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Volumn 6, Issue 7, 2011, Pages

Evolutionary patterns of RNA-based duplication in non-mammalian chordates

Author keywords

[No Author keywords available]

Indexed keywords

AGE DISTRIBUTION; ANOLIS CAROLINENSIS; ARTICLE; ASCIDIACEA; BRANCHIOSTOMA FLORIDAE; CHIMERA; CHORDATA; CIONA INTESTINALIS; CONTROLLED STUDY; GALLUS GALLUS; GASTEROSTEUS ACULEATUS; GENE DOSAGE; GENE DUPLICATION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE LOCATION; GENETIC SCREENING; GENETIC SELECTION; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN; HUMAN VERSUS ANIMAL COMPARISON; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; ORNITHORHYNCHUS ANATINUS; ORYZIAS; SPECIES COMPARISON; TAKIFUGU RUBRIPES; TETRAODON NIGROVIRIDIS; XENOPUS TROPICALIS; ZEBRA FISH; ANIMAL; CLASSIFICATION; GENETICS; GENOME; PHYLOGENY;

EID: 79960136837     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0021466     Document Type: Article
Times cited : (12)

References (52)
  • 2
  • 3
    • 1642475221 scopus 로고    scopus 로고
    • Extensive gene traffic on the mammalian X chromosome
    • Emerson JJ, Kaessmann H, Betran E, Long MY, (2004) Extensive gene traffic on the mammalian X chromosome. Science 303: 537-540.
    • (2004) Science , vol.303 , pp. 537-540
    • Emerson, J.J.1    Kaessmann, H.2    Betran, E.3    Long, M.Y.4
  • 4
    • 43249118306 scopus 로고    scopus 로고
    • Chromosomal gene movements reflect the recent origin and biology of therian sex chromosomes
    • Potrzebowski L, Vinckenbosch N, Marques AC, Chalmel F, Jegou B, et al. (2008) Chromosomal gene movements reflect the recent origin and biology of therian sex chromosomes. PLoS Biol 6: e80.
    • (2008) PLoS Biol , vol.6
    • Potrzebowski, L.1    Vinckenbosch, N.2    Marques, A.C.3    Chalmel, F.4    Jegou, B.5
  • 5
    • 0025864962 scopus 로고
    • Retroposons-seeds of evolution
    • Brosius J, (1991) Retroposons-seeds of evolution. Science 251: 753.
    • (1991) Science , vol.251 , pp. 753
    • Brosius, J.1
  • 7
  • 8
    • 0346752110 scopus 로고    scopus 로고
    • Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome
    • Zhang Z, Harrison PM, Liu Y, Gerstein M, (2003) Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res 13: 2541-2558.
    • (2003) Genome Res , vol.13 , pp. 2541-2558
    • Zhang, Z.1    Harrison, P.M.2    Liu, Y.3    Gerstein, M.4
  • 9
    • 13144282699 scopus 로고    scopus 로고
    • Sex chromosomes and male functions: where do new genes go?
    • Betran E, Emerson JJ, Kaessmann H, Long M, (2004) Sex chromosomes and male functions: where do new genes go? Cell Cycle 3: 873-875.
    • (2004) Cell Cycle , vol.3 , pp. 873-875
    • Betran, E.1    Emerson, J.J.2    Kaessmann, H.3    Long, M.4
  • 10
    • 33747465505 scopus 로고    scopus 로고
    • High rate of chimeric gene origination by retroposition in plant genomes
    • Wang W, Zheng H, Fan C, Li J, Shi J, et al. (2006) High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell 18: 1791-1802.
    • (2006) Plant Cell , vol.18 , pp. 1791-1802
    • Wang, W.1    Zheng, H.2    Fan, C.3    Li, J.4    Shi, J.5
  • 11
    • 10644283823 scopus 로고    scopus 로고
    • Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
    • Hillier LW, Miller W, Birney E, Warren W, Hardison RC, et al. (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716.
    • (2004) Nature , vol.432 , pp. 695-716
    • Hillier, L.W.1    Miller, W.2    Birney, E.3    Warren, W.4    Hardison, R.C.5
  • 12
    • 0030845714 scopus 로고    scopus 로고
    • Chicken repeat 1 (CR1) elements, which define an ancient family of vertebrate non-LTR retrotransposons, contain two closely spaced open reading frames
    • Haas NB, Grabowski JM, Sivitz AB, Burch JB, (1997) Chicken repeat 1 (CR1) elements, which define an ancient family of vertebrate non-LTR retrotransposons, contain two closely spaced open reading frames. Gene 197: 305-309.
    • (1997) Gene , vol.197 , pp. 305-309
    • Haas, N.B.1    Grabowski, J.M.2    Sivitz, A.B.3    Burch, J.B.4
  • 13
    • 0035819894 scopus 로고    scopus 로고
    • Subfamilies of CR1 non-LTR retrotransposons have different 5′UTR sequences but are otherwise conserved
    • Haas NB, Grabowski JM, North J, Moran JV, Kazazian HH, et al. (2001) Subfamilies of CR1 non-LTR retrotransposons have different 5′UTR sequences but are otherwise conserved. Gene 265: 175-183.
    • (2001) Gene , vol.265 , pp. 175-183
    • Haas, N.B.1    Grabowski, J.M.2    North, J.3    Moran, J.V.4    Kazazian, H.H.5
  • 14
    • 57749177443 scopus 로고    scopus 로고
    • RNA-based gene duplication: mechanistic and evolutionary insights
    • Kaessmann H, Vinckenbosch N, Long M, (2009) RNA-based gene duplication: mechanistic and evolutionary insights. Nat Rev Genet 10: 19-31.
    • (2009) Nat Rev Genet , vol.10 , pp. 19-31
    • Kaessmann, H.1    Vinckenbosch, N.2    Long, M.3
  • 15
    • 0036906987 scopus 로고    scopus 로고
    • Retroposed new genes out of the X in Drosophila
    • Betran E, Thornton K, Long M, (2002) Retroposed new genes out of the X in Drosophila. Genome Res 12: 1854-1859.
    • (2002) Genome Res , vol.12 , pp. 1854-1859
    • Betran, E.1    Thornton, K.2    Long, M.3
  • 16
    • 34247387864 scopus 로고    scopus 로고
    • Retrogene movement within- and between-chromosomes in the evolution of Drosophila genomes
    • Dai H, Yoshimatsu TF, Long M, (2006) Retrogene movement within- and between-chromosomes in the evolution of Drosophila genomes. Gene 385: 96-102.
    • (2006) Gene , vol.385 , pp. 96-102
    • Dai, H.1    Yoshimatsu, T.F.2    Long, M.3
  • 17
    • 34147128526 scopus 로고    scopus 로고
    • Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila
    • Bai Y, Casola C, Feschotte C, Betran E, (2007) Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila. Genome Biol 8: R11.
    • (2007) Genome Biol , vol.8
    • Bai, Y.1    Casola, C.2    Feschotte, C.3    Betran, E.4
  • 18
    • 0027905006 scopus 로고
    • Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila
    • Long M, Langley CH, (1993) Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science 260: 91-95.
    • (1993) Science , vol.260 , pp. 91-95
    • Long, M.1    Langley, C.H.2
  • 19
    • 33244496489 scopus 로고    scopus 로고
    • Evolution and development of the chordates: collagen and pharyngeal cartilage
    • Rychel AL, Smith SE, Shimamoto HT, Swalla BJ, (2006) Evolution and development of the chordates: collagen and pharyngeal cartilage. Mol Biol Evol 23: 541-549.
    • (2006) Mol Biol Evol , vol.23 , pp. 541-549
    • Rychel, A.L.1    Smith, S.E.2    Shimamoto, H.T.3    Swalla, B.J.4
  • 20
    • 78549247150 scopus 로고    scopus 로고
    • The rapid generation of chimerical genes expanding protein diversity in zebrafish
    • Fu B, Chen M, Zou M, Long M, He S, (2010) The rapid generation of chimerical genes expanding protein diversity in zebrafish. BMC Genomics 11: 657.
    • (2010) BMC Genomics , vol.11 , pp. 657
    • Fu, B.1    Chen, M.2    Zou, M.3    Long, M.4    He, S.5
  • 21
    • 0001109687 scopus 로고
    • On the Inheritance of Color in a Fresh-Water Fish, APLOCHEILUS LATIPES Temmick and Schlegel, with Special Reference to Sex-Linked Inheritance
    • 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: 554-573.
    • (1921) Genetics , vol.6 , pp. 554-573
    • Aida, T.1
  • 22
    • 0037198690 scopus 로고    scopus 로고
    • DMY is a Y-specific DM-domain gene required for male development in the medaka fish
    • 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: 559-563.
    • (2002) Nature , vol.417 , pp. 559-563
    • Matsuda, M.1    Nagahama, Y.2    Shinomiya, A.3    Sato, T.4    Matsuda, C.5
  • 23
    • 0025906872 scopus 로고
    • The evolution of sex chromosomes
    • Charlesworth B, (1991) The evolution of sex chromosomes. Science 251: 1030-1033.
    • (1991) Science , vol.251 , pp. 1030-1033
    • Charlesworth, B.1
  • 24
    • 0036897666 scopus 로고    scopus 로고
    • Slow molecular clocks in Old World monkeys, apes, and humans
    • Yi S, Ellsworth DL, Li WH, (2002) Slow molecular clocks in Old World monkeys, apes, and humans. Mol Biol Evol 19: 2191-2198.
    • (2002) Mol Biol Evol , vol.19 , pp. 2191-2198
    • Yi, S.1    Ellsworth, D.L.2    Li, W.H.3
  • 25
    • 4344713315 scopus 로고    scopus 로고
    • A mitochondrial DNA phylogeny of African clawed frogs: phylogeography and implications for polyploid evolution
    • Evans BJ, Kelley DB, Tinsley RC, Melnick DJ, Cannatella DC, (2004) A mitochondrial DNA phylogeny of African clawed frogs: phylogeography and implications for polyploid evolution. Mol Phylogenet Evol 33: 197-213.
    • (2004) Mol Phylogenet Evol , vol.33 , pp. 197-213
    • Evans, B.J.1    Kelley, D.B.2    Tinsley, R.C.3    Melnick, D.J.4    Cannatella, D.C.5
  • 26
    • 33744807179 scopus 로고    scopus 로고
    • Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling
    • Morin RD, Chang E, Petrescu A, Liao N, Griffith M, et al. (2006) Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling. Genome Res 16: 796-803.
    • (2006) Genome Res , vol.16 , pp. 796-803
    • Morin, R.D.1    Chang, E.2    Petrescu, A.3    Liao, N.4    Griffith, M.5
  • 27
    • 0037103251 scopus 로고    scopus 로고
    • A novel functional class I lineage in zebrafish (Danio rerio), carp (Cyprinus carpio), and large barbus (Barbus intermedius) showing an unusual conservation of the peptide binding domains
    • Kruiswijk CP, Hermsen TT, Westphal AH, Savelkoul HF, Stet RJ, (2002) A novel functional class I lineage in zebrafish (Danio rerio), carp (Cyprinus carpio), and large barbus (Barbus intermedius) showing an unusual conservation of the peptide binding domains. J Immunol 169: 1936-1947.
    • (2002) J Immunol , vol.169 , pp. 1936-1947
    • Kruiswijk, C.P.1    Hermsen, T.T.2    Westphal, A.H.3    Savelkoul, H.F.4    Stet, R.J.5
  • 28
    • 33646878378 scopus 로고    scopus 로고
    • Novel relationships among ten fish model species revealed based on a phylogenomic analysis using ESTs
    • Steinke D, Salzburger W, Meyer A, (2006) Novel relationships among ten fish model species revealed based on a phylogenomic analysis using ESTs. J Mol Evol 62: 772-784.
    • (2006) J Mol Evol , vol.62 , pp. 772-784
    • Steinke, D.1    Salzburger, W.2    Meyer, A.3
  • 29
    • 7244259101 scopus 로고    scopus 로고
    • Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype
    • Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, et al. (2004) Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431: 946-957.
    • (2004) Nature , vol.431 , pp. 946-957
    • Jaillon, O.1    Aury, J.M.2    Brunet, F.3    Petit, J.L.4    Stange-Thomann, N.5
  • 30
    • 0034079713 scopus 로고    scopus 로고
    • Human LINE retrotransposons generate processed pseudogenes
    • Esnault C, Maestre J, Heidmann T, (2000) Human LINE retrotransposons generate processed pseudogenes. Nat Genet 24: 363-367.
    • (2000) Nat Genet , vol.24 , pp. 363-367
    • Esnault, C.1    Maestre, J.2    Heidmann, T.3
  • 31
    • 0342313559 scopus 로고    scopus 로고
    • Frequent human genomic DNA transduction driven by LINE-1 retrotransposition
    • Pickeral OK, Makalowski W, Boguski MS, Boeke JD, (2000) Frequent human genomic DNA transduction driven by LINE-1 retrotransposition. Genome Res 10: 411-415.
    • (2000) Genome Res , vol.10 , pp. 411-415
    • Pickeral, O.K.1    Makalowski, W.2    Boguski, M.S.3    Boeke, J.D.4
  • 32
    • 0035144498 scopus 로고    scopus 로고
    • Human L1 retrotransposition: cis preference versus trans complementation
    • Wei W, Gilbert N, Ooi SL, Lawler JF, Ostertag EM, et al. (2001) Human L1 retrotransposition: cis preference versus trans complementation. Mol Cell Biol 21: 1429-1439.
    • (2001) Mol Cell Biol , vol.21 , pp. 1429-1439
    • Wei, W.1    Gilbert, N.2    Ooi, S.L.3    Lawler, J.F.4    Ostertag, E.M.5
  • 33
    • 0032103760 scopus 로고    scopus 로고
    • Repeats in genomic DNA: mining and meaning
    • Jurka J, (1998) Repeats in genomic DNA: mining and meaning. Curr Opin Struct Biol 8: 333-337.
    • (1998) Curr Opin Struct Biol , vol.8 , pp. 333-337
    • Jurka, J.1
  • 36
    • 63449122253 scopus 로고    scopus 로고
    • Burst of young retrogenes and independent retrogene formation in mammals
    • Pan D, Zhang L, (2009) Burst of young retrogenes and independent retrogene formation in mammals. PLoS ONE 4: e5040.
    • (2009) PLoS ONE , vol.4
    • Pan, D.1    Zhang, L.2
  • 38
    • 0345070506 scopus 로고    scopus 로고
    • Mutational equilibrium model of genome size evolution
    • Petrov DA, (2002) Mutational equilibrium model of genome size evolution. Theor Popul Biol 61: 531-544.
    • (2002) Theor Popul Biol , vol.61 , pp. 531-544
    • Petrov, D.A.1
  • 39
    • 37349093019 scopus 로고    scopus 로고
    • Genome organization and gene expression shape the transposable element distribution in the Drosophila melanogaster euchromatin
    • Fontanillas P, Hartl DL, Reuter M, (2007) Genome organization and gene expression shape the transposable element distribution in the Drosophila melanogaster euchromatin. PLoS Genet 3: e210.
    • (2007) PLoS Genet , vol.3
    • Fontanillas, P.1    Hartl, D.L.2    Reuter, M.3
  • 40
    • 0032893932 scopus 로고    scopus 로고
    • Preservation of duplicate genes by complementary, degenerative mutations
    • Force A, Lynch M, Pickett FB, Amores A, Yan YL, et al. (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.
    • (1999) Genetics , vol.151 , pp. 1531-1545
    • Force, A.1    Lynch, M.2    Pickett, F.B.3    Amores, A.4    Yan, Y.L.5
  • 41
    • 0034889978 scopus 로고    scopus 로고
    • A possible meiotic function of the peculiar patterns of gene expression in mammalian spermatogenic cells
    • Kleene KC, (2001) A possible meiotic function of the peculiar patterns of gene expression in mammalian spermatogenic cells. Mech Dev 106: 3-23.
    • (2001) Mech Dev , vol.106 , pp. 3-23
    • Kleene, K.C.1
  • 42
    • 34249994907 scopus 로고    scopus 로고
    • The medaka draft genome and insights into vertebrate genome evolution
    • 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: 714-719.
    • (2007) Nature , vol.447 , pp. 714-719
    • Kasahara, M.1    Naruse, K.2    Sasaki, S.3    Nakatani, Y.4    Qu, W.5
  • 43
    • 71049190885 scopus 로고    scopus 로고
    • Extensive structural renovation of retrogenes in the evolution of the Populus genome
    • Zhu Z, Zhang Y, Long M, (2009) Extensive structural renovation of retrogenes in the evolution of the Populus genome. Plant Physiol 151: 1943-1951.
    • (2009) Plant Physiol , vol.151 , pp. 1943-1951
    • Zhu, Z.1    Zhang, Y.2    Long, M.3
  • 44
    • 9244247603 scopus 로고    scopus 로고
    • Evolving protein functional diversity in new genes of Drosophila
    • Zhang J, Dean AM, Brunet F, Long M, (2004) Evolving protein functional diversity in new genes of Drosophila. Proc Natl Acad Sci U S A 101: 16246-16250.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 16246-16250
    • Zhang, J.1    Dean, A.M.2    Brunet, F.3    Long, M.4
  • 45
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5
  • 47
    • 0031573415 scopus 로고    scopus 로고
    • Comparison of DNA sequences with protein sequences
    • Pearson WR, Wood T, Zhang Z, Miller W, (1997) Comparison of DNA sequences with protein sequences. Genomics 46: 24-36.
    • (1997) Genomics , vol.46 , pp. 24-36
    • Pearson, W.R.1    Wood, T.2    Zhang, Z.3    Miller, W.4
  • 48
    • 34248669040 scopus 로고    scopus 로고
    • KaKs_Calculator: calculating Ka and Ks through model selection and model averaging
    • Zhang Z, Li J, Zhao XQ, Wang J, Wong GK, et al. (2006) KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics 4: 259-263.
    • (2006) Genomics Proteomics Bioinformatics , vol.4 , pp. 259-263
    • Zhang, Z.1    Li, J.2    Zhao, X.Q.3    Wang, J.4    Wong, G.K.5
  • 49
    • 0027403961 scopus 로고
    • Unbiased estimation of the rates of synonymous and nonsynonymous substitution
    • Li WH, (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol 36: 96-99.
    • (1993) J Mol Evol , vol.36 , pp. 96-99
    • Li, W.H.1
  • 50
    • 0027533924 scopus 로고
    • Evolution of the Zfx and Zfy genes: rates and interdependence between the genes
    • Pamilo P, Bianchi NO, (1993) Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. Mol Biol Evol 10: 271-281.
    • (1993) Mol Biol Evol , vol.10 , pp. 271-281
    • Pamilo, P.1    Bianchi, N.O.2
  • 51
    • 0030683599 scopus 로고    scopus 로고
    • PAML: a program package for phylogenetic analysis by maximum likelihood
    • Yang Z, (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13: 555-556.
    • (1997) Comput Appl Biosci , vol.13 , pp. 555-556
    • Yang, Z.1
  • 52
    • 0031897964 scopus 로고    scopus 로고
    • Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
    • Yang Z, (1998) Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol 15: 568-573.
    • (1998) Mol Biol Evol , vol.15 , pp. 568-573
    • Yang, Z.1


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