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Volumn 165, Issue 1, 2014, Pages 412-423

Evolution of gene structural complexity: An alternative-splicing-based model accounts for intron-containing retrogenes

Author keywords

[No Author keywords available]

Indexed keywords

ISOPROTEIN; RETROPOSON;

EID: 84899845433     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.113.231696     Document Type: Article
Times cited : (19)

References (61)
  • 1
    • 0035504023 scopus 로고    scopus 로고
    • Hypermutability at a poly (A/T) tract in the human germline
    • Bacon AL, Dunlop MG, Farrington SM (2001) Hypermutability at a poly (A/T) tract in the human germline. Nucleic Acids Res 29: 4405-4413
    • (2001) Nucleic Acids Res , vol.29 , pp. 4405-4413
    • Bacon, A.L.1    Dunlop, M.G.2    Farrington, S.M.3
  • 2
    • 50649109231 scopus 로고    scopus 로고
    • Genome-wide analyses of alternative splicing in plants: Opportunities and challenges
    • Barbazuk WB, Fu Y, McGinnis KM (2008) Genome-wide analyses of alternative splicing in plants: opportunities and challenges. Genome Res 18: 1381-1392
    • (2008) Genome Res , vol.18 , pp. 1381-1392
    • Barbazuk, W.B.1    Fu, Y.2    McGinnis, K.M.3
  • 3
    • 0036906987 scopus 로고    scopus 로고
    • Retroposed new genes out of the X in Drosophila
    • Betrán 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
    • Betrán, E.1    Thornton, K.2    Long, M.3
  • 4
    • 33745899048 scopus 로고    scopus 로고
    • Alternative splicing: New insights from global analyses
    • Blencowe BJ (2006) Alternative splicing: new insights from global analyses. Cell 126: 37-47
    • (2006) Cell , vol.126 , pp. 37-47
    • Blencowe, B.J.1
  • 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
    • 33846573830 scopus 로고    scopus 로고
    • Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis
    • Campbell MA, Haas BJ, Hamilton JP, Mount SM, Buell CR (2006) Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics 7: 327
    • (2006) BMC Genomics , vol.7 , pp. 327
    • Campbell, M.A.1    Haas, B.J.2    Hamilton, J.P.3    Mount, S.M.4    Buell, C.R.5
  • 8
    • 84882340111 scopus 로고    scopus 로고
    • New genes as drivers of phenotypic evolution
    • Chen S, Krinsky BH, Long M (2013) New genes as drivers of phenotypic evolution. Nat Rev Genet 14: 645-660
    • (2013) Nat Rev Genet , vol.14 , pp. 645-660
    • Chen, S.1    Krinsky, B.H.2    Long, M.3
  • 9
    • 0031968001 scopus 로고    scopus 로고
    • The involvement of cellular recombination and repair genes in RNA-mediated recombination in Saccharomyces cerevisiae
    • Derr LK (1998) The involvement of cellular recombination and repair genes in RNA-mediated recombination in Saccharomyces cerevisiae. Genetics 148: 937-945
    • (1998) Genetics , vol.148 , pp. 937-945
    • Derr, L.K.1
  • 10
    • 0026014793 scopus 로고
    • RNA-mediated recombination in S. cerevisiae
    • Derr LK, Strathern JN, Garfinkel DJ (1991) RNA-mediated recombination in S. cerevisiae. Cell 67: 355-364
    • (1991) Cell , vol.67 , pp. 355-364
    • Derr, L.K.1    Strathern, J.N.2    Garfinkel, D.J.3
  • 12
    • 0023649687 scopus 로고
    • Pseudogenes in yeast?
    • Fink GR (1987) Pseudogenes in yeast? Cell 49: 5-6
    • (1987) Cell , vol.49 , pp. 5-6
    • Fink, G.R.1
  • 13
    • 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
  • 14
    • 1942533477 scopus 로고    scopus 로고
    • Detection and evaluation of intron retention events in the human transcriptome
    • Galante PAF, Sakabe NJ, Kirschbaum-Slager N, de Souza SJ (2004) Detection and evaluation of intron retention events in the human transcriptome. RNA 10: 757-765
    • (2004) RNA , vol.10 , pp. 757-765
    • Galante, P.A.F.1    Sakabe, N.J.2    Kirschbaum-Slager, N.3    de Souza, S.J.4
  • 17
    • 4844222571 scopus 로고    scopus 로고
    • Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences
    • Iida K, Seki M, Sakurai T, Satou M, Akiyama K, Toyoda T, Konagaya A, Shinozaki K (2004) Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences. Nucleic Acids Res 32: 5096-5103
    • (2004) Nucleic Acids Res , vol.32 , pp. 5096-5103
    • Iida, K.1    Seki, M.2    Sakurai, T.3    Satou, M.4    Akiyama, K.5    Toyoda, T.6    Konagaya, A.7    Shinozaki, K.8
  • 18
    • 0031844194 scopus 로고    scopus 로고
    • Evolutionary relationship of plant catalase genes inferred from exon-intron structures: Isozyme divergence after the separation of monocots and dicots
    • Iwamoto M, Maekawa M, Saito A, Higo H, Higo K (1998) Evolutionary relationship of plant catalase genes inferred from exon-intron structures: isozyme divergence after the separation of monocots and dicots. TAG Theor Appl Genet 97: 9-19
    • (1998) TAG Theor Appl Genet , vol.97 , pp. 9-19
    • Iwamoto, M.1    Maekawa, M.2    Saito, A.3    Higo, H.4    Higo, K.5
  • 19
    • 24344459435 scopus 로고    scopus 로고
    • The evolutionary fate of MULE-mediated duplications of host gene fragments in rice
    • Juretic N, Hoen DR, Huynh ML, Harrison PM, Bureau TE (2005) The evolutionary fate of MULE-mediated duplications of host gene fragments in rice. Genome Res 15: 1292-1297
    • (2005) Genome Res , vol.15 , pp. 1292-1297
    • Juretic, N.1    Hoen, D.R.2    Huynh, M.L.3    Harrison, P.M.4    Bureau, T.E.5
  • 20
    • 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
  • 21
    • 18744390284 scopus 로고    scopus 로고
    • Selecting for functional alternative splices in ESTs
    • Kan Z, States D, Gish W (2002) Selecting for functional alternative splices in ESTs. Genome Res 12: 1837-1845
    • (2002) Genome Res , vol.12 , pp. 1837-1845
    • Kan, Z.1    States, D.2    Gish, W.3
  • 22
    • 0036226603 scopus 로고    scopus 로고
    • BLAT: The BLAST-like alignment tool
    • Kent WJ (2002) BLAT: the BLAST-like alignment tool. Genome Res 12: 656-664
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 23
    • 77951120000 scopus 로고    scopus 로고
    • Alternative splicing and evolution: Diversification, exon definition and function
    • Keren H, Lev-Maor G, Ast G (2010) Alternative splicing and evolution: diversification, exon definition and function. Nat Rev Genet 11: 345-355
    • (2010) Nat Rev Genet , vol.11 , pp. 345-355
    • Keren, H.1    Lev-Maor, G.2    Ast, G.3
  • 24
    • 33846681383 scopus 로고    scopus 로고
    • Different levels of alternative splicing among eukaryotes
    • Kim E, Magen A, Ast G (2007) Different levels of alternative splicing among eukaryotes. Nucleic Acids Res 35: 125-131
    • (2007) Nucleic Acids Res , vol.35 , pp. 125-131
    • Kim, E.1    Magen, A.2    Ast, G.3
  • 25
    • 13244292333 scopus 로고    scopus 로고
    • DEDB: A database of Drosophila melanogaster exons in splicing graph form
    • Lee BTK, Tan TW, Ranganathan S (2004) DEDB: a database of Drosophila melanogaster exons in splicing graph form. BMC Bioinformatics 5: 189
    • (2004) BMC Bioinformatics , vol.5 , pp. 189
    • Lee, B.T.K.1    Tan, T.W.2    Ranganathan, S.3
  • 26
    • 33745088890 scopus 로고    scopus 로고
    • Intron gain and loss in segmentally duplicated genes in rice
    • Lin H, Zhu W, Silva JC, Gu X, Buell CR (2006) Intron gain and loss in segmentally duplicated genes in rice. Genome Biol 7: R41
    • (2006) Genome Biol , vol.7
    • Lin, H.1    Zhu, W.2    Silva, J.C.3    Gu, X.4    Buell, C.R.5
  • 27
    • 0037062440 scopus 로고    scopus 로고
    • Intron presence-absence polymorphism in Drosophila driven by positive Darwinian selection
    • Llopart A, Comeron JM, Brunet FG, Lachaise D, Long M (2002) Intron presence-absence polymorphism in Drosophila driven by positive Darwinian selection. Proc Natl Acad Sci USA 99: 8121-8126
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 8121-8126
    • Llopart, A.1    Comeron, J.M.2    Brunet, F.G.3    Lachaise, D.4    Long, M.5
  • 28
    • 0242354129 scopus 로고    scopus 로고
    • The origin of new genes: Glimpses from the young and old
    • Long M, Betrán E, Thornton K, Wang W (2003) The origin of new genes: glimpses from the young and old. Nat Rev Genet 4: 865-875
    • (2003) Nat Rev Genet , vol.4 , pp. 865-875
    • Long, M.1    Betrán, E.2    Thornton, K.3    Wang, W.4
  • 29
    • 77956277181 scopus 로고    scopus 로고
    • Function annotation of the rice transcriptome at singlenucleotide resolution by RNA-seq
    • Lu T, Lu G, Fan D, Zhu C, Li W, Zhao Q, Feng Q, Zhao Y, Guo Y, Li W, et al (2010) Function annotation of the rice transcriptome at singlenucleotide resolution by RNA-seq. Genome Res 20: 1238-1249
    • (2010) Genome Res , vol.20 , pp. 1238-1249
    • Lu, T.1    Lu, G.2    Fan, D.3    Zhu, C.4    Li, W.5    Zhao, Q.6    Feng, Q.7    Zhao, Y.8    Guo, Y.9    Li, W.10
  • 31
    • 84861890038 scopus 로고    scopus 로고
    • Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis
    • Marquez Y, Brown JWS, Simpson C, Barta A, Kalyna M (2012) Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res 22: 1184-1195
    • (2012) Genome Res , vol.22 , pp. 1184-1195
    • Marquez, Y.1    Brown, J.W.S.2    Simpson, C.3    Barta, A.4    Kalyna, M.5
  • 34
    • 0038780670 scopus 로고    scopus 로고
    • Eukaryotic intron loss
    • Mourier T, Jeffares DC (2003) Eukaryotic intron loss. Science 300: 1393
    • (2003) Science , vol.300 , pp. 1393
    • Mourier, T.1    Jeffares, D.C.2
  • 35
    • 28844443988 scopus 로고    scopus 로고
    • Speciesspecific variation of alternative splicing and transcriptional initiation in six eukaryotes
    • Nagasaki H, Arita M, Nishizawa T, Suwa M, Gotoh O (2005) Speciesspecific variation of alternative splicing and transcriptional initiation in six eukaryotes. Gene 364: 53-62
    • (2005) Gene , vol.364 , pp. 53-62
    • Nagasaki, H.1    Arita, M.2    Nishizawa, T.3    Suwa, M.4    Gotoh, O.5
  • 37
    • 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
    • 56749098074 scopus 로고    scopus 로고
    • Deep surveying of alternative splicing complexity in the human transcriptome by highthroughput sequencing
    • Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ (2008) Deep surveying of alternative splicing complexity in the human transcriptome by highthroughput sequencing. Nat Genet 40: 1413-1415
    • (2008) Nat Genet , vol.40 , pp. 1413-1415
    • Pan, Q.1    Shai, O.2    Lee, L.J.3    Frey, B.J.4    Blencowe, B.J.5
  • 39
    • 0033990061 scopus 로고    scopus 로고
    • Flexible sequence similarity searching with the FASTA3 program package
    • Pearson WR (2000) Flexible sequence similarity searching with the FASTA3 program package. Methods Mol Biol 132: 185-219
    • (2000) Methods Mol Biol , vol.132 , pp. 185-219
    • Pearson, W.R.1
  • 40
    • 0036845822 scopus 로고    scopus 로고
    • Splitting pairs: The diverging fates of duplicated genes
    • Prince VE, Pickett FB (2002) Splitting pairs: the diverging fates of duplicated genes. Nat Rev Genet 3: 827-837
    • (2002) Nat Rev Genet , vol.3 , pp. 827-837
    • Prince, V.E.1    Pickett, F.B.2
  • 42
    • 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
  • 43
    • 59349107038 scopus 로고    scopus 로고
    • Mystery of intron gain: New data and new models
    • Roy SW, Irimia M (2009) Mystery of intron gain: new data and new models. Trends Genet 25: 67-73
    • (2009) Trends Genet , vol.25 , pp. 67-73
    • Roy, S.W.1    Irimia, M.2
  • 45
    • 65449181986 scopus 로고    scopus 로고
    • Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome
    • Severing EI, van Dijk ADJ, Stiekema WJ, van Ham RCHJ (2009) Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome. BMC Genomics 10: 154
    • (2009) BMC Genomics , vol.10 , pp. 154
    • Severing, E.I.1    van Dijk, A.D.J.2    Stiekema, W.J.3    van Ham, R.C.H.J.4
  • 49
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739
    • (2011) Mol Biol Evol , vol.28 , pp. 2731-2739
    • Tamura, K.1    Peterson, D.2    Peterson, N.3    Stecher, G.4    Nei, M.5    Kumar, S.6
  • 50
    • 0035989395 scopus 로고    scopus 로고
    • Frequent germline mutations and somatic repeat instability in DNA mismatch-repair-deficient Caenorhabditis elegans
    • Tijsterman M, Pothof J, Plasterk RHA (2002) Frequent germline mutations and somatic repeat instability in DNA mismatch-repair-deficient Caenorhabditis elegans. Genetics 161: 651-660
    • (2002) Genetics , vol.161 , pp. 651-660
    • Tijsterman, M.1    Pothof, J.2    Plasterk, R.H.A.3
  • 51
    • 33644777605 scopus 로고    scopus 로고
    • Evolutionary fate of retroposed gene copies in the human genome
    • Vinckenbosch N, Dupanloup I, Kaessmann H (2006) Evolutionary fate of retroposed gene copies in the human genome. Proc Natl Acad Sci USA 103: 3220-3225
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 3220-3225
    • Vinckenbosch, N.1    Dupanloup, I.2    Kaessmann, H.3
  • 52
    • 33646484347 scopus 로고    scopus 로고
    • Genomewide comparative analysis of alternative splicing in plants
    • Wang BB, Brendel V (2006) Genomewide comparative analysis of alternative splicing in plants. Proc Natl Acad Sci USA 103: 7175-7180
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 7175-7180
    • Wang, B.B.1    Brendel, V.2
  • 54
    • 2442576123 scopus 로고    scopus 로고
    • Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species
    • Wang W, Yu H, Long M (2004) Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species. Nat Genet 36: 523-527
    • (2004) Nat Genet , vol.36 , pp. 523-527
    • Wang, W.1    Yu, H.2    Long, M.3
  • 56
    • 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
  • 57
    • 84874710448 scopus 로고    scopus 로고
    • gKaKs: The pipeline for genomelevel Ka/Ks calculation
    • Zhang C, Wang J, Long M, Fan C (2013) gKaKs: the pipeline for genomelevel Ka/Ks calculation. Bioinformatics 29: 645-646
    • (2013) Bioinformatics , vol.29 , pp. 645-646
    • Zhang, C.1    Wang, J.2    Long, M.3    Fan, C.4
  • 58
    • 26944438711 scopus 로고    scopus 로고
    • Computational identification of 69 retroposons in Arabidopsis
    • Zhang Y, Wu Y, Liu Y, Han B (2005) Computational identification of 69 retroposons in Arabidopsis. Plant Physiol 138: 935-948
    • (2005) Plant Physiol , vol.138 , pp. 935-948
    • Zhang, Y.1    Wu, Y.2    Liu, Y.3    Han, B.4
  • 59
    • 79959408735 scopus 로고    scopus 로고
    • A cautionary note for retrocopy identification: DNA-based duplication of introncontaining genes significantly contributes to the origination of single exon genes
    • Zhang YE, Vibranovski MD, Krinsky BH, Long M (2011) A cautionary note for retrocopy identification: DNA-based duplication of introncontaining genes significantly contributes to the origination of single exon genes. Bioinformatics 27: 1749-1753
    • (2011) Bioinformatics , vol.27 , pp. 1749-1753
    • Zhang, Y.E.1    Vibranovski, M.D.2    Krinsky, B.H.3    Long, M.4
  • 60
    • 0037783258 scopus 로고    scopus 로고
    • Refined annotation of the Arabidopsis genome by complete expressed sequence tag mapping
    • Zhu W, Schlueter SD, Brendel V (2003) Refined annotation of the Arabidopsis genome by complete expressed sequence tag mapping. Plant Physiol 132: 469-484
    • (2003) Plant Physiol , vol.132 , pp. 469-484
    • Zhu, W.1    Schlueter, S.D.2    Brendel, V.3
  • 61
    • 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


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