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Volumn 2, Issue 3, 2006, Pages 113-125

Large-scale trends in the evolution of gene structures within 11 animal genomes

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALS; GENES; OPEN SYSTEMS; PROTEINS;

EID: 33645769791     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0020015     Document Type: Article
Times cited : (67)

References (56)
  • 1
  • 2
    • 0032574738 scopus 로고    scopus 로고
    • Toward a resolution of the introns early/late debate: Only phase zero introns are correlated with the structure of ancient proteins
    • U S A
    • de Souza SJ, Long M, Klein RJ, Roy S, Lin S, et al. (1998) Toward a resolution of the introns early/late debate: Only phase zero introns are correlated with the structure of ancient proteins. Proc Natl Acad Sci U S A 95: 5094-5099.
    • (1998) Proc Natl Acad Sci , vol.95 , pp. 5094-5099
    • De Souza, S.J.1    Long, M.2    Klein, R.J.3    Roy, S.4    Lin, S.5
  • 3
    • 2342473948 scopus 로고    scopus 로고
    • Molecular evolution: Introns fall into place
    • Stoltzfus A (2004) Molecular evolution: Introns fall into place. Curr Biol 14: R351-R352.
    • (2004) Curr Biol , vol.14
    • Stoltzfus, A.1
  • 4
    • 0347361692 scopus 로고    scopus 로고
    • Selective constraints on intron evolution in Drosophila
    • Parsch J (2003) Selective constraints on intron evolution in Drosophila. Genetics 165: 1843-1851.
    • (2003) Genetics , vol.165 , pp. 1843-1851
    • Parsch, J.1
  • 5
    • 3042548834 scopus 로고    scopus 로고
    • The evolutionary gain of spliceosomal introns: Sequence and phase preferences
    • Qiu WG, Schisler N, Stoltzfus A (2004) The evolutionary gain of spliceosomal introns: Sequence and phase preferences. Mol Biol Evol 21: 1252-1263.
    • (2004) Mol Biol Evol , vol.21 , pp. 1252-1263
    • Qiu, W.G.1    Schisler, N.2    Stoltzfus, A.3
  • 6
    • 15444379114 scopus 로고    scopus 로고
    • Resolution of a deep animal divergence by the pattern of intron conservation
    • U S A
    • Roy SW, Gilbert W (2005) Resolution of a deep animal divergence by the pattern of intron conservation. Proc Natl Acad Sci U S A 102: 4403-4408.
    • (2005) Proc Natl Acad Sci , vol.102 , pp. 4403-4408
    • Roy, S.W.1    Gilbert, W.2
  • 7
    • 3142749596 scopus 로고    scopus 로고
    • Prevalence of intron gain over intron loss in the evolution of paralogous gene families
    • Babenko VN, Rogozin IB, Mekhedov SL, Koonin EV (2004) Prevalence of intron gain over intron loss in the evolution of paralogous gene families. Nucleic Acids Res 32: 3724-3733.
    • (2004) Nucleic Acids Res , vol.32 , pp. 3724-3733
    • Babenko, V.N.1    Rogozin, I.B.2    Mekhedov, S.L.3    Koonin, E.V.4
  • 8
    • 10344222940 scopus 로고    scopus 로고
    • Phylogenetic mapping of intron positions: A case study of translation initiation factor eIF2gamma
    • Krauss V, Pecyna M, Kurz K, Sass H (2005) Phylogenetic mapping of intron positions: A case study of translation initiation factor eIF2gamma. Mol Biol Evol 22: 74-84.
    • (2005) Mol Biol Evol , vol.22 , pp. 74-84
    • Krauss, V.1    Pecyna, M.2    Kurz, K.3    Sass, H.4
  • 9
    • 0036888952 scopus 로고    scopus 로고
    • The evolution of spliceosomal introns
    • Lynch M, Richardson AO (2002) The evolution of spliceosomal introns. Curr Opin Genet Dev 12: 701-710.
    • (2002) Curr Opin Genet Dev , vol.12 , pp. 701-710
    • Lynch, M.1    Richardson, A.O.2
  • 10
    • 0033832676 scopus 로고    scopus 로고
    • Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment
    • Kent WJ, Zahler AM (2000) Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. Genome Res 10: 1115-1125.
    • (2000) Genome Res , vol.10 , pp. 1115-1125
    • Kent, W.J.1    Zahler, A.M.2
  • 11
    • 3843113189 scopus 로고    scopus 로고
    • Origins of recently gained introns in Caenorhabditis
    • U S A
    • Coghlan A, Wolfe KH (2004) Origins of recently gained introns in Caenorhabditis. Proc Natl Acad Sci U S A 101: 11362-11367.
    • (2004) Proc Natl Acad Sci , vol.101 , pp. 11362-11367
    • Coghlan, A.1    Wolfe, K.H.2
  • 14
  • 15
  • 16
    • 0032509302 scopus 로고    scopus 로고
    • Genome sequence of the nematode C. elegans: A platform for investigating biology
    • C. elegans Sequencing Consortium (1998) Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282: 2012-2018.
    • (1998) Science , vol.282 , pp. 2012-2018
  • 19
    • 0002636459 scopus 로고    scopus 로고
    • Annotation of the Drosophila melanogaster euchromatic genome: A systematic review
    • RESEARCH0083
    • Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, et al. (2002) Annotation of the Drosophila melanogaster euchromatic genome: A systematic review. Genome Biol 3: RESEARCH0083.
    • (2002) Genome Biol , vol.3
    • Misra, S.1    Crosby, M.A.2    Mungall, C.J.3    Matthews, B.B.4    Campbell, K.S.5
  • 22
    • 2242464840 scopus 로고    scopus 로고
    • The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins
    • Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, et al. (2002) The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins. Science 298: 2157-2167.
    • (2002) Science , vol.298 , pp. 2157-2167
    • Dehal, P.1    Satou, Y.2    Campbell, R.K.3    Chapman, J.4    Degnan, B.5
  • 23
    • 33645793935 scopus 로고    scopus 로고
    • Department of Energy Joint Genome Institute (2004) Archival data: Ciona intestinalis v1.0. Available: http://genome.jgi-psf.org/ciona4/ciona4.home. html. Accessed 25 January 2006.
    • (2004) Archival Data: Ciona Intestinalis V1.0
  • 25
    • 0023470085 scopus 로고
    • Fossil appendicularians in the Early Cambrian
    • Zhang A (1987) Fossil appendicularians in the Early Cambrian. Sci Sin [B] 30: 888-896.
    • (1987) Sci Sin [B] , vol.30 , pp. 888-896
    • Zhang, A.1
  • 29
    • 19944434180 scopus 로고    scopus 로고
    • Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution
    • Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, et al. (2005) Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution. Genome Res 15: 1-18.
    • (2005) Genome Res , vol.15 , pp. 1-18
    • Richards, S.1    Liu, Y.2    Bettencourt, B.R.3    Hradecky, P.4    Letovsky, S.5
  • 30
    • 1242352089 scopus 로고    scopus 로고
    • Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks
    • Tamura K, Subramanian S, Kumar S (2004) Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol Biol Evol 21: 36-44.
    • (2004) Mol Biol Evol , vol.21 , pp. 36-44
    • Tamura, K.1    Subramanian, S.2    Kumar, S.3
  • 31
    • 0026657738 scopus 로고
    • Splicing signals in Drosophila: Intron size, information content, and consensus sequences
    • Mount SM, Burks C, Hertz G, Stormo GD, White O, et al. (1992) Splicing signals in Drosophila: Intron size, information content, and consensus sequences. Nucleic Acids Res 20: 42554262.
    • (1992) Nucleic Acids Res , vol.20 , pp. 42554262
    • Mount, S.M.1    Burks, C.2    Hertz, G.3    Stormo, G.D.4    White, O.5
  • 32
    • 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
  • 33
    • 0037180494 scopus 로고    scopus 로고
    • The signal of ancient introns is obscured by intron density and homolog number
    • U S A
    • Roy SW, Fedorov A, Gilbert W (2002) The signal of ancient introns is obscured by intron density and homolog number. Proc Natl Acad Sci U S A 99: 15513-15517.
    • (2002) Proc Natl Acad Sci , vol.99 , pp. 15513-15517
    • Roy, S.W.1    Fedorov, A.2    Gilbert, W.3
  • 35
    • 0030425648 scopus 로고    scopus 로고
    • Molecular evidence for deep pre-Cambrian divergences among the metazoan phyla
    • Wray GA (1996) Molecular evidence for deep pre-Cambrian divergences among the metazoan phyla. Science 274: 568-573.
    • (1996) Science , vol.274 , pp. 568-573
    • Wray, G.A.1
  • 37
    • 0030023247 scopus 로고    scopus 로고
    • Determining divergence times of the major kingdoms of living organisms with a protein clock
    • Doolittle RF, Feng DF, Tsang S, Cho G, Little E (1996) Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 271: 470-477.
    • (1996) Science , vol.271 , pp. 470-477
    • Doolittle, R.F.1    Feng, D.F.2    Tsang, S.3    Cho, G.4    Little, E.5
  • 39
    • 0025878149 scopus 로고
    • Amino acid substitution matrices from an information theoretic perspective
    • Altschul SF (1991) Amino acid substitution matrices from an information theoretic perspective. J Mol Biol 219: 555-565.
    • (1991) J Mol Biol , vol.219 , pp. 555-565
    • Altschul, S.F.1
  • 40
  • 41
    • 0034649566 scopus 로고    scopus 로고
    • Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
    • Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
    • (2000) Nature , vol.408 , pp. 796-815
  • 42
    • 27844438226 scopus 로고    scopus 로고
    • Genome-scale evidence of the nematode-arthropod clade
    • Dopazo H, Dopazo J (2005) Genome-scale evidence of the nematode-arthropod clade. Genome Biol 6: R41.
    • (2005) Genome Biol , vol.6
    • Dopazo, H.1    Dopazo, J.2
  • 43
    • 0000122573 scopus 로고
    • PHYLIP-Phylogeny Inference Package (Version 3.2)
    • Felsenstein J (1993) PHYLIP-Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.
    • (1993) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 44
    • 0029982849 scopus 로고    scopus 로고
    • Bootstrap confidence levels for phylogenetic trees
    • U S A
    • Efron B, Halloran E, Holmes S (1996) Bootstrap confidence levels for phylogenetic trees. Proc Natl Acad Sci U S A 93: 13429-13434.
    • (1996) Proc Natl Acad Sci , vol.93 , pp. 13429-13434
    • Efron, B.1    Halloran, E.2    Holmes, S.3
  • 45
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • U S A
    • Henikoff S, Henikoff JG (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A 89: 10915-10919.
    • (1992) Proc Natl Acad Sci , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 46
    • 4444293128 scopus 로고    scopus 로고
    • Indel-based evolutionary distance and mouse-human divergence
    • Ogurtsov AY, Sunyaev S, Kondrashov AS (2004) Indel-based evolutionary distance and mouse-human divergence. Genome Res 14: 1610-1616.
    • (2004) Genome Res , vol.14 , pp. 1610-1616
    • Ogurtsov, A.Y.1    Sunyaev, S.2    Kondrashov, A.S.3
  • 48
    • 0037383240 scopus 로고    scopus 로고
    • Genomic clocks and evolutionary timescales
    • Blair Hedges S, Kumar S (2003) Genomic clocks and evolutionary timescales. Trends Genet 19: 200-206.
    • (2003) Trends Genet , vol.19 , pp. 200-206
    • Blair Hedges, S.1    Kumar, S.2
  • 50
    • 0028168856 scopus 로고
    • A codon-based model of nucleotide substitution for protein-coding DNA sequences
    • Goldman N, Yang Z (1994) A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 11: 725-736.
    • (1994) Mol Biol Evol , vol.11 , pp. 725-736
    • Goldman, N.1    Yang, Z.2
  • 51
    • 0033979433 scopus 로고    scopus 로고
    • Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
    • Yang Z, Nielsen R (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 17: 32-43.
    • (2000) Mol Biol Evol , vol.17 , pp. 32-43
    • Yang, Z.1    Nielsen, R.2
  • 53
    • 0012302769 scopus 로고    scopus 로고
    • An integrated computational pipeline and database to support whole-genome sequence annotation
    • RESEARCH0081
    • Mungall CJ, Misra S, Berman BP, Carlson J, Frise E, et al. (2002) An integrated computational pipeline and database to support whole-genome sequence annotation. Genome Biol 3: RESEARCH0081.
    • (2002) Genome Biol , vol.3
    • Mungall, C.J.1    Misra, S.2    Berman, B.P.3    Carlson, J.4    Frise, E.5
  • 54
    • 0031732094 scopus 로고    scopus 로고
    • A computer program for aligning a cDNA sequence with a genomic DNA sequence
    • Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W (1998) A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res 8: 967-974.
    • (1998) Genome Res , vol.8 , pp. 967-974
    • Florea, L.1    Hartzell, G.2    Zhang, Z.3    Rubin, G.M.4    Miller, W.5
  • 55
    • 33645767851 scopus 로고    scopus 로고
    • Gish WR (2005) WU-BLAST. Available: http://blast.wustl.edu. Accessed 25 January 2006.
    • (2005) WU-BLAST
    • Gish, W.R.1
  • 56
    • 0012341115 scopus 로고    scopus 로고
    • The transposable elements of the Drosophila melanogaster euchromatin: A genomics perspective
    • RESEARCH0084
    • Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, et al. (2002) The transposable elements of the Drosophila melanogaster euchromatin: A genomics perspective. Genome Biol 3: RESEARCH0084.
    • (2002) Genome Biol , vol.3
    • Kaminker, J.S.1    Bergman, C.M.2    Kronmiller, B.3    Carlson, J.4    Svirskas, R.5


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