메뉴 건너뛰기




Volumn 4, Issue 8, 2008, Pages

Evolutionary convergence on highly-conserved 3′ intron structures in intron-poor eukaryotes and insights into the ancestral eukaryotic genome

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; EUKARYOTE; GENE STRUCTURE; GENOME; GREEN ALGA; INTRON; METAZOON; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT; ANIMAL; CLASSIFICATION; COMPARATIVE STUDY; EUKARYOTIC CELL; FISH; FUNGUS; GENETICS; HUMAN; MOLECULAR EVOLUTION; PHYLOGENY; PHYSIOLOGY; PHYTOPHTHORA; PROTOZOON; RNA SPLICING; SPLICEOSOME;

EID: 50849088978     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1000148     Document Type: Article
Times cited : (64)

References (48)
  • 1
    • 15444370758 scopus 로고    scopus 로고
    • Spliceosomal introns in the deep-branching eukaryote Trichomonas vaginalis
    • Vanacova S, Yan W, Carlton JM, Johnson PJ (2005) Spliceosomal introns in the deep-branching eukaryote Trichomonas vaginalis. Proc Natl Acad Sci USA 102: 4430-4435.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 4430-4435
    • Vanacova, S.1    Yan, W.2    Carlton, J.M.3    Johnson, P.J.4
  • 2
    • 16344385067 scopus 로고    scopus 로고
    • Complex spliceosomal organization ancestral to extant eukaryotes
    • Collins L, Penny D (2005) Complex spliceosomal organization ancestral to extant eukaryotes. Mol Biol Evol 22: 1053-1066.
    • (2005) Mol Biol Evol , vol.22 , pp. 1053-1066
    • Collins, L.1    Penny, D.2
  • 3
    • 33746001953 scopus 로고    scopus 로고
    • A high density of ancient spliceosomal introns in oxymonad excavates
    • Slamovits CH, Keeling PJ (2006) A high density of ancient spliceosomal introns in oxymonad excavates. BMC Evol Biol 6: 34.
    • (2006) BMC Evol Biol , vol.6 , pp. 34
    • Slamovits, C.H.1    Keeling, P.J.2
  • 5
    • 33846528971 scopus 로고    scopus 로고
    • Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis
    • Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, et al. (2007) Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis. Science 315: 207-212.
    • (2007) Science , vol.315 , pp. 207-212
    • Carlton, J.M.1    Hirt, R.P.2    Silva, J.C.3    Delcher, A.L.4    Schatz, M.5
  • 6
    • 33747188649 scopus 로고    scopus 로고
    • Intron-rich ancestors
    • Roy SW (2006) Intron-rich ancestors. Trends Genet 22: 468-471.
    • (2006) Trends Genet , vol.22 , pp. 468-471
    • Roy, S.W.1
  • 8
    • 33745476746 scopus 로고    scopus 로고
    • Complete nucleotide sequence of the chlorarachniophyte nucleomorph: Nature's smallest nucleus
    • Gilson PR, Su V, Slamovits CH, Reith ME, Keeling PJ, et al. (2006) Complete nucleotide sequence of the chlorarachniophyte nucleomorph: Nature's smallest nucleus. Proc Natl Acad Sci 103: 9566-9571.
    • (2006) Proc Natl Acad Sci , vol.103 , pp. 9566-9571
    • Gilson, P.R.1    Su, V.2    Slamovits, C.H.3    Reith, M.E.4    Keeling, P.J.5
  • 9
    • 34250707188 scopus 로고    scopus 로고
    • Coevolution of genomic intron number and splice sites
    • Irimia M, Penny D, Roy SW (2007) Coevolution of genomic intron number and splice sites. Trends Genet 23: 321-325.
    • (2007) Trends Genet , vol.23 , pp. 321-325
    • Irimia, M.1    Penny, D.2    Roy, S.W.3
  • 10
    • 0037440652 scopus 로고    scopus 로고
    • Molecular evolution of eukaryotic genomes: Hemiascomycetous yeast spliceosomal introns
    • Bon E, Casaregola S, Blandin G, Llorente B, Neuveglise C, et al. (2003) Molecular evolution of eukaryotic genomes: hemiascomycetous yeast spliceosomal introns. Nucleic Acids Res 31: 1121-1135.
    • (2003) Nucleic Acids Res , vol.31 , pp. 1121-1135
    • Bon, E.1    Casaregola, S.2    Blandin, G.3    Llorente, B.4    Neuveglise, C.5
  • 11
    • 50849114575 scopus 로고    scopus 로고
    • Blumenthal T, Steward K (1997) C. elegans II; Riddle D, Blumenthal T, Meyer B, Priess J, eds. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. pp 117-145.
    • Blumenthal T, Steward K (1997) C. elegans II; Riddle D, Blumenthal T, Meyer B, Priess J, eds. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. pp 117-145.
  • 12
    • 0024100723 scopus 로고
    • The role of the mammalian branchpoint sequence in pre-mRNA splicing
    • Reed R, Maniatis T (1988) The role of the mammalian branchpoint sequence in pre-mRNA splicing. Genes Dev 2: 1268-1276.
    • (1988) Genes Dev , vol.2 , pp. 1268-1276
    • Reed, R.1    Maniatis, T.2
  • 13
    • 0028205987 scopus 로고
    • Branch nucleophile selection in premRNA splicing: Evidence for the bulged duplex model
    • Query CC, Moore MJ, Sharp PA (1994) Branch nucleophile selection in premRNA splicing: evidence for the bulged duplex model. Genes Dev 8: 587-597.
    • (1994) Genes Dev , vol.8 , pp. 587-597
    • Query, C.C.1    Moore, M.J.2    Sharp, P.A.3
  • 14
    • 0142247085 scopus 로고    scopus 로고
    • trans and cis splicing in trypanosomatids: Mechanism, factors, and regulation
    • Liang XH, Haritan A, Uliel S, Michaeli S (2003) trans and cis splicing in trypanosomatids: mechanism, factors, and regulation. Eukaryot Cell 2: 830-840.
    • (2003) Eukaryot Cell , vol.2 , pp. 830-840
    • Liang, X.H.1    Haritan, A.2    Uliel, S.3    Michaeli, S.4
  • 15
    • 0034634621 scopus 로고    scopus 로고
    • Mutational analysis of 3′ splice site selection during trans-splicing
    • Hummel HS, Gillespie RD, Swindle J (2000) Mutational analysis of 3′ splice site selection during trans-splicing. J Biol Chem 275: 35522-35531.
    • (2000) J Biol Chem , vol.275 , pp. 35522-35531
    • Hummel, H.S.1    Gillespie, R.D.2    Swindle, J.3
  • 16
    • 45549083628 scopus 로고    scopus 로고
    • When good transcripts go bad: Artifactual RT-PCR 'splicing' and genome analysis
    • Roy SW, Irimia M (2008) When good transcripts go bad: artifactual RT-PCR 'splicing' and genome analysis. BioEssays 30: 601-605.
    • (2008) BioEssays , vol.30 , pp. 601-605
    • Roy, S.W.1    Irimia, M.2
  • 17
    • 33746683274 scopus 로고    scopus 로고
    • Reverse transcriptase template switching and false alternative transcripts
    • Cocquet J, Chong A, Zhang G, Veitia RA (2006) Reverse transcriptase template switching and false alternative transcripts. Genomics 88: 127-131.
    • (2006) Genomics , vol.88 , pp. 127-131
    • Cocquet, J.1    Chong, A.2    Zhang, G.3    Veitia, R.A.4
  • 18
    • 34250689932 scopus 로고    scopus 로고
    • The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation
    • Palenik B, Grimwood J, Aerts A, Rouze P, Salamov A, et al. (2007) The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl Acad Sci USA 104: 7705-7710.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 7705-7710
    • Palenik, B.1    Grimwood, J.2    Aerts, A.3    Rouze, P.4    Salamov, A.5
  • 21
    • 0030857005 scopus 로고    scopus 로고
    • Functional analysis of the polypyrimidine tract in pre-mRNA splicing
    • Coolidge C, Seely R, Patton J (1997) Functional analysis of the polypyrimidine tract in pre-mRNA splicing. Nucl Acids Res 25: 888-896.
    • (1997) Nucl Acids Res , vol.25 , pp. 888-896
    • Coolidge, C.1    Seely, R.2    Patton, J.3
  • 23
    • 20444470310 scopus 로고    scopus 로고
    • Human-mouse comparative analysis reveals that branch-site plasticity contributes to splicing regulation
    • Kol G, Lev-Maor G, Ast G (2005) Human-mouse comparative analysis reveals that branch-site plasticity contributes to splicing regulation. Hum Mol Genet 14: 1559-1568.
    • (2005) Hum Mol Genet , vol.14 , pp. 1559-1568
    • Kol, G.1    Lev-Maor, G.2    Ast, G.3
  • 24
    • 0030878280 scopus 로고    scopus 로고
    • A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites
    • Tolstrup N, Rouze P, Brunak S (1997) A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites. Nucl Acids Res 25: 3159-3163.
    • (1997) Nucl Acids Res , vol.25 , pp. 3159-3163
    • Tolstrup, N.1    Rouze, P.2    Brunak, S.3
  • 25
    • 0033576591 scopus 로고    scopus 로고
    • Both subunits of U2AF recognize the 3′ splice site in Caenorhabditis elegans
    • Zorio DAR, Blumenthal T (1999) Both subunits of U2AF recognize the 3′ splice site in Caenorhabditis elegans. Nature 402: 835-838.
    • (1999) Nature , vol.402 , pp. 835-838
    • Zorio, D.A.R.1    Blumenthal, T.2
  • 26
    • 33644847698 scopus 로고    scopus 로고
    • The evolution of spliceosomal introns: Patterns, puzzles and progress
    • Roy SW, Gilbert W (2006) The evolution of spliceosomal introns: patterns, puzzles and progress. Nat Rev Genet 7: 211-221.
    • (2006) Nat Rev Genet , vol.7 , pp. 211-221
    • Roy, S.W.1    Gilbert, W.2
  • 27
    • 38049029652 scopus 로고    scopus 로고
    • Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes
    • Schwartz S, Silva J, Burstein D, Pupko T, Eyras E, et al. (2008) Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes. Genome Res 18: 88-103.
    • (2008) Genome Res , vol.18 , pp. 88-103
    • Schwartz, S.1    Silva, J.2    Burstein, D.3    Pupko, T.4    Eyras, E.5
  • 28
    • 44349155377 scopus 로고    scopus 로고
    • Computational screen for spliceosomal RNA genes aids in defining the phylogenetic distribution of major and minor spliceosomal components
    • Dávila López M, Rosenblad MA, Samuelsson T (2008) Computational screen for spliceosomal RNA genes aids in defining the phylogenetic distribution of major and minor spliceosomal components. Nucl Acids Res 36: 3001-3010.
    • (2008) Nucl Acids Res , vol.36 , pp. 3001-3010
    • Dávila López, M.1    Rosenblad, M.A.2    Samuelsson, T.3
  • 29
    • 12144268815 scopus 로고    scopus 로고
    • Genetic distance in housekeeping genes between Plasmodium falciparum and Plasmodium reichenowi and within P. falciparum
    • Tanabe K, Sakihama N, Hattori T, Ranford-Cartwright L, Goldman I, et al. (2004) Genetic distance in housekeeping genes between Plasmodium falciparum and Plasmodium reichenowi and within P. falciparum. J Mol Evol 59: 687-694.
    • (2004) J Mol Evol , vol.59 , pp. 687-694
    • Tanabe, K.1    Sakihama, N.2    Hattori, T.3    Ranford-Cartwright, L.4    Goldman, I.5
  • 30
    • 20444376117 scopus 로고    scopus 로고
    • Evolution of noncoding and silent coding sites in the Plasmodium falciparum and Plasmodium reichenowi genomes
    • Neafsey DE, Hartl DL, Berriman M (2005) Evolution of noncoding and silent coding sites in the Plasmodium falciparum and Plasmodium reichenowi genomes. Mol Biol Evol 22: 1621-1626.
    • (2005) Mol Biol Evol , vol.22 , pp. 1621-1626
    • Neafsey, D.E.1    Hartl, D.L.2    Berriman, M.3
  • 31
    • 0037197986 scopus 로고    scopus 로고
    • Intron evolution as a population-genetic process
    • Lynch M (2002) Intron evolution as a population-genetic process. Proc Natl Acad Sci USA 99: 6118-6123.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 6118-6123
    • Lynch, M.1
  • 32
    • 38349125022 scopus 로고    scopus 로고
    • Translational control of intron splicing in eukaryotes
    • Jaillon O, Bouhouche K, Gout J-F, Aury J-M, Noel B, et al. (2008) Translational control of intron splicing in eukaryotes. Nature 451: 359-362.
    • (2008) Nature , vol.451 , pp. 359-362
    • Jaillon, O.1    Bouhouche, K.2    Gout, J.-F.3    Aury, J.-M.4    Noel, B.5
  • 33
    • 0032247416 scopus 로고    scopus 로고
    • Evolutionary fates and origins of U12-type introns
    • Burge CB, Padgett RA, Sharp PA (1998) Evolutionary fates and origins of U12-type introns. Mol Cell 2: 773-785.
    • (1998) Mol Cell , vol.2 , pp. 773-785
    • Burge, C.B.1    Padgett, R.A.2    Sharp, P.A.3
  • 34
    • 33750336226 scopus 로고    scopus 로고
    • An early evolutionary origin for the minor spliceosome
    • Russell AG, Charette JM, Spencer DF, Gray MW (2006) An early evolutionary origin for the minor spliceosome. Nature 443: 863-866.
    • (2006) Nature , vol.443 , pp. 863-866
    • Russell, A.G.1    Charette, J.M.2    Spencer, D.F.3    Gray, M.W.4
  • 35
    • 84872246297 scopus 로고    scopus 로고
    • New maximum likelihood estimators for eukaryotic intron evolution
    • Nguyen H, Yoshihama M, Kenmochi N (2005) New maximum likelihood estimators for eukaryotic intron evolution. PLoS Comput Biol 1: e79.
    • (2005) PLoS Comput Biol , vol.1
    • Nguyen, H.1    Yoshihama, M.2    Kenmochi, N.3
  • 36
    • 21044447550 scopus 로고    scopus 로고
    • Analysis of evolution of exon-intron structure of eukaryotic genes
    • Rogozin I, Sverdlov A, Babenko V, Koonin E (2005) Analysis of evolution of exon-intron structure of eukaryotic genes. Brief Bioinform 6: 118-134.
    • (2005) Brief Bioinform , vol.6 , pp. 118-134
    • Rogozin, I.1    Sverdlov, A.2    Babenko, V.3    Koonin, E.4
  • 38
    • 15944384932 scopus 로고    scopus 로고
    • Conservation versus parallel gains in intron evolution
    • Sverdlov A, Rogozin I, Babenko V, Koonin E (2005) Conservation versus parallel gains in intron evolution. Nucl Acids Res 33: 1741-1748.
    • (2005) Nucl Acids Res , vol.33 , pp. 1741-1748
    • Sverdlov, A.1    Rogozin, I.2    Babenko, V.3    Koonin, E.4
  • 39
    • 36349026377 scopus 로고    scopus 로고
    • Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing
    • Irimia M, Rukov JL, Penny D, Roy SW (2007) Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing. BMC Evol Biol 7: 188.
    • (2007) BMC Evol Biol , vol.7 , pp. 188
    • Irimia, M.1    Rukov, J.L.2    Penny, D.3    Roy, S.W.4
  • 40
    • 41649111671 scopus 로고    scopus 로고
    • Intron mis-splicing: No alternative?
    • Roy S, Irimia M (2008) Intron mis-splicing: no alternative? Genome Biology 9: 208.
    • (2008) Genome Biology , vol.9 , pp. 208
    • Roy, S.1    Irimia, M.2
  • 41
    • 0035953753 scopus 로고    scopus 로고
    • The highly reduced genome of an enslaved algal nucleus
    • Douglas S, Zauner S, Fraunholz M, Beaton M, Penny S, et al. (2001) The highly reduced genome of an enslaved algal nucleus. Nature 410: 1091-1096.
    • (2001) Nature , vol.410 , pp. 1091-1096
    • Douglas, S.1    Zauner, S.2    Fraunholz, M.3    Beaton, M.4    Penny, S.5
  • 42
    • 11144354393 scopus 로고    scopus 로고
    • Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D
    • Matsuzaki M, Misumi O, Shin-i T, Maruyama S, Takahara M, et al. (2004) Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature 428: 653-657.
    • (2004) Nature , vol.428 , pp. 653-657
    • Matsuzaki, M.1    Misumi, O.2    Shin-i, T.3    Maruyama, S.4    Takahara, M.5
  • 43
    • 34848894621 scopus 로고    scopus 로고
    • Genomic Minimalism in the Early Diverging Intestinal Parasite Giardia lamblia
    • Morrison HG, McArthur AG, Gillin FD, Aley SB, Adam RD, et al. (2007) Genomic Minimalism in the Early Diverging Intestinal Parasite Giardia lamblia. Science 317: 1921-1926.
    • (2007) Science , vol.317 , pp. 1921-1926
    • Morrison, H.G.1    McArthur, A.G.2    Gillin, F.D.3    Aley, S.B.4    Adam, R.D.5
  • 44
    • 38849108817 scopus 로고    scopus 로고
    • Dicyema Pax6 and Zic: Tool-kit genes in a highly simplified bilaterian
    • Aruga J, Odaka YS, Kamiya A, Furuya H (2007) Dicyema Pax6 and Zic: tool-kit genes in a highly simplified bilaterian. BMC Evol Biol 7: 201.
    • (2007) BMC Evol Biol , vol.7 , pp. 201
    • Aruga, J.1    Odaka, Y.S.2    Kamiya, A.3    Furuya, H.4
  • 45
    • 36348934556 scopus 로고    scopus 로고
    • Intron-rich gene structure in the intracellular plant parasite Plasmodiophora brassicae
    • Bulman S, Ridgway HJ, Eady C, Conner AJ (2007) Intron-rich gene structure in the intracellular plant parasite Plasmodiophora brassicae. Protist 158: 423-433.
    • (2007) Protist , vol.158 , pp. 423-433
    • Bulman, S.1    Ridgway, H.J.2    Eady, C.3    Conner, A.J.4
  • 46
    • 4644345013 scopus 로고    scopus 로고
    • Coding properties of Oxytricha trifallax ( Sterkiella histriomuscorum) macronuclear chromosomes: Analysis of a pilot genome project
    • Cavalcanti ARO, Stover NA, Orecchia L, Doak TG, Landweber LF (2004) Coding properties of Oxytricha trifallax ( Sterkiella histriomuscorum) macronuclear chromosomes: analysis of a pilot genome project. Chromosoma V113: 69-76.
    • (2004) Chromosoma , vol.113 , pp. 69-76
    • Cavalcanti, A.R.O.1    Stover, N.A.2    Orecchia, L.3    Doak, T.G.4    Landweber, L.F.5
  • 47
    • 12544255323 scopus 로고    scopus 로고
    • The real 'kingdoms' of eukaryotes
    • Simpson A, Roger A (2004) The real 'kingdoms' of eukaryotes. Curr Biol 14: R693-R696.
    • (2004) Curr Biol , vol.14
    • Simpson, A.1    Roger, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.