–1121. doi: 10.1126/science.281.5380.1119 · DOI
  140. Volff JN (2005) Genome evolution and biodiversity in teleost fish. Heredity 94:280–294. doi: 10.1038/sj.hdy.6800635 · DOI
  141. Werthand CR, Windham MD (1991) A model for divergent, allopatric speciation of polyploid pteridophytes resulting from silencing of duplicate-gene expression. Am Nat 137:515–526. doi: 10.1086/285180 · DOI
  142. Wolfe KH (2001) Yesterday’s polyploids and the mystery of diploidization. Nat Rev Genet 2:333–341. doi: 10.1038/35072009 · DOI
  143. Yamanoue Y, Miya M, Inoue JG, Matsuura K, Nishida M (2006) The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetraodontiformes) and divergence time estimation among model organisms in fishes. Genes Genet Syst 8:29–39. doi: 10.1266/ggs.81.29 · DOI
  144. Yamanoue Y, Miya M, Matsuura K, Katoh M, Sakai H, Nishida M (2008) A new perspective on phylogeny and evolution of tetraodontiform fishes (Pisces: Acanthopterygii) based on whole mitochondrial genome sequences: Basal ecological diversification? BMC Evol Biol 8:212. doi: 10.1186/1471-2148-8-212 · DOI
  145. Yamanoue Y, Miya M, Matsuura K, Miyazawa S, Tsukamoto N, Doi H, Takahashi H, Mabuchi K, Nishida M, Sakai H (2009) Explosive speciation of Takifugu: another use of fugu as a model system for evolutionary biology. Mol Biol Evol 26:623–629. doi: 10.1093/molbev/msn283 · DOI
  146. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555–556. doi: 10.1093/bioinformatics/13.5.555 · DOI
  147. Yu WP, Yew K, Rajasegaran V, Venkatesh B (2007) Sequencing and comparative analysis of fugu protocadherin clusters reveal diversity of protocadherin genes among teleosts. BMC Evol Biol 7:49. doi: 10.1186/1471-2148-7-49 · DOI
  148. Zhang J (2003) Evolution by gene duplication: an update. Trends Ecol Evol 18:292–298. doi: 10.1016/S0169-5347(03)00033-8 · DOI · Paper page
  149. Zhou R, Cheng H, Tiersch TR (2001) Differential genome duplication and fish diversity. Rev Fish Biol Fish 11:331–337. doi: 10.1023/A:1021395506705 · DOI

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Metadata

Authors
Sato, Y., & Nishida, M.
Affiliations
  • National Institute of Genetics (JP)
  • The University of Tokyo (JP)
Corresponding author
Sato, Yukuto
ORCID
Venue
Environmental Biology of Fishes
Publisher
Springer Science and Business Media LLC
Published
2010-02-26
Volume
88
Issue
2
Pages
169-188
ISSN
  • 0378-1909 (ISSN-L)
  • 1573-5133
DOI
10.1007/s10641-010-9628-7
OpenAlex
W2119119333
Cited by
94
References
6
Citations by year
2026: 6 · 2025: 3 · 2024: 3 · 2023: 5 · 2022: 6 · 2021: 7 · 2020: 3 · 2019: 6 · 2018: 10 · 2017: 1 · 2016: 11 · 2015: 6 · 2014: 9 · 2013: 6 · 2012: 7
FWCI
6.42
Type
journal article
Language
en
Open access
closed
Licence
www.springer.com/tdm (tdm)
Locations
Environmental Biology of Fishes (publishedVersion)
Funders
Japan Society for the Promotion of Science
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
whole-genome duplication, teleosts, vertebrate genome evolution, duplicate genes, synteny analysis, Tetraodon, medaka, chromosomal rearrangements, tetrapod evolution, Actinopterygii

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