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  • Chloroplast DNA  (5)
  • Inverted repeat  (5)
  • Cell & Developmental Biology  (2)
  • 1
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    BioEssays 2 (1985), S. 263-267 
    ISSN: 0265-9247
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The small, relatively constant size and conservative evolution of chloroplast DNA (cpDNA) make it an ideal molecule for tracing the evolutionary history of plant species. At lower taxonomic levels, cpDNA variation is easily and conveniently assayed by comparing restriction patterns and maps, while at higher taxonomic levels, DNA sequencing and inversion analysis are the methods of choice for comparing chloroplast genomes. The study of cpDNA variation has already yielded important new insights into the origin and evolution of many agriculturally important crop plants, and promises to significantly enhance our phylogenetic understanding of the major lines of descent among land plants and algae.
    Additional Material: 4 Ill.
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    BioEssays 17 (1995), S. 1005-1008 
    ISSN: 0265-9247
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The most common form of the CO2-fixing enzyme rubisco is a form I enzyme, heretofore found universally in oxygenic phototrophs (cyanobacteria and plastids) and widely in proteobacteria. Two groups(1-4), however, now report that in dinoflagellate plastids the usual form I rubisco has been replaced by the distantly related form II enzyme, known previously only from anaerobic proteobacteria. This raises the important question of how such an oxygensensitive rubisco could function in an aerobic organism. Moreover, the dinoflagellate rubisco has unusual molecular properties: it is encoded as a polyprotein, by nuclear (rather than plastid) genes, and these genes contain noncanonical spliceosomal introns. The nuclear location and alphaproteobacterial affinity of dinoflagellate rubisco genes hint at a possible mitochondrial origin and highlight the extraordinary richness of lateral gene transfers, both between and within organisms, that have occurred during rubisco evolution.
    Additional Material: 1 Ill.
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  • 3
    ISSN: 1432-1432
    Keywords: Chloroplast DNA ; Rearrangements ; Inversions ; Intron loss ; Homoplasy ; Ranunculaceae ; Anemone complex
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Chloroplast DNA cleavage sites for 10 restriction enzymes were mapped for 46 species representing all sections of Anemone, four closely related genera (Clematis, Pulsatilla, Hepatica, and Knowltonia), and three more distantly related outgroups (Caltha, Ranunculus, and Adonis). Comparison of the maps revealed that the chloroplast genomes of Anemone and related genera have sustained an unusual number and variety of rearrangements. A single inversion of a 42-kb segment was found in the large single-copy region of Adonis aestivalis. Two types of rearrangements were found in the chloroplast genome of Clematis, Anemone, Pulsatilla, Hepatica, and Knowltonia: An approximately 4-kb expansion of the inverted repeat and four inversions within the large single-copy region. These rearrangements support the monophyletic status of these genera, clearly separating them from Caltha, Ranunculus, and Adonis. Two further inversions were found in two Clematis species and three Anemone species. While appearing to support a monophyletic grouping for these taxa, these two inversions conflict with data from both chloroplast restriction sites and morphology and are better interpreted as having occurred twice independently. These are the first two documented cases of homoplastic inversions in chloroplast DNA. Finally, the second intron of the chloroplast rps12 gene was shown to have been lost in the common ancestor of the same three Anemone species that feature the two homoplastic inversions.
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  • 4
    ISSN: 1432-0983
    Keywords: Restriction maps ; Gene organization ; Chloroplast DNA ; Inversion ; Asteraceae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have cloned into plasmids 17 of 18 lettuce chloroplast DNA SacI fragments covering 96% of the genome. The cloned fragments were used to construct cleavage maps for 10 restriction enzymes for the chloroplast genomes of lettuce (Lactuca sativa) and Barnadesia caryophylla, two distantly related species in the sunflower family (Asteraceae). Both genomes are approximately 151 kb in size and contain a 25 kb inverted repeat. We also mapped the position and orientation of 37 chloroplast DNA genes. The mapping studies reveal that chloroplast DNAs of lettuce and Barnadesia differ by a 22 kb inversion in the large single copy region. Barnadesia has retained the primitive land plant genome arrangement, while the inversion has occurred in a lettuce lineage. The endpoints of the derived lettuce inversion were located by comparison to the well-characterized spinach and tobacco genomes. Both endpoints are located in intergenic spacers within tRNA gene clusters; one cluster being located downstream from the atpA gene and the other upstream from the psbD gene. The endpoint near the atpA gene is very close to one endpoint of a 20 kb inversion in wheat (Howe et al. 1983; Quigley and Weil 1985). Comparison of the restriction site maps gives an estimated sequence divergence of 3.7% for the lettuce and Barnadesia genomes. This value is relatively low compared to previous estimates for other angiosperm groups, suggesting a high degree of sequence conservation in the Asteraceae.
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Current genetics 10 (1986), S. 823-833 
    ISSN: 1432-0983
    Keywords: Inverted repeat ; Gene order ; Chloroplast genome arrangement ; Vascular plant
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have constructed the first physical map of a gymnosperm chloroplast genome and compared its organization with those of a fern and several angiosperms by heterologous filter hybridization. The chloroplast genome of the gymnosperm Ginkgo biloba consists of a 158 kb circular chromosome that contains a ribosomal RNA-encoding inverted repeat approximately 17 kb in size. Gene mapping experiments demonstrate a remarkable similarity in the linear order and absolute positions of the ribosomal RNA genes and of 17 protein genes in the cpDNAs of Ginkgo biloba, the fern Osmunda cinnamomea and the angiosperm Spinacia oleracea. Moreover, filter hybridizations using as probes cloned fragments that cover the entirety of the angiosperm chloroplast genome reveal a virtually colinear arrangement of homologous sequence elements in these genomes representing three divisions of vascular plants that diverged some 200–400 million years ago. The only major difference in chloroplast genome structure among these vascular plants involves the size of the rRNA-encoding inverted repeat, which is only 10 kb in Osmunda, 17 kb in Ginkgo, and about 25 kb in most angiosperms. This size variation appears to be the result of spreading of the repeat through previously single copy sequences, or the reverse process of shrinkage, unaccompanied by any overall change in genome complexity.
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  • 6
    ISSN: 1432-0983
    Keywords: Inverted repeat ; Colinearity ; Flip-flop recombination ; Fern chloroplast DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The evolution and recombination of chloroplast genome structure in the fern genus Osmunda were studied by comparative restriction site mapping and filter hybridization of chloroplast DNAs (cpDNAs) from three species — 0. cinnamomea, 0. claytoniana and 0. regalis. The three 144 kb circular genomes were found to be colinear in organization, indicating that no major inversions or transpositions had occurred during the approximately 70 million years since their radiation from a common ancestor. Although overall size and sequence arrangement are highly conserved in the three genomes, they differ by an extensive series of small deletions and insertions, ranging in size from 50 bp to 350 by and scattered more or less at random throughout the circular chromosomes. All three chloroplast genomes contain a large inverted repeat of approximately 10 kb in size. However, hybridizations using cloned fragments from the 0. cinnamomea and 0. regalis genomes revealed the absence of any dispersed repeats in at least 50% of the genome. Analysis with restriction enzymes that fail to cleave the 10 kb inverted repeat indicated that each of the three fern chloroplast genomes exists as an equimolar population of two isomeric circles differing only in the relative orientation of their two single copy regions. These two inversion isomers are inferred to result from high frequency intramolecular recombination between paired inverted repeat segments. In all aspects of their general organization, recombinational heterogeneity, and extent of structural rearrangement and length mutation, these fern chloroplast genomes resemble very closely the chloroplast genomes of most angiosperms.
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  • 7
    ISSN: 1432-0983
    Keywords: Chloroplast genome evolution ; Ribosomal RNA and protein genes ; Inverted repeat ; Restriction endonucleases
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Chloroplast DNA from the fern Osmunda einnamomea was isolated by a sucrose gradient procedure utilizing PEG to stabilize chloroplasts. Analysis with the restriction endonucleases PvuII, Sacl and BstEII indicates a chloroplast genome size of 144 kb. A physical map of the fragments produced by these three enzymes was constructed by filter hybridizations using purified PvuII fragments as hybridization probes. The Osmunda chloroplast genome is circular and contains an inverted repeat 8–13 kb in size. Gene probes from tobacco, corn and spinach were used to map the positions of six genes on the Osmunda chloroplast chromosome. The 16S and 23S ribosomal RNAs are encoded by duplicate genes which lie within the inverted repeat. Genes for the large subunit of ribulose-1,5-bisphosphate carboxylase, a photosystem II polypeptide, and the alpha and beta subunits of chloroplast coupling factor are located in three different segments of the large single copy region. The Osmunda chloroplast genome is remarkably similar in size, conformation, physical organization, and map positions of known genes, to chloroplast DNA from a number of angiosperms. The major difference between chloroplast DNA from this fern and angiosperms is that the inverted repeat is smaller in Osmunda (8–13 kb) than in angiosperms (22–25 kb).
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  • 8
    ISSN: 1432-2048
    Keywords: Chlorophyll a/b-binding protein ; Chloroplast DNA ; Phytochrome (RNA levels) ; RNA levels, light ; Pisum (light and RNA) ; Ribulosebisphosphate carboxylase ; Vigna
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have examined phytochrome effects on the abundance of transcripts from several nuclear and chloroplast genes in buds of dark-grown pea seedlings and primary leaves of dark-grown mung-bean seedlings. Probes for nuclear-coded RNAs were selected from a library of cDNA clones and included those corresponding to the small subunit (SS) of ribulosebisphosphate carboxylase and a chlorophyll a/b binding protein (AB). Transcripts from chloroplast genes for RuBP carboxylase large subunit (LS) and a 32,000-dalton photosystem II polypeptide (PII) were assayed with cloned fragments of the chloroplast genome. In addition, we present data on transcripts from a number of other nuclear genes of unknown function, several of which change in abundance during light-induced development. Transcript levels were measured as a proportion of total RNA by a dot blot assay in which RNA from different tissues or stages is fixed to nitrocellulose and hybridized with 32P-labeled probes prepared from cloned DNAs. Several patterns of induction can be seen. For example, although both SS and AB RNAs show positive, red/far-red reversible responses in both pea and mung bean, in pea buds the induction ratio for SS RNA is much higher than that for AB RNA, while just the reverse is true for mung-bean leaves. In addition, treatment with lowfluence red light produces full induction of the pea AB RNA, while SS RNA in the same tissue does not reach a maximum steady-state level until after about 24 h of supplementary high-intensity white light. In pea buds, chloroplast genes (LS, PII) also show clear responses to phytochrome, as measured by the steady-state levels of their RNA products. Chloroplast DNA levels (as a fraction of the total cellular DNA) show the same response pattern, which may indicate that in peas many of the light effects we see are related to a general stimulation of chloroplast development. In mung beans, the levels of plastid DNA and RNA are already quite high in the leaves of 7-d dark-grown seedlings, and light effects are much less pronounced. The results are consistent with the notion that chloroplast development is arrested at a later stage in dark-grown mung-bean leaves than in etiolated pea buds.
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  • 9
    ISSN: 1432-0983
    Keywords: Gene mapping ; Rearrangements ; Chloroplast DNA evolution ; Inverted repeat
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Cloned genes from tobacco, spinach, and pea were used as hybridization probes to localize 36 protein genes on the chloroplast chromosomes of four legumes — mung bean, common bean, soybean, and pea. The first three chloroplast DNAs (cpDNAs), all of which retain a large inverted repeat, have an identical gene order with but one exception. A 78 kb segment encompassing nearly the entire large single copy region is inverted in mung bean and common bean relative to soybean and non-legumes. The simplest evolutionary explanation for this difference is a 78 kb inversion, with one endpoint between rps8 and infA and the second between psbA and rpl2. However, we can not rule out a two-step re-arrangement (consisting of successive expansion and contraction of the inverted repeat) leading to the relocation of a block of six ribosomal protein genes (rps19-rps8) from one end of the large single copy region to the other. Analysis of gene locations in pea cpDNA, which lacks the large inverted repeat, combined with cross-hybridization studies using 59 clones covering the mung bean genome, leads to a refined picture of the position and nature of the numerous rearrangements previously described in the pea genome. A minimum of eight large inversions are postulated to account for these rearrangements. None of these inversions disrupt groups of genes that are transcriptionally linked in angiosperm cpDNA. Rather, the end-points of inversions are associated with relatively spacer-rich segments of the genome, many of which contain tRNA genes. All of the pea-specific inversions are shown to be positionally distinct from those recently described in a closely related legume, broad bean.
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  • 10
    ISSN: 1432-0983
    Keywords: Chloroplast DNA ; tRNA import ; Plastid gene translation ; Pseudogene ; Non-photosynthetic plants
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We recently reported that the gene for chloroplast tRNACys(GCA) is a pseudogene in the plastid DNA of Epifagus virginiana, a non-photosynthetic parastic flowering plant in the family Orobanchaceae. Since this is the only tRNACys gene in the plastid genome, and since Epifagus appears to possess a functional plastid translational apparatus, it seems probable that nuclear-encoded tRNAs are imported into plastids to effect translation. In this study we have surveyed species closely related to Epifagus to establish how widespread the loss of this tRNA gene has been. We find that Conopholis americana, another non-photosynthetic parasite, lacks the gene altogether, but that seven closely-related photosythetic plants (both parasitic and free-living) maintain an intact chloroplast tRNACys gene. Thus, the tRNACys gene appears to have become non-functional at the same time that photosynthetic ability was lost. This may be because the levels of putatively imported tRNAs are sufficient to meet the demands of plastid gene expression under nonphotosynthetic conditions only.
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