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Volumn 483, Issue 1-2, 2011, Pages 63-71

Genome structure analysis of molluscs revealed whole genome duplication and lineage specific repeat variation

Author keywords

Cephalopods; Genome components; Genome duplication; Next generation sequencing; Repetitive elements

Indexed keywords

DNA;

EID: 79960230372     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2011.05.027     Document Type: Article
Times cited : (38)

References (50)
  • 1
    • 77952533015 scopus 로고    scopus 로고
    • Characterization of a novel SINE superfamily from invertebrates: "Ceph-SINEs" from the genomes of squids and cuttlefish
    • Akasaki T., Nikaido M., Nishihara H., Tsuchiya K., Segawa S., Okada N. Characterization of a novel SINE superfamily from invertebrates: "Ceph-SINEs" from the genomes of squids and cuttlefish. Gene 2010, 454:8-19.
    • (2010) Gene , vol.454 , pp. 8-19
    • Akasaki, T.1    Nikaido, M.2    Nishihara, H.3    Tsuchiya, K.4    Segawa, S.5    Okada, N.6
  • 2
    • 0028685490 scopus 로고
    • Fitting a mixture model by expectation maximization to discover motifs in biopolymers
    • Bailey T.L., Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 1994, 2:28-36.
    • (1994) Proc. Int. Conf. Intell. Syst. Mol. Biol. , vol.2 , pp. 28-36
    • Bailey, T.L.1    Elkan, C.2
  • 3
    • 0034831138 scopus 로고    scopus 로고
    • Segmental duplications: organization and impact within the current human genome project assembly
    • Bailey J.A., Yavor A.M., Massa H.F., Trask B.J., Eichler E.E. Segmental duplications: organization and impact within the current human genome project assembly. Genome Res. 2001, 11:1005-1017.
    • (2001) Genome Res. , vol.11 , pp. 1005-1017
    • Bailey, J.A.1    Yavor, A.M.2    Massa, H.F.3    Trask, B.J.4    Eichler, E.E.5
  • 4
    • 33644927549 scopus 로고    scopus 로고
    • The hemocyanin from a living fossil, the cephalopod Nautilus pompilius: protein structure, gene organization, and evolution
    • Bergmann S., Lieb B., Ruth P., Markl J. The hemocyanin from a living fossil, the cephalopod Nautilus pompilius: protein structure, gene organization, and evolution. J. Mol. Evol. 2006, 62:362-374.
    • (2006) J. Mol. Evol. , vol.62 , pp. 362-374
    • Bergmann, S.1    Lieb, B.2    Ruth, P.3    Markl, J.4
  • 5
    • 3142700743 scopus 로고    scopus 로고
    • Widespread paleopolyploidy in model plant species inferred from age distributions of duplicated genes
    • Blanc G., Wolfe K.H. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicated genes. Plant Cell 2004, 16:1667-1678.
    • (2004) Plant Cell , vol.16 , pp. 1667-1678
    • Blanc, G.1    Wolfe, K.H.2
  • 6
    • 1342287785 scopus 로고    scopus 로고
    • A molecular and karyological approach to the taxonomy of Nautilus
    • Bonnaud L., Ozouf-Costaz C., Boucher-Rodini R. A molecular and karyological approach to the taxonomy of Nautilus. CR Biol. 2004, 327:133-138.
    • (2004) CR Biol. , vol.327 , pp. 133-138
    • Bonnaud, L.1    Ozouf-Costaz, C.2    Boucher-Rodini, R.3
  • 7
    • 3042615882 scopus 로고    scopus 로고
    • Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs
    • Chevreux B., Pfisterer T., Drescher B., Driesel A.J., Muller W.E., Wetter T., Suhai S. Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res. 2004, 14:1147-1159.
    • (2004) Genome Res. , vol.14 , pp. 1147-1159
    • Chevreux, B.1    Pfisterer, T.2    Drescher, B.3    Driesel, A.J.4    Muller, W.E.5    Wetter, T.6    Suhai, S.7
  • 8
    • 0036569564 scopus 로고    scopus 로고
    • Flow cytometry measurement of the DNA contents of G0/G1 diploid cells from three different teleost fish species
    • Ciudad J., Cid E., Velasco A., Lara J.M., Aijón J., Orfao A. Flow cytometry measurement of the DNA contents of G0/G1 diploid cells from three different teleost fish species. Cytometry 2002, 48:20-25.
    • (2002) Cytometry , vol.48 , pp. 20-25
    • Ciudad, J.1    Cid, E.2    Velasco, A.3    Lara, J.M.4    Aijón, J.5    Orfao, A.6
  • 9
    • 0017085802 scopus 로고
    • A colony bank containing synthetic Col El hybrid plasmids representative of the entire E. coli genome
    • Clarke L., Carbon J. A colony bank containing synthetic Col El hybrid plasmids representative of the entire E. coli genome. Cell 1976, 9:91-99.
    • (1976) Cell , vol.9 , pp. 91-99
    • Clarke, L.1    Carbon, J.2
  • 10
    • 70349318211 scopus 로고    scopus 로고
    • The impact of retrotransposons on human genome evolution
    • Cordeaux R., Batzer M.A. The impact of retrotransposons on human genome evolution. Nat. Rev. Genet. 2009, 10:691-703.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 691-703
    • Cordeaux, R.1    Batzer, M.A.2
  • 11
    • 77958600477 scopus 로고    scopus 로고
    • Cost-effective, species-specific microsatellite development for the endangered Dwarf Bulrush (Typha minima) using next-generation sequencing technology
    • Csencsics D., Brodbeck S., Holderegger R. Cost-effective, species-specific microsatellite development for the endangered Dwarf Bulrush (Typha minima) using next-generation sequencing technology. J. Hered. 2010, 101:789-793.
    • (2010) J. Hered. , vol.101 , pp. 789-793
    • Csencsics, D.1    Brodbeck, S.2    Holderegger, R.3
  • 13
    • 0043209733 scopus 로고    scopus 로고
    • Telomeres in the chicken: genome stability and chromosome ends
    • Delany M.E., Daniels L.M., Swanberg S.E., Taylor H.A. Telomeres in the chicken: genome stability and chromosome ends. Poult. Sci. 2003, 82:917-926.
    • (2003) Poult. Sci. , vol.82 , pp. 917-926
    • Delany, M.E.1    Daniels, L.M.2    Swanberg, S.E.3    Taylor, H.A.4
  • 14
    • 37549029474 scopus 로고    scopus 로고
    • DNA transposons and the evolution of eukaryotic genomes
    • Feschotte C., Pritham E.J. DNA transposons and the evolution of eukaryotic genomes. Annu. Rev. Genet. 2007, 41:331-368.
    • (2007) Annu. Rev. Genet. , vol.41 , pp. 331-368
    • Feschotte, C.1    Pritham, E.J.2
  • 16
    • 34948898172 scopus 로고    scopus 로고
    • A model of segmental duplication formation in Drosophila melanogaster
    • Fiston-Lavier A.S., Anxolabehere D., Quesneville H. A model of segmental duplication formation in Drosophila melanogaster. Genome Res. 2007, 17:1458-1470.
    • (2007) Genome Res. , vol.17 , pp. 1458-1470
    • Fiston-Lavier, A.S.1    Anxolabehere, D.2    Quesneville, H.3
  • 17
    • 0028168856 scopus 로고
    • A codon-based model of nucleotide substitution for protein-coding DNA sequences
    • Goldman N., Yang Z. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 1994, 11:725-736.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 725-736
    • Goldman, N.1    Yang, Z.2
  • 19
    • 3242738257 scopus 로고    scopus 로고
    • Lineage-specific expansion of KRAB zinc-finger transcription factor genes: implications for the evolution of vertebrate regulatory networks
    • Hamilton A.T., Huntley S., Kim J., Branscomb E., Stubbs L. Lineage-specific expansion of KRAB zinc-finger transcription factor genes: implications for the evolution of vertebrate regulatory networks. Cold Spring Harb. Symp. Quant. Biol. 2003, 68:131-140.
    • (2003) Cold Spring Harb. Symp. Quant. Biol. , vol.68 , pp. 131-140
    • Hamilton, A.T.1    Huntley, S.2    Kim, J.3    Branscomb, E.4    Stubbs, L.5
  • 23
    • 1542513556 scopus 로고    scopus 로고
    • Mobile elements: drivers of genome evolution
    • Kazazian H.H. Mobile elements: drivers of genome evolution. Science 2004, 303:1626-1632.
    • (2004) Science , vol.303 , pp. 1626-1632
    • Kazazian, H.H.1
  • 24
    • 33750831582 scopus 로고    scopus 로고
    • Annotation, submission and screening of repetitive elements in Repbase: Repbase Submitter and Censor
    • Kohany O., Gentles A.J., Hankus L., Jurka J. Annotation, submission and screening of repetitive elements in Repbase: Repbase Submitter and Censor. BMC Bioinforma. 2006, 7:474.
    • (2006) BMC Bioinforma. , vol.7 , pp. 474
    • Kohany, O.1    Gentles, A.J.2    Hankus, L.3    Jurka, J.4
  • 26
    • 56549086632 scopus 로고    scopus 로고
    • A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes
    • Kurtz S., Narechania A., Stein J., Ware D. A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics 2008, 9:517.
    • (2008) BMC Genomics , vol.9 , pp. 517
    • Kurtz, S.1    Narechania, A.2    Stein, J.3    Ware, D.4
  • 27
    • 0023988195 scopus 로고
    • Genomic mapping by fingerprinting random clones: a mathematical analysis
    • Lander E.S., Waterman M.S. Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics 1988, 2:231-239.
    • (1988) Genomics , vol.2 , pp. 231-239
    • Lander, E.S.1    Waterman, M.S.2
  • 28
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • Lander E.S., et al. Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
    • (2001) Nature , vol.409 , pp. 860-921
    • Lander, E.S.1
  • 30
    • 0027261149 scopus 로고
    • Mapping simple repeated DNA sequences in heterochromatin of Drosophila melanogaster
    • Lohe A.R., Hilliker A.J., Roberts P.A. Mapping simple repeated DNA sequences in heterochromatin of Drosophila melanogaster. Genetics 1993, 134:1149-1174.
    • (1993) Genetics , vol.134 , pp. 1149-1174
    • Lohe, A.R.1    Hilliker, A.J.2    Roberts, P.A.3
  • 31
    • 0031754413 scopus 로고    scopus 로고
    • Pathological consequences of sequence duplications in the human genome
    • Mazzarella R., Schlessinger D. Pathological consequences of sequence duplications in the human genome. Genome Res. 1998, 8:1007-1021.
    • (1998) Genome Res. , vol.8 , pp. 1007-1021
    • Mazzarella, R.1    Schlessinger, D.2
  • 32
    • 0000263297 scopus 로고
    • BAR DUPLICATION
    • Muller H.J. BAR DUPLICATION. Science 1936, 83:528-530.
    • (1936) Science , vol.83 , pp. 528-530
    • Muller, H.J.1
  • 34
    • 0034500239 scopus 로고    scopus 로고
    • Polyploid incidence and evolution
    • Otto S.P., Whitton J. Polyploid incidence and evolution. Annu. Rev. Genet. 2000, 34:401-437.
    • (2000) Annu. Rev. Genet. , vol.34 , pp. 401-437
    • Otto, S.P.1    Whitton, J.2
  • 35
    • 0014807030 scopus 로고
    • Relative growth, nucleic acid content and cell numbers of the brain in Octopus vulgaris (Lamarck)
    • Packard A., Albergoni V. Relative growth, nucleic acid content and cell numbers of the brain in Octopus vulgaris (Lamarck). J. Exp. Biol. 1970, 52:539-552.
    • (1970) J. Exp. Biol. , vol.52 , pp. 539-552
    • Packard, A.1    Albergoni, V.2
  • 37
    • 77958609381 scopus 로고    scopus 로고
    • When technology meets conservation: increased microsatellite marker production using 454 genome sequencing on the endangered Okaloosa Darter (Etheostoma okaloosae)
    • Saarinen E.V., Austin J.D. When technology meets conservation: increased microsatellite marker production using 454 genome sequencing on the endangered Okaloosa Darter (Etheostoma okaloosae). J. Hered. 2010, 101:784-788.
    • (2010) J. Hered. , vol.101 , pp. 784-788
    • Saarinen, E.V.1    Austin, J.D.2
  • 38
    • 77955505201 scopus 로고    scopus 로고
    • Dating and functional characterization of duplicated genes in the apple (Malus domestica Borkh.) by analyzing EST data
    • Sanzol J. Dating and functional characterization of duplicated genes in the apple (Malus domestica Borkh.) by analyzing EST data. BMC Plant Biol. 2010, 10:87.
    • (2010) BMC Plant Biol. , vol.10 , pp. 87
    • Sanzol, J.1
  • 39
    • 77952690602 scopus 로고    scopus 로고
    • Utility of sequenced genomes for microsatellite marker development in non-model organisms: a case study of functionally important genes in nine-spined sticklebacks (Pungitius pungitius)
    • Shikano T., Ramadevi J., Shimada Y., Merilä J. Utility of sequenced genomes for microsatellite marker development in non-model organisms: a case study of functionally important genes in nine-spined sticklebacks (Pungitius pungitius). BMC Genomics 2010, 11:334.
    • (2010) BMC Genomics , vol.11 , pp. 334
    • Shikano, T.1    Ramadevi, J.2    Shimada, Y.3    Merilä, J.4
  • 40
    • 34548774532 scopus 로고    scopus 로고
    • Deep molluscan phylogeny: synthesis of palaeontological and neontological data
    • Sigwart J.D., Sutton M.D. Deep molluscan phylogeny: synthesis of palaeontological and neontological data. Proc. Biol. Sci. 2007, 274:2413-2419.
    • (2007) Proc. Biol. Sci. , vol.274 , pp. 2413-2419
    • Sigwart, J.D.1    Sutton, M.D.2
  • 41
    • 33947303168 scopus 로고    scopus 로고
    • Transposable elements and the epigenetic regulation of the genome
    • Slotkin R.K., Martienssen R. Transposable elements and the epigenetic regulation of the genome. Nat. Rev. Genet. 2007, 8:272-285.
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 272-285
    • Slotkin, R.K.1    Martienssen, R.2
  • 42
    • 34250789278 scopus 로고    scopus 로고
    • Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey
    • Swaminathan K., Varala K., Hudson M.E. Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey. BMC Genomics 2007, 8:132.
    • (2007) BMC Genomics , vol.8 , pp. 132
    • Swaminathan, K.1    Varala, K.2    Hudson, M.E.3
  • 43
    • 0036100845 scopus 로고    scopus 로고
    • Zinc finger gene clusters and tandem gene duplication
    • Tang M., Waterman M., Yooseph S. Zinc finger gene clusters and tandem gene duplication. J. Comput. Biol. 2002, 9:429-446.
    • (2002) J. Comput. Biol. , vol.9 , pp. 429-446
    • Tang, M.1    Waterman, M.2    Yooseph, S.3
  • 44
  • 45
    • 0036907035 scopus 로고    scopus 로고
    • Generalized gap model for bacterial artificial chromosome clone fingerprint mapping and shotgun sequencing
    • Wendl M.C., Waterston R.H. Generalized gap model for bacterial artificial chromosome clone fingerprint mapping and shotgun sequencing. Genome Res. 2002, 12:1943-1949.
    • (2002) Genome Res. , vol.12 , pp. 1943-1949
    • Wendl, M.C.1    Waterston, R.H.2
  • 46
    • 41049088756 scopus 로고    scopus 로고
    • Eukaryotic transposable elements: teaching old genomes newtricks
    • Oxford University Press, NewYork, L. Caporale (Ed.)
    • Wessler S.R. Eukaryotic transposable elements: teaching old genomes newtricks. The Implicit Genome 2006, 138-165. Oxford University Press, NewYork. L. Caporale (Ed.).
    • (2006) The Implicit Genome , pp. 138-165
    • Wessler, S.R.1
  • 47
    • 0345731466 scopus 로고    scopus 로고
    • Enrichment of gene-coding sequences in maize by genome filtration
    • Whitelaw C.A., et al. Enrichment of gene-coding sequences in maize by genome filtration. Science 2003, 302:2118-2120.
    • (2003) Science , vol.302 , pp. 2118-2120
    • Whitelaw, C.A.1
  • 48
    • 79952425617 scopus 로고    scopus 로고
    • A novel abundance-based algorithm for binning metagenomic sequences using l-tuples
    • Wu Y.W., Ye Y. A novel abundance-based algorithm for binning metagenomic sequences using l-tuples. J. Comput. Biol. 2011, 18:523-534.
    • (2011) J. Comput. Biol. , vol.18 , pp. 523-534
    • Wu, Y.W.1    Ye, Y.2
  • 49
    • 0001461778 scopus 로고
    • Normal embryonic stages of the pygmy cuttlefish, Idiosepius pygmaeus paradoxus Ortmann
    • Yamamoto M. Normal embryonic stages of the pygmy cuttlefish, Idiosepius pygmaeus paradoxus Ortmann. Zool. Sci. 1988, 5:989-999.
    • (1988) Zool. Sci. , vol.5 , pp. 989-999
    • Yamamoto, M.1
  • 50
    • 35349006401 scopus 로고    scopus 로고
    • Fosmid library construction and initial analysis of end sequences in Zhikong scallop (Chlamys farreri)
    • Zhang L., Bao Z., Cheng J., Li H., Huang X., Wang S., Zhang C., Hu J. Fosmid library construction and initial analysis of end sequences in Zhikong scallop (Chlamys farreri). Mar. Biotechnol. (NY) 2007, 9:606-612.
    • (2007) Mar. Biotechnol. (NY) , vol.9 , pp. 606-612
    • Zhang, L.1    Bao, Z.2    Cheng, J.3    Li, H.4    Huang, X.5    Wang, S.6    Zhang, C.7    Hu, J.8


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.