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de Heij HT, Lustig H, Moeskops DJ, Bovenberg WA, Bisanz C, Groot GS. Chloroplast DNAs of Spinacia, Petunia and Spirodela have a similar gene organization. Curr Genet 2013; 7:1-6. [PMID: 24173111 DOI: 10.1007/bf00365673] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/1982] [Indexed: 11/25/2022]
Abstract
We have located the positions of the genes coding for the α, β and ε subunits of the ATPase complex on Spirodela oligorhiza chloroplast DNA by means of heterologous hybridization with Spinacia cpDNA fragments.The overall cpDNA sequence organization of Petunia hybrida and Spirodela was compared. We hybridized well-characterized, cloned Spirodela cpDNA fragments with size fractionated Petunia cpDNA digested by Sall. It appears that the monocotyledonous Spirodela and the dicotyledonous Petunia cpDNA share a common sequence organization around their entire circumference. These observations, together with data reported in the literature, indicate a strikingly similar genetic organization of the chloroplast genome in widely divergent plants.
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Affiliation(s)
- H T de Heij
- Biochemical Laboratory, Free University, de Boelelaan 1083, 1081, HV Amsterdam, The Netherlands
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2
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Abstract
A complete clone bank representing the chloroplast DNA from Vicia faba has been constructed. A total of 15 fragments (10 Pst1, 1 Pst1-EcoR1 and 4 Sal1 fragments) were inserted into the vector pBR322 and transformed into the E. coli strain HB101. The cloned fragments were used as the main tools in constructing the physical map of Vicia faba for the restriction endonucleases Pst1, Kpn1 and Xho1. The identity of the cloned fragments was demonstrated by restriction analysis and blot hybridization. The information generated was used to construct the map. The 16S and 23S rRNA genes and the gene for the large subunit of ribulose-1,5-bisphosphate carboxylase have been positioned on the map using heterologous probes. The orientation of the gene for the large subunit of RuBP carboxylase has also been determined.
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Rauwolf U, Golczyk H, Meurer J, Herrmann RG, Greiner S. Molecular marker systems for Oenothera genetics. Genetics 2008; 180:1289-306. [PMID: 18791241 PMCID: PMC2581935 DOI: 10.1534/genetics.108.091249] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Accepted: 08/21/2008] [Indexed: 11/18/2022] Open
Abstract
The genus Oenothera has an outstanding scientific tradition. It has been a model for studying aspects of chromosome evolution and speciation, including the impact of plastid nuclear co-evolution. A large collection of strains analyzed during a century of experimental work and unique genetic possibilities allow the exchange of genetically definable plastids, individual or multiple chromosomes, and/or entire haploid genomes (Renner complexes) between species. However, molecular genetic approaches for the genus are largely lacking. In this study, we describe the development of efficient PCR-based marker systems for both the nuclear genome and the plastome. They allow distinguishing individual chromosomes, Renner complexes, plastomes, and subplastomes. We demonstrate their application by monitoring interspecific exchanges of genomes, chromosome pairs, and/or plastids during crossing programs, e.g., to produce plastome-genome incompatible hybrids. Using an appropriate partial permanent translocation heterozygous hybrid, linkage group 7 of the molecular map could be assigned to chromosome 9.8 of the classical Oenothera map. Finally, we provide the first direct molecular evidence that homologous recombination and free segregation of chromosomes in permanent translocation heterozygous strains is suppressed.
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Affiliation(s)
- Uwe Rauwolf
- Ludwig-Maximilians-Universität München, Lehrstuhl für Botanik, Department Biologie I, Munich, Germany
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Greiner S, Wang X, Rauwolf U, Silber MV, Mayer K, Meurer J, Haberer G, Herrmann RG. The complete nucleotide sequences of the five genetically distinct plastid genomes of Oenothera, subsection Oenothera: I. sequence evaluation and plastome evolution. Nucleic Acids Res 2008; 36:2366-78. [PMID: 18299283 PMCID: PMC2367718 DOI: 10.1093/nar/gkn081] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Revised: 02/01/2008] [Accepted: 02/08/2008] [Indexed: 12/02/2022] Open
Abstract
The flowering plant genus Oenothera is uniquely suited for studying molecular mechanisms of speciation. It assembles an intriguing combination of genetic features, including permanent translocation heterozygosity, biparental transmission of plastids, and a general interfertility of well-defined species. This allows an exchange of plastids and nuclei between species often resulting in plastome-genome incompatibility. For evaluation of its molecular determinants we present the complete nucleotide sequences of the five basic, genetically distinguishable plastid chromosomes of subsection Oenothera (=Euoenothera) of the genus, which are associated in distinct combinations with six basic genomes. Sizes of the chromosomes range from 163 365 bp (plastome IV) to 165 728 bp (plastome I), display between 96.3% and 98.6% sequence similarity and encode a total of 113 unique genes. Plastome diversification is caused by an abundance of nucleotide substitutions, small insertions, deletions and repetitions. The five plastomes deviate from the general ancestral design of plastid chromosomes of vascular plants by a subsection-specific 56 kb inversion within the large single-copy segment. This inversion disrupted operon structures and predates the divergence of the subsection presumably 1 My ago. Phylogenetic relationships suggest plastomes I-III in one clade, while plastome IV appears to be closest to the common ancestor.
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Affiliation(s)
- Stephan Greiner
- Department Biologie I, Bereich Botanik, Ludwig-Maximilians-Universität, Menzinger Strasse 67, 80 638 Munich and MIPS/IBI Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Ingolstädter Landstrasse 1, 85 764 Neuherberg, Germany
| | - Xi Wang
- Department Biologie I, Bereich Botanik, Ludwig-Maximilians-Universität, Menzinger Strasse 67, 80 638 Munich and MIPS/IBI Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Ingolstädter Landstrasse 1, 85 764 Neuherberg, Germany
| | - Uwe Rauwolf
- Department Biologie I, Bereich Botanik, Ludwig-Maximilians-Universität, Menzinger Strasse 67, 80 638 Munich and MIPS/IBI Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Ingolstädter Landstrasse 1, 85 764 Neuherberg, Germany
| | - Martina V. Silber
- Department Biologie I, Bereich Botanik, Ludwig-Maximilians-Universität, Menzinger Strasse 67, 80 638 Munich and MIPS/IBI Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Ingolstädter Landstrasse 1, 85 764 Neuherberg, Germany
| | - Klaus Mayer
- Department Biologie I, Bereich Botanik, Ludwig-Maximilians-Universität, Menzinger Strasse 67, 80 638 Munich and MIPS/IBI Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Ingolstädter Landstrasse 1, 85 764 Neuherberg, Germany
| | - Jörg Meurer
- Department Biologie I, Bereich Botanik, Ludwig-Maximilians-Universität, Menzinger Strasse 67, 80 638 Munich and MIPS/IBI Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Ingolstädter Landstrasse 1, 85 764 Neuherberg, Germany
| | - Georg Haberer
- Department Biologie I, Bereich Botanik, Ludwig-Maximilians-Universität, Menzinger Strasse 67, 80 638 Munich and MIPS/IBI Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Ingolstädter Landstrasse 1, 85 764 Neuherberg, Germany
| | - Reinhold G. Herrmann
- Department Biologie I, Bereich Botanik, Ludwig-Maximilians-Universität, Menzinger Strasse 67, 80 638 Munich and MIPS/IBI Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Ingolstädter Landstrasse 1, 85 764 Neuherberg, Germany
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Bohnert HJ, Löffelhardt W. Cyanelle DNA fromCyanophora paradoxaexists in two forms due to intramolecular recombination. FEBS Lett 2001. [DOI: 10.1016/0014-5793(82)80777-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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O'Kane SL. Clone bank and physical map of Lopezia miniata Lag. ex DC. ssp. miniata (Onagraceae) chloroplast DNA. BIOCHEM SYST ECOL 1995. [DOI: 10.1016/0305-1978(95)00041-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Sundberg SD, Denton MF, Rehner SA. Structural map of Sedum oreganum (Crassulaceae) chloroplast DNA. BIOCHEM SYST ECOL 1990. [DOI: 10.1016/0305-1978(90)90085-t] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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9
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Chloroplast Genomes as Genetic Markers. ACTA ACUST UNITED AC 1989. [DOI: 10.1007/978-3-642-74454-9_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Sears BB, Herrmann RG. Plastome mutation affecting the chloroplast ATP synthase involves a post-transcriptional defect. Curr Genet 1985; 9:521-8. [PMID: 2897251 DOI: 10.1007/bf00434057] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In a plastid genome (plastome) mutation of Oenothera hookeri, at least two of the plastome-coded polypeptides (the beta and epsilon subunits) of the chloroplast ATP synthase are directly affected. As in other plastid chromosomes, the genes for the beta and epsilon subunits are located next to each other on the Oenothera ptDNA molecule and are cotranscribed. Immunoanalysis and peptide mapping of in vivo products suggests that a fusion of the two genes may have occurred in the plastome mutant. In contrast to the in vivo data, in vitro translation of the RNA using a heterologous system results in polypeptides which cannot be distinguished from those of wild-type. In addition, neither the mRNA sizes nor plastid DNA restriction fragment patterns differ from wild-type. To reconcile the paradox of these results, it is suggested that either a defect in a translational signal or some other post-transcriptional event is responsible for the mutant phenotype.
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Affiliation(s)
- B B Sears
- Botanisches Institut der Universität Düsseldorf, Federal Republic of Germany
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11
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Spielmann A, Ortiz W, Stutz E. The soybean chloroplast genome: Construction of a circular restriction site map and location of DNA regions encoding the genes for rRNAs, the large subunit of the ribulose-1,5-bisphosphate carboxylase and the 32 KD protein of the photosystem II reaction center. ACTA ACUST UNITED AC 1983. [DOI: 10.1007/bf00330317] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Vedel F, Mathieu C. Physical and gene mapping of chloroplast DNA from normal and cytoplasmic male sterile (radish cytoplasm) lines of Brassica napus. Curr Genet 1983; 7:13-20. [DOI: 10.1007/bf00365675] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/1982] [Indexed: 10/26/2022]
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13
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Physical mappings of chloroplast DNA from liverwort Marchantia polymorpha L. cell suspension cultures. ACTA ACUST UNITED AC 1983. [DOI: 10.1007/bf00326047] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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14
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The barley chloroplast genome: Physical structure and transcriptional activity in vivo. ACTA ACUST UNITED AC 1983. [DOI: 10.1007/bf02906170] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Gordon KH, Crouse EJ, Bohnert HJ, Herrmann RG. Physical mapping of differences in chloroplast DNA of the five wild-type plastomes in Oenothera subsection Euoenothera. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1982; 61:373-384. [PMID: 24270500 DOI: 10.1007/bf00272860] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/1980] [Accepted: 08/15/1980] [Indexed: 06/02/2023]
Abstract
1) DNA has been isolated from the five genetically distinguishable plastid types of Oenothera, subsection Euoenothera. DNA of plastomes I to IV was obtained from plants with identical nuclear backgrounds containing the genotype AA of Oenothera hookeri whereas the DNA of plastome V came from Oenothera argillicola (genotype CC). 2) The DNAs of the five basic Euoenothera wild-type plastomes can be distinguished by restriction endonuclease analysis with Sal I, Pst I, Kpn I, Eco RI and Bam HI. The fragment patterns exhibit distinct common features as well as some degree of variability. 3) Physical maps for the circular DNAs of plastome I, II, III and V could be constructed using the previously detailed map of plastome IV DNA (Gordon et al. 1981). This has been achieved by comparing the cleavage products generated by restriction endonucleases Sal I, Pst I and Kpn I which collectively result in 36 sites in each of the five plastome DNAs, and by hybridization of radioactively labelled chloroplast rRNA or chloroplast cRNA probes of spinach to Southern blots of appropriate restriction digests. The data show that the overall fragment order is the same for all five plastome DNAs. Each DNA molecule is segmentally organized into four regions represented by a large duplicated sequence in inverted orientation whose copies are separated by two single-copy segments. 4) The alterations in position of restriction sites among the Euoenothera plastome DNAs result primarily from insertions/deletions. Eleven size differences of individual fragments in the Sal I, Pst I and Kpn I patterns measuring 0.1-0.8 Md (150-1,200 bp) relative to plastome IV DNA have been located. Most changes were found in the larger of the two single-copy regions of the five plastomes. Changes in the duplication are always found in both copies. This suggests the existence of an editing mechanism that, in natural populations, equalizes or transposes any change in one copy of the repeat to the equivalent site of the other copy. 5) Detailed mapping of the two rDNA regions of the five plastomes, using the restriction endonucleases Eco RI and Bam HI which each recognize more than 60 cleavage sites per DNA molecule, disclosed a 0.3 Md deletion in plastome III DNA and a 0.1 Md insertion in plastome V DNA relative to DNA of plastome IV, I and II. These changes are most probably located in the spacer between the genes for 16S and 23S rRNA and are found in both rDNA units.
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Affiliation(s)
- K H Gordon
- Botanisches Institut der Universität Düsseldorf, Düsseldorf, Germany
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Palmer JD, Thompson WF. Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost. Cell 1982; 29:537-50. [PMID: 6288261 DOI: 10.1016/0092-8674(82)90170-2] [Citation(s) in RCA: 294] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We examined the arrangement of sequences common to seven angiosperm chloroplast genomes. The chloroplast DNAs of spinach, petunia and cucumber are essentially colinear. They share with the corn chloroplast genome a large inversion of approximately 50 kb relative to the genomes of three legumes--mung bean, pea and broad bean. There is one additional rearrangement, a second, smaller inversion within the 50 kb inversion, which is specific to the corn genome. These two changes are the only detectable rearrangements that have occurred during the evolution of the species examined (corn, spinach, petunia, cucumber and mung bean) whose chloroplast genomes contain a large inverted repeat sequence of 22-25 kb. In contrast, we find extensive sequence rearrangements in comparing the pea and broad bean genomes, both of which have deleted one entire segment of the inverted repeat, and also in comparing each of these to the mung bean genome. Thus there is a relatively stable arrangement of sequences in those genomes with the inverted repeat and a much more dynamic arrangement in those that have lost it. We discuss several explanations for this correlation, including the possibility that the inverted repeat may play a direct role in maintaining a conserved arrangement of chloroplast DNA sequences.
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Chu NM, Tewari KK. Arrangement of the ribosomal RNA genes in chloroplast DNA of Leguminosae. ACTA ACUST UNITED AC 1982. [DOI: 10.1007/bf00422907] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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19
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The Cooperation of Nuclear and Plastid Genomes in Plastid Biogenesis and Differentiation. ACTA ACUST UNITED AC 1982. [DOI: 10.1016/s0015-3796(82)80025-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Electron microscopical localisation of the 23S and 16S rRNA genes within an inverted repeat for two chromoplast DNAs. Curr Genet 1981; 4:25-8. [DOI: 10.1007/bf00376782] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/1981] [Indexed: 10/26/2022]
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21
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A physical map of Nicotiana tabacum plastid DNA including the location of structural genes for ribosomal RNAs and the large subunit of ribulose bisphosphate carboxylase/oxygenase. Curr Genet 1981; 3:189-204. [DOI: 10.1007/bf00429821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/1981] [Indexed: 10/26/2022]
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Bohnert HJ, Gordon KH, Crouse EJ. Homologies among ribosomal RNA and messenger RNA genes in chloroplasts, mitochondria and E. coli. MOLECULAR & GENERAL GENETICS : MGG 1980; 179:539-45. [PMID: 7003301 DOI: 10.1007/bf00271743] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Labelled chloroplast rRNAs from Spinacia oleracea were hybridized to restriction endonuclease digests of chloroplast DNA from Oenothera hookeri and Euglena gracilis, to mitochondrial DNA of Acanthamoeba castellanii, and to DNA of the E. coli rrn B operon in the transducing phage lambda rifd 18. The degree of homology is greatest for the 16S rRNA gene. Greater than 90% occurs between the two higher plant genes, 80% homology to the lower plant gene, 60%-70% homology to the bacterial gene, and 20% homology to the mitochondrial gene. The degree of hybridization varied considerably for the 23S and the 5S rRNA genes. Very high homology exists between the two higher plant genes, only about 50% homology for both the Euglena and bacterial genes, and no significant homology for the mitochondrial genes. These results show that any chloroplast (or E. coli) rRNA may be used as a probe to identify rRNA genes in other ctDNAs. Two RNA populations, each enriched for a different ctDNA-encoded mRNA, proved useful in the location of these genes on both higher plant ctDNAs. No significant hybridization was obtained using these probes to the Euglena ctDNA which seems to be too distantly related.
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Gordon KH, Hildebrandt JW, Bohnert HJ, Herrmann RG, Schmitt JM. Analysis of the plastid DNA in an Oenothera plastome mutant deficient in ribulose bisphosphate carboxylase. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1980; 57:203-7. [PMID: 24301093 DOI: 10.1007/bf00264671] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/27/1979] [Indexed: 05/14/2023]
Abstract
Plastid DNA of the light green Oenothera plastome mutant sigma, from plastome I, which is deficient in ribulose bisphosphate carboxylase, has been compared with wild-type chloroplast DNA from plastome I and the related plastome IV. For this, double digestions with the restriction endonucleases Sal I, Pst I and Kpn I were used. Chloroplast DNA from plastomes I and IV differs in the sizes of several fragments, with the changes being from under 0.1 to about 0.6 Md in size. In the cleavage patterns of the mutant DNA compared to the wild-type DNA from plastome I, the only differences observed are two possible deletions of less than 0.1 Md from a fragment known to partly cover the genes for the ribosomal RNAs and from a fragment located in the small single-copy region of the molecule. It is concluded that the ribulose bisphosphate carboxylase deficiency in this mutant is not caused by a major deletion in the plastid DNA.
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Affiliation(s)
- K H Gordon
- Botanisches Institut der Universität, Düsseldorf, Federal Republic of Germany
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