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Volumn 25, Issue 3, 2008, Pages 603-615

The mitochondrial genome of the gymnosperm Cycas taitungensis contains a novel family of short interspersed elements, Bpu sequences, and abundant RNA editing sites

Author keywords

Cycas; Mitochondrial genome; Mobile elements; Repeats; RNA editing sites

Indexed keywords

ADENINE; MITOCHONDRIAL DNA; RESTRICTION ENDONUCLEASE; RNA; THYMINE;

EID: 39749142161     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msn009     Document Type: Article
Times cited : (134)

References (46)
  • 1
    • 0344719444 scopus 로고    scopus 로고
    • Evolution of mitochondrial gene content: Gene loss and transfer to the nucleus
    • Adams KL, Palmer JD. 2003. Evolution of mitochondrial gene content: gene loss and transfer to the nucleus. Mol Phylogenet Evol. 29:380-395.
    • (2003) Mol Phylogenet Evol , vol.29 , pp. 380-395
    • Adams, K.L.1    Palmer, J.D.2
  • 2
    • 0037162534 scopus 로고    scopus 로고
    • Punctuated evolution of mitochondrial gene content: High and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution
    • Adams KL, Qiu YL, Stoutemyer M, Palmer JD. 2002. Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. Proc Natl Acad Sci USA. 99:9905-9912.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 9905-9912
    • Adams, K.L.1    Qiu, Y.L.2    Stoutemyer, M.3    Palmer, J.D.4
  • 3
    • 0033555906 scopus 로고    scopus 로고
    • Tandem repeats finder: A program to analyze DNA sequences
    • Benson G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27:573-580.
    • (1999) Nucleic Acids Res , vol.27 , pp. 573-580
    • Benson, G.1
  • 4
    • 11144228905 scopus 로고    scopus 로고
    • Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella
    • Bergthorsson U, Richardson AO, Young GJ, Goertzen LR, Palmer JD. 2004. Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. Proc Natl Acad Sci USA. 101:17747-17752.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 17747-17752
    • Bergthorsson, U.1    Richardson, A.O.2    Young, G.J.3    Goertzen, L.R.4    Palmer, J.D.5
  • 5
    • 2442517979 scopus 로고    scopus 로고
    • Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes
    • Chaw SM, Chang CC, Chen HL, Li WH. 2004. Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes. J Mol Evol. 58:424-441.
    • (2004) J Mol Evol , vol.58 , pp. 424-441
    • Chaw, S.M.1    Chang, C.C.2    Chen, H.L.3    Li, W.H.4
  • 6
    • 25144494505 scopus 로고    scopus 로고
    • A phylogeny of cycads (Cycadales) inferred from chloroplast matK gene, trnK intron, and nuclear rDNA ITS region
    • Chaw SM, Walters TW, Chang CC, Hu SH, Chen SH. 2005. A phylogeny of cycads (Cycadales) inferred from chloroplast matK gene, trnK intron, and nuclear rDNA ITS region. Mol Phylogenet Evol. 37:214-234.
    • (2005) Mol Phylogenet Evol , vol.37 , pp. 214-234
    • Chaw, S.M.1    Walters, T.W.2    Chang, C.C.3    Hu, S.H.4    Chen, S.H.5
  • 7
    • 0031012107 scopus 로고    scopus 로고
    • Molecular phylogeny of extant gymnosperms and seed plant evolution: Analysis of nuclear 18S rRNA sequences
    • Chaw SM, Zharkikh A, Sung HM, Lau TC, Li WH. 1997. Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences. Mol Biol Evol. 14:56-68.
    • (1997) Mol Biol Evol , vol.14 , pp. 56-68
    • Chaw, S.M.1    Zharkikh, A.2    Sung, H.M.3    Lau, T.C.4    Li, W.H.5
  • 8
    • 0032564449 scopus 로고    scopus 로고
    • Explosive invasion of plant mitochondria by a group I intron
    • Cho Y, Qiu YL, Kuhlman P, Palmer JD. 1998. Explosive invasion of plant mitochondria by a group I intron. Proc Natl Acad Sci USA. 95:14244-14249.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 14244-14249
    • Cho, Y.1    Qiu, Y.L.2    Kuhlman, P.3    Palmer, J.D.4
  • 9
    • 11144234440 scopus 로고    scopus 로고
    • Clifton SW, Minx P, Fauron CM, et al. (13 co-authors). 2004. Sequence and comparative analysis of the maize NB mitochondrial genome. Plant Physiol. 136:3486-3503.
    • Clifton SW, Minx P, Fauron CM, et al. (13 co-authors). 2004. Sequence and comparative analysis of the maize NB mitochondrial genome. Plant Physiol. 136:3486-3503.
  • 11
    • 10344257212 scopus 로고    scopus 로고
    • Ancestors of trans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosses with vascular plants
    • Groth-Malonek M, Pruchner D, Grewe F, Knoop V. 2005. Ancestors of trans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosses with vascular plants. Mol Biol Evol. 22:117-125.
    • (2005) Mol Biol Evol , vol.22 , pp. 117-125
    • Groth-Malonek, M.1    Pruchner, D.2    Grewe, F.3    Knoop, V.4
  • 12
    • 0344442430 scopus 로고    scopus 로고
    • The complete nucleotide sequence and RNA editing content of the mitochondrial genome of rapeseed (Brassica napus L.): Comparative analysis of the mitochondrial genomes of rapeseed and Arabidopsis thaliana
    • Handa H. 2003. The complete nucleotide sequence and RNA editing content of the mitochondrial genome of rapeseed (Brassica napus L.): comparative analysis of the mitochondrial genomes of rapeseed and Arabidopsis thaliana. Nucleic Acids Res. 31:5907-5916.
    • (2003) Nucleic Acids Res , vol.31 , pp. 5907-5916
    • Handa, H.1
  • 13
    • 0025910413 scopus 로고
    • Editing of a chloroplast mRNA by creation of an initiation codon
    • Hoch B, Maier RM, Appel K, Igloi GL, Kossel H. 1991. Editing of a chloroplast mRNA by creation of an initiation codon. Nature. 353:178-180.
    • (1991) Nature , vol.353 , pp. 178-180
    • Hoch, B.1    Maier, R.M.2    Appel, K.3    Igloi, G.L.4    Kossel, H.5
  • 15
    • 0029822746 scopus 로고    scopus 로고
    • Targeting presequence acquisition after mitochondrial gene transfer to the nucleus occurs by duplication of existing targeting signals
    • Kadowaki K, Kubo N, Ozawa K, Hirai A. 1996. Targeting presequence acquisition after mitochondrial gene transfer to the nucleus occurs by duplication of existing targeting signals. EMBO J. 15:6652-6661.
    • (1996) EMBO J , vol.15 , pp. 6652-6661
    • Kadowaki, K.1    Kubo, N.2    Ozawa, K.3    Hirai, A.4
  • 17
    • 4744343662 scopus 로고    scopus 로고
    • The mitochondrial DNA of land plants: Peculiarities in phylogenetic perspective
    • Knoop V. 2004. The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective. Curr Genet. 46:123-139.
    • (2004) Curr Genet , vol.46 , pp. 123-139
    • Knoop, V.1
  • 18
    • 12744253474 scopus 로고    scopus 로고
    • A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts
    • Kotera E, Tasaka M, Shikanai T. 2005. A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts. Nature. 433:326-330.
    • (2005) Nature , vol.433 , pp. 326-330
    • Kotera, E.1    Tasaka, M.2    Shikanai, T.3
  • 19
    • 0034235831 scopus 로고    scopus 로고
    • The complete nucleotide sequence of the mitochondrial genome of sugar beet (Beta vulgaris L.) reveals a novel gene for tRNA(Cys)(GCA)
    • Kubo T, Nishizawa S, Sugawara A, Itchoda N, Estiati A, Mikami T. 2000. The complete nucleotide sequence of the mitochondrial genome of sugar beet (Beta vulgaris L.) reveals a novel gene for tRNA(Cys)(GCA). Nucleic Acids Res. 28:2571-2576.
    • (2000) Nucleic Acids Res , vol.28 , pp. 2571-2576
    • Kubo, T.1    Nishizawa, S.2    Sugawara, A.3    Itchoda, N.4    Estiati, A.5    Mikami, T.6
  • 20
    • 3242810318 scopus 로고    scopus 로고
    • MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment
    • Kumar S, Tamura K, Nei M. 2004. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform. 5:150-163.
    • (2004) Brief Bioinform , vol.5 , pp. 150-163
    • Kumar, S.1    Tamura, K.2    Nei, M.3
  • 22
    • 0030854739 scopus 로고    scopus 로고
    • tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
    • Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955-964.
    • (1997) Nucleic Acids Res , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 23
    • 4043172772 scopus 로고    scopus 로고
    • Lurin C, Andres C, Aubourg S, et al. 19 co-authors. 2004. Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell. 16:2089-2103.
    • Lurin C, Andres C, Aubourg S, et al. 19 co-authors. 2004. Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell. 16:2089-2103.
  • 24
    • 0031027524 scopus 로고    scopus 로고
    • Evolution of trans-splicing plant mitochondrial introns in pre-Permian times
    • Malek O, Brennicke A, Knoop V. 1997. Evolution of trans-splicing plant mitochondrial introns in pre-Permian times. Proc Natl Acad Sci USA. 94:553-558.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 553-558
    • Malek, O.1    Brennicke, A.2    Knoop, V.3
  • 25
    • 0031789680 scopus 로고    scopus 로고
    • Trans-splicing group II introns in plant mitochondria: The complete set of cis-arranged homologs in ferns, fern allies, and a hornwort
    • Malek O, Knoop V. 1998. Trans-splicing group II introns in plant mitochondria: the complete set of cis-arranged homologs in ferns, fern allies, and a hornwort. RNA. 4:1599-1609.
    • (1998) RNA , vol.4 , pp. 1599-1609
    • Malek, O.1    Knoop, V.2
  • 26
    • 0029066770 scopus 로고
    • Structure and activities of group II introns
    • Michel F, Ferat JL. 1995. Structure and activities of group II introns. Annu Rev Biochem. 64:435-461.
    • (1995) Annu Rev Biochem , vol.64 , pp. 435-461
    • Michel, F.1    Ferat, J.L.2
  • 27
    • 25444502084 scopus 로고    scopus 로고
    • Mower JP. 2005. PREP-Mt: predictive RNA editor for plant mitochondrial genes. BMC Bioinformatics. 6:96.
    • Mower JP. 2005. PREP-Mt: predictive RNA editor for plant mitochondrial genes. BMC Bioinformatics. 6:96.
  • 28
    • 35748939098 scopus 로고    scopus 로고
    • Computational analysis of RNA editing sites in plant mitochondrial genomes reveals similar information content and a sporadic distribution of editing sites
    • Mulligan RM, Chang KL, Chou CC. 2007. Computational analysis of RNA editing sites in plant mitochondrial genomes reveals similar information content and a sporadic distribution of editing sites. Mol Biol Evol. 24:1971-1981.
    • (2007) Mol Biol Evol , vol.24 , pp. 1971-1981
    • Mulligan, R.M.1    Chang, K.L.2    Chou, C.C.3
  • 29
    • 0036456491 scopus 로고    scopus 로고
    • The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: Frequent DNA sequence acquisition and loss during the evolution of flowering plants
    • Notsu Y, Masood S, Nishikawa T, Kubo N, Akiduki G, Nakazono M, Hirai A, Kadowaki K. 2002. The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants. Mol Genet Genomics. 268:434-445.
    • (2002) Mol Genet Genomics , vol.268 , pp. 434-445
    • Notsu, Y.1    Masood, S.2    Nishikawa, T.3    Kubo, N.4    Akiduki, G.5    Nakazono, M.6    Hirai, A.7    Kadowaki, K.8
  • 30
    • 0026443330 scopus 로고
    • Mitochondrial DNA of Marchantia polymorpha as a single circular form with no incorporation of foreign DNA
    • Oda K, Kohchi T, Ohyama K. 1992. Mitochondrial DNA of Marchantia polymorpha as a single circular form with no incorporation of foreign DNA. Biosci Biotechnol Biochem. 56:132-135.
    • (1992) Biosci Biotechnol Biochem , vol.56 , pp. 132-135
    • Oda, K.1    Kohchi, T.2    Ohyama, K.3
  • 31
    • 28544439733 scopus 로고    scopus 로고
    • Ogihara Y, Yamazaki Y, Murai K, et al. (14 co-authors). 2005. Structural dynamics of cereal mitochondrial genomes as revealed by complete nucleotide sequencing of the wheat mitochondrial genome. Nucleic Acids Res. 33:6235-6250.
    • Ogihara Y, Yamazaki Y, Murai K, et al. (14 co-authors). 2005. Structural dynamics of cereal mitochondrial genomes as revealed by complete nucleotide sequencing of the wheat mitochondrial genome. Nucleic Acids Res. 33:6235-6250.
  • 32
    • 33750303564 scopus 로고    scopus 로고
    • Qiu YL, Li L, Wang B, et al. (13 co-authors). 2006. The deepest divergences in land plants inferred from phylogenomic evidence. Proc Natl Acad Sci USA. 103:15511-15516.
    • Qiu YL, Li L, Wang B, et al. (13 co-authors). 2006. The deepest divergences in land plants inferred from phylogenomic evidence. Proc Natl Acad Sci USA. 103:15511-15516.
  • 33
    • 16444376278 scopus 로고    scopus 로고
    • A novel additional group II intron distinguishes the mitochondrial rps3 gene in gymnosperms
    • Regina TM, Picardi E, Lopez L, Pesole G, Quagliariello C. 2005. A novel additional group II intron distinguishes the mitochondrial rps3 gene in gymnosperms. J Mol Evol. 60:196-206.
    • (2005) J Mol Evol , vol.60 , pp. 196-206
    • Regina, T.M.1    Picardi, E.2    Lopez, L.3    Pesole, G.4    Quagliariello, C.5
  • 34
    • 0035283304 scopus 로고    scopus 로고
    • Reducing the genome size of organelles favours gene transfer to the nucleus
    • Selosse M, Albert B, Godelle B. 2001. Reducing the genome size of organelles favours gene transfer to the nucleus. Trends Ecol Evol. 16:135-141.
    • (2001) Trends Ecol Evol , vol.16 , pp. 135-141
    • Selosse, M.1    Albert, B.2    Godelle, B.3
  • 35
    • 33645074681 scopus 로고    scopus 로고
    • RNA editing in plant organelles: Machinery, physiological function and evolution
    • Shikanai T. 2006. RNA editing in plant organelles: machinery, physiological function and evolution. Cell Mol Life Sci. 63:698-708.
    • (2006) Cell Mol Life Sci , vol.63 , pp. 698-708
    • Shikanai, T.1
  • 37
    • 0002432955 scopus 로고
    • Morphology and systematics of the Cycadales
    • Stevenson DW. 1990. Morphology and systematics of the Cycadales. Mem N Y Bot Gard. 57:8-15.
    • (1990) Mem N Y Bot Gard , vol.57 , pp. 8-15
    • Stevenson, D.W.1
  • 38
    • 0027158760 scopus 로고
    • A rapid CTAB DNA isolation technique useful for RAPD fingerprinting and other PCR applications
    • Stewart CN Jr, Via LE. 1993. A rapid CTAB DNA isolation technique useful for RAPD fingerprinting and other PCR applications. Biotechniques. 14:748-750.
    • (1993) Biotechniques , vol.14 , pp. 748-750
    • Stewart Jr, C.N.1    Via, L.E.2
  • 39
    • 15044341867 scopus 로고    scopus 로고
    • The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: Comparative analysis of mitochondrial genomes in higher plants
    • Sugiyama Y, Watase Y, Nagase M, Makita N, Yagura S, Hirai A, Sugiura M. 2005. The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants. Mol Genet Genomics. 272:603-615.
    • (2005) Mol Genet Genomics , vol.272 , pp. 603-615
    • Sugiyama, Y.1    Watase, Y.2    Nagase, M.3    Makita, N.4    Yagura, S.5    Hirai, A.6    Sugiura, M.7
  • 40
    • 33847669179 scopus 로고    scopus 로고
    • The mitochondrial genome of the moss Physcomitrella patens sheds new light on mitochondrial evolution in land plants
    • Terasawa K, Odahara M, Kabeya Y, Kikugawa T, Sekine Y, Fujiwara M, Sato N. 2007. The mitochondrial genome of the moss Physcomitrella patens sheds new light on mitochondrial evolution in land plants. Mol Biol Evol. 24:699-709.
    • (2007) Mol Biol Evol , vol.24 , pp. 699-709
    • Terasawa, K.1    Odahara, M.2    Kabeya, Y.3    Kikugawa, T.4    Sekine, Y.5    Fujiwara, M.6    Sato, N.7
  • 41
    • 0042922459 scopus 로고    scopus 로고
    • The mitochondrial genome of Chara vulgaris: Insights into the mitochondrial DNA architecture of the last common ancestor of green algae and land plants
    • Turmel M, Otis C, Lemieux C. 2003. The mitochondrial genome of Chara vulgaris: insights into the mitochondrial DNA architecture of the last common ancestor of green algae and land plants. Plant Cell. 15:1888-1903.
    • (2003) Plant Cell , vol.15 , pp. 1888-1903
    • Turmel, M.1    Otis, C.2    Lemieux, C.3
  • 42
    • 0031021278 scopus 로고    scopus 로고
    • The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides
    • Unseld M, Marienfeld JR, Brandt P, Brennicke A. 1997. The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides. Nat Genet. 15:57-61.
    • (1997) Nat Genet , vol.15 , pp. 57-61
    • Unseld, M.1    Marienfeld, J.R.2    Brandt, P.3    Brennicke, A.4
  • 43
    • 34548410837 scopus 로고    scopus 로고
    • Transfer of chloroplast genomic DNA to mitochondrial genome occurred at least 300 MYA
    • Wang D, Wu YW, Chun-Chieh Shih A, Wu CS, Wang YN, Chaw SM. 2007. Transfer of chloroplast genomic DNA to mitochondrial genome occurred at least 300 MYA. Mol Biol Evol. 24:2040-2048.
    • (2007) Mol Biol Evol , vol.24 , pp. 2040-2048
    • Wang, D.1    Wu, Y.W.2    Chun-Chieh Shih, A.3    Wu, C.S.4    Wang, Y.N.5    Chaw, S.M.6
  • 44
    • 1842584947 scopus 로고    scopus 로고
    • Applied bioinformatics for the identification of regulatory elements
    • Wasserman WW, Sandelin A. 2004. Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet. 5:276-287.
    • (2004) Nat Rev Genet , vol.5 , pp. 276-287
    • Wasserman, W.W.1    Sandelin, A.2
  • 45
    • 0026029987 scopus 로고
    • A termination codon is created by RNA editing in the petunia atp9 transcript
    • Wintz H, Hanson MR. 1991. A termination codon is created by RNA editing in the petunia atp9 transcript. Curr Genet. 19:61-64.
    • (1991) Curr Genet , vol.19 , pp. 61-64
    • Wintz, H.1    Hanson, M.R.2
  • 46
    • 34548108492 scopus 로고    scopus 로고
    • Chloroplast genome (cpDNA) of Cycas taitungensis and 56 cp protein-coding genes of Gnetum parvifolium: Insights into cpDNA evolution and phylogeny of extant seed plants
    • Wu CS, Wang YN, Liu SM, Chaw SM. 2007. Chloroplast genome (cpDNA) of Cycas taitungensis and 56 cp protein-coding genes of Gnetum parvifolium: insights into cpDNA evolution and phylogeny of extant seed plants. Mol Biol Evol. 24:1366-1379.
    • (2007) Mol Biol Evol , vol.24 , pp. 1366-1379
    • Wu, C.S.1    Wang, Y.N.2    Liu, S.M.3    Chaw, S.M.4


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