메뉴 건너뛰기




Volumn 10, Issue , 2009, Pages

Comparative genomics and evolution of conserved noncoding elements (CNE) in rainbow trout

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME; FISH GENETICS; GENE DUPLICATION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC MARKER; GENETIC VARIABILITY; GENOME; GENOMICS; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; RAINBOW TROUT; SALMON; UNINDEXED SEQUENCE; VERTEBRATE; ZEBRA FISH; ANIMAL; CHROMOSOME MAP; COMPARATIVE GENOMIC HYBRIDIZATION; DNA SEQUENCE; GENETICS; HUMAN; ORYZIAS; SYNTENY; UNTRANSLATED REGION;

EID: 67650763462     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-278     Document Type: Article
Times cited : (10)

References (64)
  • 2
    • 0036613237 scopus 로고    scopus 로고
    • Extensive genomic duplication during early chordate evolution
    • 12032567
    • McLysaght A Hokamp K Wolfe KH Extensive genomic duplication during early chordate evolution Nat Genet 2002, 31:200-204. 12032567
    • (2002) Nat Genet , vol.31 , pp. 200-204
    • McLysaght, A.1    Hokamp, K.2    Wolfe, K.H.3
  • 4
    • 1242274629 scopus 로고    scopus 로고
    • Major events in the genome evolution of vertebrates: Paranome age and size differ considerably between ray-finned fishes and land vertebrates
    • 341801 14757817
    • Vandepoele K De Vos W Taylor JS Meyer A Peer Van de Y 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 USA 2004, 101:1638-1643. 341801 14757817
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 1638-1643
    • Vandepoele, K.1    De Vos, W.2    Taylor, J.S.3    Meyer, A.4    Peer, Y.5
  • 5
    • 26444603772 scopus 로고    scopus 로고
    • Two rounds of whole genome duplication in the ancestral vertebrate
    • 1197285 16128622
    • Dehal P Boore JL Two rounds of whole genome duplication in the ancestral vertebrate PLoS Biol 2005, 3:e314. 1197285 16128622
    • (2005) PLoS Biol , vol.3
    • Dehal, P.1    Boore, J.L.2
  • 6
    • 33745067419 scopus 로고    scopus 로고
    • The gain and loss of genes during 600 million years of vertebrate evolution
    • 1779523 16723033
    • Blomme T Vandepoele K De Bodt S Simillion C Maere S Peer Van de Y The gain and loss of genes during 600 million years of vertebrate evolution Genome Biol 2006, 7:R43. 1779523 16723033
    • (2006) Genome Biol , vol.7
    • Blomme, T.1    Vandepoele, K.2    De Bodt, S.3    Simillion, C.4    Maere, S.5    Peer, Y.6
  • 7
    • 33644553076 scopus 로고    scopus 로고
    • Tetraodon genome analysis provides further evidence for whole-genome duplication in the ray-finned fish lineage
    • Christoffels A Brenner S Venkatesh B Tetraodon genome analysis provides further evidence for whole-genome duplication in the ray-finned fish lineage Comp Biochem Physiol D: Genomics Proteomics 2006, 1:13-19.
    • (2006) Comp Biochem Physiol D: Genomics Proteomics , vol.1 , pp. 13-19
    • Christoffels, A.1    Brenner, S.2    Venkatesh, B.3
  • 8
    • 0035344021 scopus 로고    scopus 로고
    • Yesterday's polyploids and the mystery of diploidization
    • 11331899
    • Wolfe KH Yesterday's polyploids and the mystery of diploidization Nat Rev Genet 2001, 2:333-341. 11331899
    • (2001) Nat Rev Genet , vol.2 , pp. 333-341
    • Wolfe, K.H.1
  • 9
    • 5044230820 scopus 로고    scopus 로고
    • Computational approaches to unveiling ancient genome duplications
    • 15510166
    • de Peer YV Computational approaches to unveiling ancient genome duplications Nat Rev Genet 2004, 5:752-763. 15510166
    • (2004) Nat Rev Genet , vol.5 , pp. 752-763
    • de Peer, Y.V.1
  • 10
    • 56549119570 scopus 로고    scopus 로고
    • Turning a hobby into a job: How duplicated genes find new functions
    • 19015656
    • Conant GC Wolfe KH Turning a hobby into a job: How duplicated genes find new functions Nat Rev Genet 2008, 9:938-950. 19015656
    • (2008) Nat Rev Genet , vol.9 , pp. 938-950
    • Conant, G.C.1    Wolfe, K.H.2
  • 12
    • 2442697672 scopus 로고    scopus 로고
    • A medaka gene map: The trace of ancestral vertebrate proto-chromosomes revealed by comparative gene mapping
    • 479108 15078856
    • Naruse K Tanaka M Mita K Shima A Postlethwait J Mitani H A medaka gene map: The trace of ancestral vertebrate proto-chromosomes revealed by comparative gene mapping Genome Res 2004, 14:820-828. 479108 15078856
    • (2004) Genome Res , vol.14 , pp. 820-828
    • Naruse, K.1    Tanaka, M.2    Mita, K.3    Shima, A.4    Postlethwait, J.5    Mitani, H.6
  • 15
    • 34548420992 scopus 로고    scopus 로고
    • Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates
    • 1950894 17652425
    • Nakatani Y Takeda H Kohara Y Morishita S Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates Genome Res 2007, 17:1254-1265. 1950894 17652425
    • (2007) Genome Res , vol.17 , pp. 1254-1265
    • Nakatani, Y.1    Takeda, H.2    Kohara, Y.3    Morishita, S.4
  • 16
    • 0030972920 scopus 로고    scopus 로고
    • Secondary tetrasomic segregation of MDH-B and preferential pairing of homeologues in rainbow trout
    • 1207878 9093860
    • Allendorf FW Danzmann RG Secondary tetrasomic segregation of MDH-B and preferential pairing of homeologues in rainbow trout Genetics 1997, 145:1083-1092. 1207878 9093860
    • (1997) Genetics , vol.145 , pp. 1083-1092
    • Allendorf, F.W.1    Danzmann, R.G.2
  • 17
    • 0002590589 scopus 로고
    • Tetraploidy and the evolution of salmonid fishes
    • New York: Plenum Press Corp. Turner JB
    • Allendorf FW Thorgaard GH Tetraploidy and the evolution of salmonid fishes Evolutionary genetics of fishes New York: Plenum Press Corp. Turner JB 1984, 1-53.
    • (1984) Evolutionary Genetics of Fishes , pp. 1-53
    • Allendorf, F.W.1    Thorgaard, G.H.2
  • 19
    • 18544392753 scopus 로고    scopus 로고
    • A microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) characterized by large sex-specific differences in recombination rates
    • 1461176 10880492
    • Sakamoto T Danzmann RG Gharbi K Howard P Ozaki A Khoo SK Woram RA Okamoto N Ferguson MM Holm LE et al A microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) characterized by large sex-specific differences in recombination rates Genetics 2000, 155:1331-1345. 1461176 10880492
    • (2000) Genetics , vol.155 , pp. 1331-1345
    • Sakamoto, T.1    Danzmann, R.G.2    Gharbi, K.3    Howard, P.4    Ozaki, A.5    Khoo, S.K.6    Woram, R.A.7    Okamoto, N.8    Ferguson, M.M.9    Holm, L.E.10
  • 21
    • 0348231044 scopus 로고    scopus 로고
    • A genetic linkage map for Arctic charr (Salvelinus alpinus): Evidence for higher recombination rates and segregation distortion in hybrid versus pure strain mapping parents
    • 15060583
    • Woram RA McGowan C Stout JA Gharbi K Ferguson MM Hoyheim B Davidson EA Davidson WS Rexroad C Danzmann RG A genetic linkage map for Arctic charr (Salvelinus alpinus): Evidence for higher recombination rates and segregation distortion in hybrid versus pure strain mapping parents Genome 2004, 47:304-315. 15060583
    • (2004) Genome , vol.47 , pp. 304-315
    • Woram, R.A.1    McGowan, C.2    Stout, J.A.3    Gharbi, K.4    Ferguson, M.M.5    Hoyheim, B.6    Davidson, E.A.7    Davidson, W.S.8    Rexroad, C.9    Danzmann, R.G.10
  • 23
    • 33646188556 scopus 로고    scopus 로고
    • A linkage map for brown trout (Salmo trutta): Chromosome homeologies and comparative genome organization with other salmonid fish
    • 1456399 16452148
    • Gharbi K Gautier A Danzmann RG Gharbi S Sakamoto T Hoyheim B Taggart JB Cairney M Powell R Krieg F et al A linkage map for brown trout (Salmo trutta): Chromosome homeologies and comparative genome organization with other salmonid fish Genetics 2006, 172:2405-2419. 1456399 16452148
    • (2006) Genetics , vol.172 , pp. 2405-2419
    • Gharbi, K.1    Gautier, A.2    Danzmann, R.G.3    Gharbi, S.4    Sakamoto, T.5    Hoyheim, B.6    Taggart, J.B.7    Cairney, M.8    Powell, R.9    Krieg, F.10
  • 24
    • 27744471365 scopus 로고    scopus 로고
    • Evidence for Hox gene duplication in rainbow trout (Oncorhynchus mykiss): A tetraploid model species
    • 16315109
    • Moghadam HK Ferguson MM Danzmann RG Evidence for Hox gene duplication in rainbow trout (Oncorhynchus mykiss): A tetraploid model species J Mol Evol 2005, 61:804-818. 16315109
    • (2005) J Mol Evol , vol.61 , pp. 804-818
    • Moghadam, H.K.1    Ferguson, M.M.2    Danzmann, R.G.3
  • 25
    • 27744588853 scopus 로고    scopus 로고
    • Evolution of Hox clusters in Salmonidae: A comparative analysis between Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss)
    • 16205980
    • Moghadam HK Ferguson MM Danzmann RG Evolution of Hox clusters in Salmonidae: A comparative analysis between Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) J Mol Evol 2005, 61:636-649. 16205980
    • (2005) J Mol Evol , vol.61 , pp. 636-649
    • Moghadam, H.K.1    Ferguson, M.M.2    Danzmann, R.G.3
  • 26
    • 32244432718 scopus 로고    scopus 로고
    • A comparative analysis of the rainbow trout genome with 2 other species of fish (Arctic charr and Atlantic salmon) within the tetraploid derivative Salmonidae family (subfamily: Salmoninae)
    • 16391673
    • Danzmann RG Cairney M Davidson WS Ferguson MM Gharbi K Guyomard R Holm LE Leder E Okamoto N Ozaki A et al A comparative analysis of the rainbow trout genome with 2 other species of fish (Arctic charr and Atlantic salmon) within the tetraploid derivative Salmonidae family (subfamily: Salmoninae) Genome 2005, 48:1037-1051. 16391673
    • (2005) Genome , vol.48 , pp. 1037-1051
    • Danzmann, R.G.1    Cairney, M.2    Davidson, W.S.3    Ferguson, M.M.4    Gharbi, K.5    Guyomard, R.6    Holm, L.E.7    Leder, E.8    Okamoto, N.9    Ozaki, A.10
  • 29
    • 33645519275 scopus 로고    scopus 로고
    • Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis
    • 1457030 16533910
    • McEwen GK Woolfe A Goode D Vavouri T Callaway H Elgar G Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis Genome Res 2006, 16:451-465. 1457030 16533910
    • (2006) Genome Res , vol.16 , pp. 451-465
    • McEwen, G.K.1    Woolfe, A.2    Goode, D.3    Vavouri, T.4    Callaway, H.5    Elgar, G.6
  • 31
    • 38949097100 scopus 로고    scopus 로고
    • Large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock
    • 18056681
    • Stephen S Pheasant M Makunin IV Mattick JS Large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock Mol Biol Evol 2008, 25:402-408. 18056681
    • (2008) Mol Biol Evol , vol.25 , pp. 402-408
    • Stephen, S.1    Pheasant, M.2    Makunin, I.V.3    Mattick, J.S.4
  • 33
    • 58649118651 scopus 로고    scopus 로고
    • Rapidly evolving fish genomes and teleost diversity
    • 19095434
    • Ravi V Venkatesh B Rapidly evolving fish genomes and teleost diversity Curr Opin Genet Dev 2008, 18:544-550. 19095434
    • (2008) Curr Opin Genet Dev , vol.18 , pp. 544-550
    • Ravi, V.1    Venkatesh, B.2
  • 35
    • 39049141215 scopus 로고    scopus 로고
    • Chapter 12: Organization of conserved elements near key developmental regulators in vertebrate genomes
    • 18282512
    • Woolfe A Elgar G Chapter 12: Organization of conserved elements near key developmental regulators in vertebrate genomes Adv Genet 2008, 61:307-338. 18282512
    • (2008) Adv Genet , vol.61 , pp. 307-338
    • Woolfe, A.1    Elgar, G.2
  • 37
    • 13144295005 scopus 로고    scopus 로고
    • Conserved non-genic sequences - An unexpected feature of mammalian genomes
    • 15716910
    • Dermitzakis ET Reymond A Antonarakis SE Conserved non-genic sequences - an unexpected feature of mammalian genomes Nat Rev Genet 2005, 6:151-157. 15716910
    • (2005) Nat Rev Genet , vol.6 , pp. 151-157
    • Dermitzakis, E.T.1    Reymond, A.2    Antonarakis, S.E.3
  • 41
    • 7244259100 scopus 로고    scopus 로고
    • Megabase deletions of gene deserts result in viable mice
    • 15496924
    • Nobrega MA Zhu Y Plajzer-Frick I Afzal V Rubin EM Megabase deletions of gene deserts result in viable mice Nature 2004, 431:988-993. 15496924
    • (2004) Nature , vol.431 , pp. 988-993
    • Nobrega, M.A.1    Zhu, Y.2    Plajzer-Frick, I.3    Afzal, V.4    Rubin, E.M.5
  • 43
    • 45449096267 scopus 로고    scopus 로고
    • Tuning in to the signals: Noncoding sequence conservation in vertebrate genomes
    • 18514361
    • Elgar G Vavouri T Tuning in to the signals: Noncoding sequence conservation in vertebrate genomes Trends Genet 2008, 24:344-352. 18514361
    • (2008) Trends Genet , vol.24 , pp. 344-352
    • Elgar, G.1    Vavouri, T.2
  • 44
  • 46
    • 67650745549 scopus 로고    scopus 로고
    • ENSEMBL
    • ENSEMBL http://www.ensembl.org
  • 48
    • 34748817478 scopus 로고    scopus 로고
    • Genomic organization of the igf1, igf2, myf5, myf6 and grf/pacap genes across Salmoninae genera
    • 17894566
    • Moghadam HK Ferguson MM Rexroad CE 3rd Coulibaly I Danzmann RG Genomic organization of the igf1, igf2, myf5, myf6 and grf/pacap genes across Salmoninae genera Anim Genet 2007, 38:527-532. 17894566
    • (2007) Anim Genet , vol.38 , pp. 527-532
    • Moghadam, H.K.1    Ferguson, M.M.2    Rexroad III, C.E.3    Coulibaly, I.4    Danzmann, R.G.5
  • 49
    • 33845710168 scopus 로고    scopus 로고
    • A type I and type II microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) with presumptive coverage of all chromosome arms
    • 1698487 17137492
    • Guyomard R Mauger S Tabet-Canale K Martineau S Genet C Krieg F Quillet E A type I and type II microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) with presumptive coverage of all chromosome arms BMC Genomics 2006, 7:302. 1698487 17137492
    • (2006) BMC Genomics , vol.7 , pp. 302
    • Guyomard, R.1    Mauger, S.2    Tabet-Canale, K.3    Martineau, S.4    Genet, C.5    Krieg, F.6    Quillet, E.7
  • 50
    • 33749000852 scopus 로고    scopus 로고
    • Conserved distances between vertebrate highly conserved elements
    • 16923797
    • Sun H Skogerbo G Chen R Conserved distances between vertebrate highly conserved elements Hum Mol Genet 2006, 15:2911-2922. 16923797
    • (2006) Hum Mol Genet , vol.15 , pp. 2911-2922
    • Sun, H.1    Skogerbo, G.2    Chen, R.3
  • 51
    • 33745591114 scopus 로고    scopus 로고
    • Genetic evidence for complex speciation of humans and chimpanzees
    • 16710306
    • Patterson N Richter DJ Gnerre S Lander ES Reich D Genetic evidence for complex speciation of humans and chimpanzees Nature 2006, 441:1103-1108. 16710306
    • (2006) Nature , vol.441 , pp. 1103-1108
    • Patterson, N.1    Richter, D.J.2    Gnerre, S.3    Lander, E.S.4    Reich, D.5
  • 53
    • 0035096956 scopus 로고    scopus 로고
    • Chromosome evolution in the Salmonidae (Pisces): An update
    • 11325050
    • Phillips R Ráb P Chromosome evolution in the Salmonidae (Pisces): An update Biol Rev Camb Philos Soc 2001, 76:1-25. 11325050
    • (2001) Biol Rev Camb Philos Soc , vol.76 , pp. 1-25
    • Phillips, R.1    Ráb, P.2
  • 56
    • 67650751729 scopus 로고
    • Cary, North Carolina: SAS Institute
    • SAS Cary, North Carolina: SAS Institute 1990
    • (1990)
  • 58
    • 67650718336 scopus 로고    scopus 로고
    • Primer3 http://frodo.wi.mit.edu/
    • Primer3
  • 59
    • 84986500438 scopus 로고
    • A simplified protocol for routine total DNA isolation from salmonid fishes
    • Taggart JB Hynes RA Prodohl PA Ferguson A A simplified protocol for routine total DNA isolation from salmonid fishes J Fish Biol 1992, 40:963-965.
    • (1992) J Fish Biol , vol.40 , pp. 963-965
    • Taggart, J.B.1    Hynes, R.A.2    Prodohl, P.A.3    Ferguson, A.4
  • 60
    • 0031890821 scopus 로고    scopus 로고
    • Identification of two QTL influencing upper temperature tolerance in three rainbow trout (Oncorhynchus mykiss) half-sib families
    • Jackson TR Ferguson MM Danzmann RG Fishback AG Ihssen PE O'Connell M Crease TJ Identification of two QTL influencing upper temperature tolerance in three rainbow trout (Oncorhynchus mykiss) half-sib families Heredity 1998, 80:143-151.
    • (1998) Heredity , vol.80 , pp. 143-151
    • Jackson, T.R.1    Ferguson, M.M.2    Danzmann, R.G.3    Fishback, A.G.4    Ihssen, P.E.5    O'Connell, M.6    Crease, T.J.7
  • 61
    • 0024595101 scopus 로고
    • Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms
    • 286999 2565038
    • Orita M Iwahana H Kanazawa H Hayashi K Sekiya T Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms Proc Natl Acad Sci USA 1989, 86:2766-2770. 286999 2565038
    • (1989) Proc Natl Acad Sci USA , vol.86 , pp. 2766-2770
    • Orita, M.1    Iwahana, H.2    Kanazawa, H.3    Hayashi, K.4    Sekiya, T.5
  • 62
    • 0027233353 scopus 로고
    • Screening for molecular pathologies in Lesch-Nyhan syndrome
    • 8318989
    • Boyd M Lanyon WG Connor JM Screening for molecular pathologies in Lesch-Nyhan syndrome Hum Mutat 1993, 2:127-130. 8318989
    • (1993) Hum Mutat , vol.2 , pp. 127-130
    • Boyd, M.1    Lanyon, W.G.2    Connor, J.M.3
  • 63
    • 0027433113 scopus 로고
    • Conformation-sensitive gel electrophoresis for rapid detection of single-base differences in double-stranded PCR products and DNA fragments: Evidence for solvent-induced bends in DNA heteroduplexes
    • 47767 8234293
    • Ganguly A Rock M Prockop D Conformation-sensitive gel electrophoresis for rapid detection of single-base differences in double-stranded PCR products and DNA fragments: Evidence for solvent-induced bends in DNA heteroduplexes Proc Natl Acad Sci USA 1993, 90:10325-10329. 47767 8234293
    • (1993) Proc Natl Acad Sci USA , vol.90 , pp. 10325-10329
    • Ganguly, A.1    Rock, M.2    Prockop, D.3
  • 64
    • 3142665525 scopus 로고    scopus 로고
    • GOstat: Find statistically overrepresented Gene Ontologies within a group of genes
    • 14962934
    • Beissbarth T Speed TP GOstat: Find statistically overrepresented Gene Ontologies within a group of genes Bioinformatics 2004, 20:1464-1465. 14962934
    • (2004) Bioinformatics , vol.20 , pp. 1464-1465
    • Beissbarth, T.1    Speed, T.P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.