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Volumn 7, Issue 5, 2006, Pages

Intron gain and loss in segmentally duplicated genes in rice

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; PLANT DNA;

EID: 33745088890     PISSN: 1474760X     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2006-7-5-r41     Document Type: Article
Times cited : (113)

References (53)
  • 1
    • 0037058978 scopus 로고    scopus 로고
    • Large-scale comparison of intron positions among animal, plant, and fungal genes
    • Fedorov A, Merican AF, Gilbert W: Large-scale comparison of intron positions among animal, plant, and fungal genes. Proc Natl Acad Sci USA 2002, 99:16128-16133.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 16128-16133
    • Fedorov, A.1    Merican, A.F.2    Gilbert, W.3
  • 2
    • 0042921194 scopus 로고    scopus 로고
    • Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution
    • Rogozin IB, Wolf YI, Sorokin AV, Mirkin BG, Koonin EV: Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr Biol 2003, 13:1512-1517.
    • (2003) Curr Biol , vol.13 , pp. 1512-1517
    • Rogozin, I.B.1    Wolf, Y.I.2    Sorokin, A.V.3    Mirkin, B.G.4    Koonin, E.V.5
  • 3
    • 0023649687 scopus 로고
    • Pseudogenes in yeast?
    • Fink GR: Pseudogenes in yeast? Cell 1987, 49:5-6.
    • (1987) Cell , vol.49 , pp. 5-6
    • Fink, G.R.1
  • 6
    • 4143150876 scopus 로고    scopus 로고
    • Preferential loss and gain of introns in 3′ portions of genes suggests a reverse-transcription mechanism of intron insertion
    • Sverdlov AV, Babenko VN, Rogozin IB, Koonin EV: Preferential loss and gain of introns in 3′ portions of genes suggests a reverse-transcription mechanism of intron insertion. Gene 2004, 338:85-91.
    • (2004) Gene , vol.338 , pp. 85-91
    • Sverdlov, A.V.1    Babenko, V.N.2    Rogozin, I.B.3    Koonin, E.V.4
  • 9
    • 0029585511 scopus 로고
    • Evolution of the intron-exon structure of eukaryotic genes
    • Long M, de Souza SJ, Gilbert W: Evolution of the intron-exon structure of eukaryotic genes. Curr Opin Genet Dev 1995, 5:774-778.
    • (1995) Curr Opin Genet Dev , vol.5 , pp. 774-778
    • Long, M.1    de Souza, S.J.2    Gilbert, W.3
  • 10
    • 0029858773 scopus 로고    scopus 로고
    • Introns and reading frames: Correlation between splicing sites and their codon positions
    • Tomita M, Shimizu N, Brutlag DL: Introns and reading frames: correlation between splicing sites and their codon positions. Mol Biol Evol 1996, 13:1219-1223.
    • (1996) Mol Biol Evol , vol.13 , pp. 1219-1223
    • Tomita, M.1    Shimizu, N.2    Brutlag, D.L.3
  • 12
    • 0027771868 scopus 로고
    • On the ancient nature of introns
    • Gilbert W, Glynias M: On the ancient nature of introns. Gene 1993, 135:137-144.
    • (1993) Gene , vol.135 , pp. 137-144
    • Gilbert, W.1    Glynias, M.2
  • 13
    • 3042548834 scopus 로고    scopus 로고
    • The evolutionary gain of spliceosomal introns: Sequence and phase preferences
    • Qiu WG, Schisler N, Stoltzfus A: The evolutionary gain of spliceosomal introns: sequence and phase preferences. Mol Biol Evol 2004, 21:1252-1263.
    • (2004) Mol Biol Evol , vol.21 , pp. 1252-1263
    • Qiu, W.G.1    Schisler, N.2    Stoltzfus, A.3
  • 14
    • 3843113189 scopus 로고    scopus 로고
    • Origins of recently gained introns in Caenorhabditis
    • Coghlan A, Wolfe KH: Origins of recently gained introns in Caenorhabditis. Proc Natl Acad Sci USA 2004, 101:11362-11367.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 11362-11367
    • Coghlan, A.1    Wolfe, K.H.2
  • 15
    • 0037795455 scopus 로고    scopus 로고
    • Large-scale comparison of intron positions in mammalian genes shows intron loss but no gain
    • Roy SW, Fedorov A, Gilbert W: Large-scale comparison of intron positions in mammalian genes shows intron loss but no gain. Proc Natl Acad Sci USA 2003, 100:7158-7162.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 7158-7162
    • Roy, S.W.1    Fedorov, A.2    Gilbert, W.3
  • 16
    • 17644379051 scopus 로고    scopus 로고
    • Rates of intron loss and gain: Implications for early eukaryotic evolution
    • Roy SW, Gilbert W: Rates of intron loss and gain: implications for early eukaryotic evolution. Proc Natl Acad Sci USA 2005, 102:5773-5778.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 5773-5778
    • Roy, S.W.1    Gilbert, W.2
  • 19
    • 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: Prevalence of intron gain over intron loss in the evolution of paralogous gene families. Nucleic Acids Res 2004, 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
  • 21
    • 84907150192 scopus 로고    scopus 로고
    • The map-based sequence of the rice genome
    • International Rice Genome Sequencing Project:
    • International Rice Genome Sequencing Project: The map-based sequence of the rice genome. Nature 2005, 436:793-800.
    • (2005) Nature , vol.436 , pp. 793-800
  • 23
    • 0024712231 scopus 로고
    • Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data
    • Wolfe KH, Gouy M, Yang YW, Sharp PM, Li WH: Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc Natl Acad Sci USA 1989, 86:6201-6205.
    • (1989) Proc Natl Acad Sci USA , vol.86 , pp. 6201-6205
    • Wolfe, K.H.1    Gouy, M.2    Yang, Y.W.3    Sharp, P.M.4    Li, W.H.5
  • 24
    • 0028973842 scopus 로고    scopus 로고
    • The origin and early diversification of angiosperms
    • Crane PR, Friis EM, Pedersen KR: The origin and early diversification of angiosperms. Nature 2002, 374:27-33.
    • (2002) Nature , vol.374 , pp. 27-33
    • Crane, P.R.1    Friis, E.M.2    Pedersen, K.R.3
  • 25
    • 3042836334 scopus 로고    scopus 로고
    • Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics
    • Paterson AH, Bowers JE, Chapman BA: Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci USA 2004, 101:9903-9908.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 9903-9908
    • Paterson, A.H.1    Bowers, J.E.2    Chapman, B.A.3
  • 26
    • 0141564555 scopus 로고    scopus 로고
    • Evidence that rice and other cereals are ancient aneuploids
    • Vandepoele K, Simillion C, Van de Peer Y: Evidence that rice and other cereals are ancient aneuploids. Plant Cell 2003, 15:2192-2202.
    • (2003) Plant Cell , vol.15 , pp. 2192-2202
    • Vandepoele, K.1    Simillion, C.2    Van de Peer, Y.3
  • 27
    • 14244250895 scopus 로고    scopus 로고
    • Duplication and DNA segmental loss in the rice genome: Implications for diploidization
    • Wang X, Shi X, Hao B, Ge S, Luo J: Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol 2005, 165:937-946.
    • (2005) New Phytol , vol.165 , pp. 937-946
    • Wang, X.1    Shi, X.2    Hao, B.3    Ge, S.4    Luo, J.5
  • 28
    • 2342554268 scopus 로고    scopus 로고
    • Building genomic profiles for uncovering segmental homology in the twilight zone
    • Simillion C, Vandepoele K, Saeys Y, Van de Peer Y: Building genomic profiles for uncovering segmental homology in the twilight zone. Genome Res 2004, 14:1095-1106.
    • (2004) Genome Res , vol.14 , pp. 1095-1106
    • Simillion, C.1    Vandepoele, K.2    Saeys, Y.3    Van de Peer, Y.4
  • 29
    • 4143051590 scopus 로고    scopus 로고
    • Ancestral genome duplication in rice
    • Guyot R, Keller B: Ancestral genome duplication in rice. Genome 2004, 47:610-614.
    • (2004) Genome , vol.47 , pp. 610-614
    • Guyot, R.1    Keller, B.2
  • 30
    • 3042599701 scopus 로고    scopus 로고
    • Accelerated rates of intron gain/loss and protein evolution in duplicate genes in human and mouse malaria parasites
    • Castillo-Davis CI, Bedford TB, Hartl DL: Accelerated rates of intron gain/loss and protein evolution in duplicate genes in human and mouse malaria parasites. Mol Biol Evol 2004, 21:1422-1427.
    • (2004) Mol Biol Evol , vol.21 , pp. 1422-1427
    • Castillo-Davis, C.I.1    Bedford, T.B.2    Hartl, D.L.3
  • 31
    • 0031737389 scopus 로고    scopus 로고
    • The recent origins of spliceosomal introns revisited
    • Logsdon JM Jr: The recent origins of spliceosomal introns revisited. Curr Opin Genet Dev 1998, 8:637-648.
    • (1998) Curr Opin Genet Dev , vol.8 , pp. 637-648
    • Logsdon Jr., J.M.1
  • 32
    • 3843106810 scopus 로고    scopus 로고
    • Worm genomes hold the smoking guns of intron gain
    • Logsdon JM Jr: Worm genomes hold the smoking guns of intron gain. Proc Natl Acad Sci USA 2004, 101:11195-11196.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 11195-11196
    • Logsdon Jr., J.M.1
  • 33
    • 0032753460 scopus 로고    scopus 로고
    • Association of intron phases with conservation at splice site sequences and evolution of spliceosomal introns
    • Long M, Deutsch M: Association of intron phases with conservation at splice site sequences and evolution of spliceosomal introns. Mol Biol Evol 1999, 16:1528-1534.
    • (1999) Mol Biol Evol , vol.16 , pp. 1528-1534
    • Long, M.1    Deutsch, M.2
  • 34
    • 0345548556 scopus 로고    scopus 로고
    • Genomic characterization of Rim2/Hipa elements reveals a CACTA-like transposon superfamily with unique features in the rice genome
    • Wang GD, Tian PF, Cheng ZK, Wu G, Jiang JM, Li DB, Li Q, He ZH: Genomic characterization of Rim2/Hipa elements reveals a CACTA-like transposon superfamily with unique features in the rice genome. Mol Genet Genomics 2003, 270:234-242.
    • (2003) Mol Genet Genomics , vol.270 , pp. 234-242
    • Wang, G.D.1    Tian, P.F.2    Cheng, Z.K.3    Wu, G.4    Jiang, J.M.5    Li, D.B.6    Li, Q.7    He, Z.H.8
  • 35
    • 0020710981 scopus 로고
    • Pseudogenes for human small nuclear RNA U3 appear to arise by integration of self-primed reverse transcripts of the RNA into new chromosomal sites
    • Bernstein LB, Mount SM, Weiner AM: Pseudogenes for human small nuclear RNA U3 appear to arise by integration of self-primed reverse transcripts of the RNA into new chromosomal sites. Cell 1983, 32:461-472.
    • (1983) Cell , vol.32 , pp. 461-472
    • Bernstein, L.B.1    Mount, S.M.2    Weiner, A.M.3
  • 36
    • 0020701499 scopus 로고
    • How mammalian RNA returns to its genome
    • Lewin R: How mammalian RNA returns to its genome. Science 1983, 219:1052-1054.
    • (1983) Science , vol.219 , pp. 1052-1054
    • Lewin, R.1
  • 37
    • 3543107924 scopus 로고    scopus 로고
    • A phylogeny of Caenorhabditis reveals frequent loss of introns during nematode evolution
    • Cho S, Jin SW, Cohen A, Ellis RE: A phylogeny of Caenorhabditis reveals frequent loss of introns during nematode evolution. Genome Res 2004, 14:1207-1220.
    • (2004) Genome Res , vol.14 , pp. 1207-1220
    • Cho, S.1    Jin, S.W.2    Cohen, A.3    Ellis, R.E.4
  • 38
    • 0025087346 scopus 로고
    • Exon mutations uncouple 5′ splice site selection from U1 snRNA pairing
    • Seraphin B, Rosbash M: Exon mutations uncouple 5′ splice site selection from U1 snRNA pairing. Cell 1990, 63:619-629.
    • (1990) Cell , vol.63 , pp. 619-629
    • Seraphin, B.1    Rosbash, M.2
  • 39
    • 0019946342 scopus 로고
    • A single-base change at a splice site in a beta 0-thalassemic gene causes abnormal RNA splicing
    • Treisman R, Proudfoot NJ, Shander M, Maniatis T: A single-base change at a splice site in a beta 0-thalassemic gene causes abnormal RNA splicing. Cell 1982, 29:903-911.
    • (1982) Cell , vol.29 , pp. 903-911
    • Treisman, R.1    Proudfoot, N.J.2    Shander, M.3    Maniatis, T.4
  • 40
    • 0029829071 scopus 로고    scopus 로고
    • SPINDLY, a tetratricopeptide repeat protein involved in gibberellin signal transduction in Arabidopsis
    • Jacobsen SE, Binkowski KA, Olszewski NE: SPINDLY, a tetratricopeptide repeat protein involved in gibberellin signal transduction in Arabidopsis. Proc Natl Acad Sci USA 1996, 93:9292-9296.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 9292-9296
    • Jacobsen, S.E.1    Binkowski, K.A.2    Olszewski, N.E.3
  • 41
    • 33745101230 scopus 로고    scopus 로고
    • Washington University BLAST Archives
    • Washington University BLAST Archives [http://blast.wustl.edu]
  • 42
    • 12344335569 scopus 로고    scopus 로고
    • DAGchainer: A tool for mining segmental genome duplications and synteny
    • Haas BJ, Delcher AL, Wortman JR, Salzberg SL: DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics 2004, 20:3643-3646.
    • (2004) Bioinformatics , vol.20 , pp. 3643-3646
    • Haas, B.J.1    Delcher, A.L.2    Wortman, J.R.3    Salzberg, S.L.4
  • 44
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 45
    • 84873055436 scopus 로고    scopus 로고
    • The TIGR Arabidopsis thaliana Database
    • The TIGR Arabidopsis thaliana Database [http://www.tigr.org/tdb/e2k1/ath1/]
  • 47
    • 84886758064 scopus 로고    scopus 로고
    • The TIGR Maize Database
    • The TIGR Maize Database [http://maize.tigr.org/]
  • 48
    • 33745077214 scopus 로고    scopus 로고
    • TIGR Assembled Sorghum Bicolor [ftp://ftp.tigr.org/pub/data/MAIZE/Sorghum_assembly/ASB.gz]
    • TIGR Assembled Sorghum Bicolor [ftp://ftp.tigr.org/pub/data/MAIZE/Sorghum_assembly/ASB.gz]
  • 49
    • 33745077816 scopus 로고    scopus 로고
    • The JGI Populus trichocarpa Genome WebSite
    • The JGI Populus trichocarpa Genome WebSite [http://genome.jgi-psf.org/PoptrI/PoptrI.home.html]
  • 50
    • 0034065724 scopus 로고    scopus 로고
    • Ab initio gene finding in Drosophila genomic DNA
    • Salamov AA, Solovyev VV: Ab initio gene finding in Drosophila genomic DNA. Genome Res 2000, 10:516-522.
    • (2000) Genome Res , vol.10 , pp. 516-522
    • Salamov, A.A.1    Solovyev, V.V.2
  • 51
    • 0031792828 scopus 로고    scopus 로고
    • Models of amino acid substitution and applications to mitochondrial protein evolution
    • Yang Z, Nielsen R, Hasegawa M: Models of amino acid substitution and applications to mitochondrial protein evolution. Mol Biol Evol 1998, 15:1600-1611.
    • (1998) Mol Biol Evol , vol.15 , pp. 1600-1611
    • Yang, Z.1    Nielsen, R.2    Hasegawa, M.3
  • 52
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang Z: PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 1997, 13:555-556.
    • (1997) Comput Appl Biosci , vol.13 , pp. 555-556
    • Yang, Z.1
  • 53
    • 0029812835 scopus 로고    scopus 로고
    • Substitution rate comparisons between grasses and palms: Synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL
    • Gaut BS, Morton BR, McCaig BC, Clegg MT: Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc Natl Acad Sci USA 1996, 93:10274-10279.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 10274-10279
    • Gaut, B.S.1    Morton, B.R.2    McCaig, B.C.3    Clegg, M.T.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.