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Chloroplast DNA of black pine retains a residual inverted repeat lacking rRNA genes: nucleotide sequences of trnQ, trnK, psbA, trnI and trnH and the absence of rps16

Summary

A physical map of black pine (Pinus thunbergii) chloroplast DNA (120 kb) was constructed and two separate portions of its nucleotide sequence were determined. One portion contains trnQ-UUG, ORF510, ORF83, trnK-UUU (ORF515 in the trnK intron), ORF22, psbA, trnI-CAU (on the opposing strand) and trnH-GUG, in that order. Sequence analysis of another portion revealed the presence of a 495 by inverted repeat containing trnI-CAU and the 3′ end of psbA but lacking rRNA genes. The position of trnI-CAU is unique because most chloroplast DNAs have no gene between psbA and trnH (trnI-CAU is usually located further downstream). Black pine chloroplast DNA lacks rps16, which has been found between trnQ and trnK in angiosperm chloroplast DNAs, but possesses ORF510 instead. This ORF is highly homologous to ORF513 found in the corresponding region of liverwort chloroplast DNA and ORF563 located downstream from trnT in Chlamydomonas moewusii chloroplast DNA. A possible pathway for the evolution of black pine chloroplast DNA is discussed.

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References

  • Aldrich J, Cherney BW, Williams C, Merlin E (1988) Sequence analysis of the junction of the large single copy region and the large inverted repeat in the petunia chloroplast genome. Curr Genet 14:487–492

    Google Scholar 

  • Bonitz SG, Coruzzi G, Thalenfeld BE, Tzagoloff A (1980) Assembly of the mitochondrial membrane system. J Biol Chem 255:11927–11941

    Google Scholar 

  • Boyer SK, Mullet JE (1988a) Pea chloroplast tRNA-Lys (UUU) gene: transcription and analysis of an intron-containing gene. Photosynthesis Res 17:7–12

    Google Scholar 

  • Boyer SK, Mullet JE (1988b) Sequence and transcript map of barley chloroplast psbA gene. Nucleic Acids Res 16:8184

    Google Scholar 

  • Eisermann A, Tiller K, Link G (1990) In vitro transcription and DNA binding characteristics of chloroplast and etioplast extracts from mustard (Sinapis alba) indicate differential usage of the psbA promoter. EMBO J 9:3981–3987

    Google Scholar 

  • Herdenberger F, Pillay DTN, Steinmetz A (1990) Sequence of the trnH gene and the inverted repeat structure deletion site of the broad bean chloroplast genome. Nucleic Acids Res 18:1297

    Google Scholar 

  • Hipkins VD, Tsai CH, Strauss SH (1990) Sequence of the gene for the large subunit of ribulose 1,5-bisphosphate carboxylase from a gymnosperm, Douglas fir. Plant Mol Biol 15:505–507

    Google Scholar 

  • Hiratsuka J, Shimada H, Whittier RF, Ishibashi T, Sakamoto M, Mori M, Kondo C, Honji Y, Sun CR, Meng BY, Li Y, Kanno A, Nishizawa Y, Hirai A, Shinozaki K, Sugiura M (1989) The complete sequence of the rice (Oryza sativa) chloroplast genome: Intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Mol Gen Genet 217:185–194

    Google Scholar 

  • Koller B, Delius H (1980) Vicia faba chloroplast DNA has only one set of ribosomal RNA genes as shown by partial denaturation mapping and R-loop analysis. Mol Gen Genet 178:261–269

    Google Scholar 

  • Kondo T, Ishibashi T, Shibata M, Hirai A (1986) Isolation of chloroplast DNA from Pinus. Plant Cell Physiol 27:741–744

    Google Scholar 

  • Lidholm J, Gustafsson P (1991) A three-step model for the rearrangement of the chloroplast trnK-psbA region of the gymnosperm Pinus contorta. Nucleic Acids Res 19:2881–2887

    Google Scholar 

  • Lidholm J, Szmidt AE, Hällgren JE, Gustafsson P (1988) The chloroplast genomes of conifers lack one of the rRNA-encoding inverted repeats. Mol Gen Genet 212:6–10

    Google Scholar 

  • Lidholm J, Szmidt A, Gustafsson P (1991) Duplication of the psbA gene on the chloroplast genome of two Pinus species. Mol Gen Genet 226:345–352

    Google Scholar 

  • Link G (1984) DNA sequence requirements for the accurate transcription of a protein-coding plastid gene in a plastid in vitro system from mustard (Sinapis alba L.). EMBO J 3:1697–1704

    Google Scholar 

  • Maier RM, Dory I, Igloi G, Kössel H (1990) The ndhH genes of gramminean plastomes are linked with the junctions between small single copy and inverted repeat regions. Curr Genet 18:245–250

    Google Scholar 

  • Mukai Y, Yamamoto N, Odani K, Shinohara K (1991) Structure and expression of a gene for the large subunit of ribulose-1,5bisphosphate carboxylase/oxygenase from pine. Plant Cell Physiol 32:273–282

    Google Scholar 

  • Neuhaus H, Link G (1987) The chloroplast tRNA-Lys (UUU) gene from mustard (Sinapis alba) contains a class H intron potentially coding for a maturase-related polypeptide. Curr Genet 11:251–257

    Google Scholar 

  • Neuhaus H, Scholz A, Link G (1989) Structure and expression of a split chloroplast gene from mustard (Sinapis alba): ribosomal protein gene rps16 reveals unusual transcriptional features and complex RNA maturation. Curr Genet 15:63–70

    Google Scholar 

  • Nickelsen J, Link G (1990) Nucleotide sequence of the mustard chloroplast genes trnH and rps19. Nucleic Acids Res 18:1051

    Google Scholar 

  • Palmer JD (1985) Comparative organization of chloroplast genomes. Annu Rev Genet 19:325–354

    Google Scholar 

  • Palmer JD, Thompson WF (1981) Rearrangements in the chloroplast genomes of mung bean and pea. Proc Natl Acad Sci USA 78:5533–5537

    Google Scholar 

  • Palmer JD, Osorio B, Aldrich J, Thompson WF (1987) Chloroplast DNA evolution among legumes: Loss of a large inverted repeat occurred prior to other sequence rearrangements. Curr Genet 11:275–286

    Google Scholar 

  • Richard M, Bellemare G (1990) Nucleotide sequence of Chlamydomonas moewusii chloroplastic tRNA-Thr. Nucleic Acids Res 18:3061

    Google Scholar 

  • Sexton TB, Jones JT, Mullet JE (1990) Sequence and transcriptional analysis of the barley ctDNA region upstream of pshD psbC encoding trnK(UUU), rps16 trnQ(UUG), psbK, psbl and trnS (GCU). Curr Genet 17:445–454

    Google Scholar 

  • Shimada H, Sugiura M (1991) Fine structural features of the chloroplast genome: comparison of the sequenced chloroplast genomes. Nucleic Acids Res 19:983–995

    Google Scholar 

  • Shinozaki K, Deno H, Sugita M, Kuramitsu S, Sugiura M (1986) Intron in the gene for the ribosomal proteins S16 of tobacco chloroplast and its conserved boundary sequences. Mol Gen Genet 202:1–5

    Google Scholar 

  • Strauss SH, Palmer JD, Howe GT, Doerksen AH (1988) Chloroplast genomes of two conifers lack a large inverted repeat and are extensively rearranged. Proc Natl Acad Sci USA 85:3898–3902

    Google Scholar 

  • Sugita M, Sugiura M (1984) Nucleotide sequence and transcription of the gene for the 32,000 dalton thylakoid membrane protein from Nicotiana tabacum. Mol Gen Genet 195:308–313

    Google Scholar 

  • Sugita M, Kato A, Shimada H, Sugiura M (1984) Sequence analysis of the junctions between a large inverted repeat and single-copy regions in tobacco chloroplast DNA. Mol Gen Genet 194:200–205

    Google Scholar 

  • Sugita M, Shinozaki K, Sugiura M (1985) Tobacco chloroplast tRNA-Lys (UUU) gene contains a 2.5-kilobase-pair intron: An open reading frame and a conserved boundary sequence in the intron. Proc Natl Acad Sci USA 82:3557–3561

    Google Scholar 

  • Sugiura M (1989) The chloroplast chromosomes in land plants. Annu Rev Cell Biol 5:51–70

    Google Scholar 

  • Sugiura M, Kusuda J (1979) Molecular cloning of tobacco chloroplast ribosomal RNA genes. Mol Gen Genet 172:137–141

    Google Scholar 

  • Sugiura M, Shinozaki K, Zaita N, Kusuda M, Kumano M (1986) Clone bank of the tobacco (Nicotiana tabacum) chloroplast genome as a set overlapping restriction endonuclease fragments: mapping of eleven ribosomal protein genes. Plant Sci 44:211–216

    Google Scholar 

  • Tsai CH, Strauss SH (1989) Dispersed repetitive sequences in the chloroplast genome of Douglas-fir. Curr Genet 16:211–218

    Google Scholar 

  • Umesono K, Inokuchi H, Shiki Y, Takeuchi M, Chang Z, Fukuzawa H, Kohchi T, Shirai H, Ohyama K, Ozeki H (1988) Structure and organization of Marchantia polymorpha chloroplast genome 11. Gene organization of the large single copy region from rps'12 to atpB. J Mol Biol 203:299–331

    Google Scholar 

  • White EE (1990) Chloroplast DNA in Pinus monticola, 1. Physical map. Theor Appl Genet 79:119–124

    Google Scholar 

  • Wolfe KH (1988) The site of deletion of the inverted repeat in pea chloroplast DNA contains duplicated gene fragments. Curr Genet 13:97–99

    Google Scholar 

  • Woodbury NW, Dobres M, Thompson WF (1989) The identification and localization of 33 pea chloroplast transcription initiation sites. Curr Genet 16:433–445

    Google Scholar 

  • Zurawski G, Bottomley W, Whitfeld PR (1984) Junctions of the large single copy region and the inverted repeats in Spinacia oleracea and Nicotiana debneyi chloroplast DNA: Sequence of the genes for tRNA-His and the ribosomal proteins S 19 and L2. Nucleic Acids Res 12:6547–6558

    Google Scholar 

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Communicated by R. Hagemann

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Tsudzuki, J., Nakashima, K., Tsudzuki, T. et al. Chloroplast DNA of black pine retains a residual inverted repeat lacking rRNA genes: nucleotide sequences of trnQ, trnK, psbA, trnI and trnH and the absence of rps16 . Molec. Gen. Genet. 232, 206–214 (1992). https://doi.org/10.1007/BF00279998

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  • DOI: https://doi.org/10.1007/BF00279998

Key words

  • Black pine
  • Chloroplast DNA
  • Inverted repeat
  • psbA
  • rps16