Integration of the genetic map and genome assembly of fugu facilitates insights into distinct features of genome evolution in teleosts and mammals

Genome Biology and Evolution

Volumn 3, Issue 1, 2011, Pages 424-442

  Kai, Wataru ^a   Kikuchi, Kiyoshi ^a   Tohari, Sumanty ^b   Chew, Ah Keng ^b   Tay, Alice ^b   Fujiwara, Atushi ^c   Hosoya, Sho ^a   Suetake, Hiroaki ^a   Naruse, Kiyoshi ^d   Brenner, Sydney ^b   Suzuki, Yuzuru ^a   Venkatesh, Byrappa ^b  

^a UNIVERSITY OF TOKYO   (Japan)

^b INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Singapore)

^c FISHERIES RESEARCH AGENCY   (Japan)

^d NATIONAL INSTITUTE FOR BASIC BIOLOGY   (Japan)

Author keywords

Conserved synteny; Genetic map; Genome evolution; Pufferfish; Rearrangement; Recombination

Indexed keywords

MICROSATELLITE DNA;

ANIMAL; ARTICLE; CHROMOSOME; CHROMOSOME MAP; DNA SEQUENCE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE ORDER; GENE REARRANGEMENT; GENETICS; GENOME; HUMAN; MAMMAL; MOLECULAR EVOLUTION; MOUSE; NUCLEOTIDE SEQUENCE; OPOSSUM; ORYZIAS; PHYLOGENY; PUFFER FISH; TETRAODONTIFORMES;

ANIMALS; CHROMOSOME MAPPING; CHROMOSOMES; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; GENE ORDER; GENE REARRANGEMENT; GENOME; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; MAMMALS; MICE; MICROSATELLITE REPEATS; OPOSSUMS; ORYZIAS; PHYLOGENY; SEQUENCE ANALYSIS, DNA; TAKIFUGU; TETRAODONTIFORMES;

DIDELPHIDAE; MAMMALIA; ORYZIINAE; TAKIFUGU; TAKIFUGU RUBRIPES; TELEOSTEI; TETRAODON; TETRAODONTIDAE; VERTEBRATA;

EID: 79960102692     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evr041     Document Type: Article

References (78)

1. Aparicio S, et al. 2002. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science. 297:1301-1310. (Pubitemid 34913162)
2. Araki H, Berejikian BA, Ford MJ, Blouin MS. 2008. Fitness of hatcheryreared salmonids in the wild. Evol Appl. 1:342-355.
3. Benton MJ, Donoghue PCJ. 2007. Paleontological evidence to date the tree of life. Mol Biol Evol. 24:26-53. (Pubitemid 46026279)
4. Beye M, et al. 2006. Exceptionally high levels of recombination across the honey bee genome. Genome Res. 16:1339-1344. (Pubitemid 44664676)
5. Brenner S, et al. 1993. Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome. Nature. 366: 265-268. (Pubitemid 23359708)
6. Charlesworth D, Charlesworth B, Marais G. 2005. Steps in the evolution of heteromorphic sex chromosomes. Heredity. 95:118-128. (Pubitemid 41133194)
7. Colosimo PF, et al. 2004. The genetic architecture of parallel armor plate reduction in threespine sticklebacks. PLoS Biol. 2:e109.
8. Comeron JM, Williford A, Kliman RM. 2008. The Hill-Robertson effect: evolutionally consequences of weak selection and linkage in finite populations. Heredity. 100:19-31. (Pubitemid 350293641)
9. DeWoody JA, Avise JC. 2000. Microsatellite variation in marine, freshwater and anadromous fishes compared with other animals. J Fish Biol. 56:461-473.
10. Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450:203-218.
11. Fujita S. 1967. Artificial interspecific and intergeneric hybridizations among the Tetraodontid puffer (preliminary report). Jpn J Michurin Biol. 3:5-11.
12. Fujita S, Abe T. 1992. Induction of ovarian maturation and development of eggs, larvae, and juveniles of the purple puffer Takifugu porphyreus reared in the laboratory. Nippon Suisan Gakkaishi. 58:1627-1632.
13. Fujiwara A, Fujiwara M, Nishida-Umehara C, Abe S, Masaoka T. 2007. Characterization of Japanese flounder karyotype by chromosome bandings and fluorescence in situ hybridization with DNA markers. Genetica. 131:267-274. (Pubitemid 47632155)
14. Fujiwara A, et al. 2001. Improved fish lymphocyte culture for chromosome preparation. Genetica. 111:77-89. (Pubitemid 34115216)
15. Goode DK, Snell P, Smith SF, Cooke JE, Elgar G. 2005. Highly conserved regulatory elements around the SHH gene may contribute to the maintenance of conserved synteny across human chromosome 7q36.3. Genomics. 86:172-181. (Pubitemid 40917222)
16. Groenen MAM, et al. 2009. A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate. Genome Res. 19:510-519.
17. Hauser L, Carvalho GR. 2008. Paradigm shifts in marine fisheries genetics: ugly hypotheses slain by beautiful facts. Fish Fish. 9:333-362.
18. Hill MM, et al. 2008. The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution. Genome Res. 18:1369-1379.
19. Hillier LD, et al. 2007. Comparison of C. elegans and C. briggasae genome sequences reveals extensive conservation of chromosome organization and synteny. PLoS Biol. 5:e167.
20. Hurley I, Hale ME, Prince VE. 2005. Duplication events and the evolution of segmental identity. Evol Dev. 7:556-567. (Pubitemid 41711652)
21. Hurley IA, et al. 2007. A new time-scale for ray-finned fish evolution. Proc Biol Sci. 22:489-498. (Pubitemid 47055521)
22. International Chicken Genome Sequencing Consortium. 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 432: 695-716.
23. Jaillon O, et al. 2004. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature. 431:946-957.
24. Kai W, et al. 2005. A genetic linkage map for the tiger pufferfish, Takifugu rubripes. Genetics. 171:227-238. (Pubitemid 41437553)
25. Kasahara M, et al. 2007. The medaka draft genome and insights into vertebrate genome evolution. Nature. 447:714-719. (Pubitemid 46889726)
26. Kato A, Doi H, Nakada T, Sakai H, Hirose S. 2005. Takifugu obscurus is a euryhaline fugu species very close to Takifugu rubripes and suitable for studying osmoregulation. BMC Physiol. 5:18.
27. Kikuchi K, et al. 2007. The sex-determining locus in the tiger pufferfish, Takifugu rubripes. Genetics. 175:2039-2042. (Pubitemid 46789984)
28. Kirkpatrick M. 2010. How and why chromosome inversions evolve. PLoS Biol. 8:e1000501.
29. Kocher TD. 2004. Adaptive evolution and explosive speciation: the cichlid fish model. Nat Rev Genet. 5:288-298. (Pubitemid 38435624)
30. Kong A, et al. 2002. A high-resolution recombination map of the human genome. Nat Genet. 31:241-247.
31. Kumar S, Subramanian S. 2002. Mutation rates in mammalian genomes. Proc Natl Acad Sci U S A. 99:803-808. (Pubitemid 34106591)
32. Lander ES, et al. 1987. MapMaker: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics. 1:174-181.
33. Lenormand T. 2003. The evolution of sex dimorphism in recombination. Genetics. 163:811-822. (Pubitemid 36314560)
34. Lenormand T, Dutheil J. 2005. Recombination difference between sexes: a role for haploid selection. PLoS Biol. 3:e63.
35. Lercher MJ, Hurst LD. 2003. Imprinted chromosomal regions of the human genome have unusually high recombination rates. Genetics. 165:1629-1632. (Pubitemid 38020278)
36. Li WH, Ellsworth DL, Krushkal J, Chang BH, Hewett-Emmett D. 1996. Rate of nucleotide substitution in primates and rodents and the generation-time effect hypothesis. Mol Phylogenet Evol. 5:182-187. (Pubitemid 126317003)
37. Lynch M, Conery J. 2000. The evolutionary fate and consequences of gene duplication. Science. 290:1151-1155.
38. Lynch M, Force AG. 2000. The origin of interspecific genomic incompatibility via gene duplication. Am Nat. 156:590-605. (Pubitemid 32013275)
39. Lynch M, O'Hely M. 2001. Captive breeding and the genetic fitness of natural populations. Conserv Genet. 2:363-378. (Pubitemid 33635447)
40. Masuda Y, Shinohara N, Takahashi Y, Tabeta O, Matsuura K. 1991. Occurrence of natural hybrid between pufferfishes, Takifugu xanthopterus and T. vermicularis, in Ariake bay, Kyushu, Japan. Nippon Suisan Gakkaishi. 57:1247-1255.
41. McLysaght A, Enright AJ, Skrabanek L, Wolfe KH. 2000. Estimation of synteny conservation and genome compaction between pufferfish (Fugu) and human. Yeast. 17:22-36. (Pubitemid 30406795)
42. Meyer A, Van de Peer Y. 2005. From 2R to 3R: evidence for a fishspecific genome duplication (FSGD). Bioessays. 27:937-945. (Pubitemid 41415948)
43. Mikkelsen TS, et al. 2007. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature. 447:167-178.
44. Miyaki K, Tabeta O, Kayano H. 1995. Karyotypes in six species of pufferfishes genus Takifugu (Tetraodontidae, Tetraodontiformes). Fish Sci. 61:594-598.
45. Myers S, Bottolo L, Freeman C, McVean G, Donnelly P. 2005. A finescale map of recombination rates and hotspots across the human genome. Science. 310:321-324. (Pubitemid 41457199)
46. 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. (Pubitemid 47360900)
47. Naruse K, et al. 2004. A medaka gene map: the trace of ancestral vertebrate proto-chromosomes revealed by comparative gene mapping. Genome Res. 14:820-828. (Pubitemid 38660498)
48. Nelson JS. 2006. Fishes of the world, 4th ed. New York: John Wiley and Sons, Inc.
49. Ogawa K. 1991. Redescription of Heterobothrium tetrodomis (Goto, 1984) (Monogenea: Diclidophoridae) and other related new species from puffers of genus Takifugu (Teleost: tetraodontidae). Jpn J Parasitol. 40:388-396.
50. Ohno S. 1970. Evolution by gene duplication. New York: Springer-Verlag.
51. Ohta T. 2002. Near-neutrality in evolution of genes and gene regulation. Proc Natl Acad Sci U S A. 99:16134-16137. (Pubitemid 35462761)
52. Oleksyk TK, Smith MW, O'Brien SJ. 2010. Genome-wide scans for footprints of natural selection. Philos Trans R Soc B. 365:185-205.
53. Pennacchio LA, et al. 2006. In vivo enhancer analysis of human conserved non-coding sequences. Nature. 444:499-502. (Pubitemid 44809068)
54. Rodionov AV. 1996. Micro vs. macro: structural-functional organization of avian micro-and macrochromosomes. Genetika. 32:597-608. (Pubitemid 126763308)
55. Sakamoto T, et al. 2000. A microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) characterization by large sex-specific differences in recombination rates. Genetics. 155:1331-1345. (Pubitemid 30463441)
56. Schuelke M. 2000. An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol. 18:233-234. (Pubitemid 30091190)
57. Sémon M, Wolfe KH. 2007a. Rearrangement rate following the wholegenome duplication in teleost. Mol Biol Evol. 24:860-867. (Pubitemid 46355810)
58. Sémon M, Wolfe KH. 2007b. Reciprocal gene loss between Tetraodon and zebrafish after whole genome duplication in their ancestor. Trends Genet. 23:108-112. (Pubitemid 46275143)
59. Shifman S, et al. 2006. A high-resolution single nucleotide polymorphism genetic map of the mouse genome. PLoS Biol. 4:e395.
60. Singer A, et al. 2002. Sex-specific recombination rates in zebrafish (Danio rerio). Genetics. 160:649-657. (Pubitemid 34194537)
61. Small KS, Brudno M, Hill MM, Sidow A. 2007. Extreme genomic variation in a natural population. Proc Natl Acad Sci U S A. 104:5698-5703. (Pubitemid 47175743)
62. Stephen S, Pheasant M, Makunin IV, Mattick JS. 2008. Large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock. Mol Biol Evol. 25:402-408. (Pubitemid 351231613)
63. Streelman JT, Peichel CL, Parichy DM. 2007. Development genetics of adaptation in fishes: the case for novelty. Annu Rev Ecol Evol Syst. 38:655-681.
64. Suda Y, et al. 2009. Evolution of Otx paralogue usages in early patterning of the vertebrate head. Dev Biol. 325:282-295.
65. Tanaka K, Takehana Y, Naruse K, Hamaguchi S, Sakaizumi M. 2007. Evidence for different origins of sex chromosomes in closely related Oryzias fishes: substitution of the master sex-determining gene. Genetics. 177:2075-2081. (Pubitemid 350276989)
66. Tesler G. 2002. GRIMM: genome rearrangements web sever. Bioinformatics. 18:492-493. (Pubitemid 34284955)
67. The Cold Spring Harbor Laboratory, Washington University Genome Sequencing Center, PE Biosystems Arabidopsis Sequencing Consortium. 2000. The complete sequence of a heterochromatic island from a higher eukaryote. Cell. 100:377-386.
68. Topp CN, Dawe RK. 2006. Reinterpreting pericentromeric heterochromatin. Curr Opin Plant Biol. 9:647-653. (Pubitemid 44537842)
69. Uno Y. 1955. Spawning habit and early development of a puffer, Fugu (Torafugu) niphobles (Jordan et Snyder). J Tokyo Univ Fish. 41: 169-183.
70. 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 consiserably between ray-finned fishes and land vertebrates. Proc Natl Acad Sci U S A. 101:1638-1643. (Pubitemid 38234207)
71. Volff JN. 2005. Genome evolution and biodiversity in teleost fish. Heredity. 94:280-294.
72. Woods IG, et al. 2005. The zebrafish gene map defines ancestral vertebrate chromosome. Genome Res. 15:1307-1314. (Pubitemid 41247922)
73. Woolfe A, Elgar G. 2007. Comparative genomics using Fugu reveals insights into regulatory subfunctionalization. Genome Biol. 8:R53.
74. Woolfe A, et al. 2005. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol. 3:e7.
75. Yamanoue Y, et al. 2009. Explosive speciation of Takifugu: another use of fugu as a model system for evolutionary biology. Mol Biol Evol. 26:623-629.
76. Yeo G, Hoon S, Venkatesh B, Burge CB. 2004. Variation in sequence and organization of splicing regulatory elements in vertebrate genes. Proc Natl Acad Sci U S A. 101:15700-15705. (Pubitemid 39473551)
77. Yu N, et al. 2001. Global patterns of human DNA sequence variation in a 10-kb region on chromosome 1. Mol Biol Evol. 18:214-222. (Pubitemid 32118866)
78. Yu Q, et al. 2009. A physical map of the papaya genome with integrated genetic map and genome sequence. BMC Genomics. 10:371.