The physical properties and renaturation kinetics of DNA extracted from isolated chloroplasts of Acetabulavia meditewanea has been studied. 3 It has a buoyant density of 1.702 g/cm³ , which corresponds to a base composition of 42.8% G+C. When melted in SSC, Acetabulavia chloroplast DNA has a Tm of 86.7°, corresponding to a base composition of 43% G+C. The close agreement of the base compositions calculated from the buoyant density and the melting temperature indicates the absence of unusual bases in Acetdbularia meditewanea chloroplast DNA. In 0.1 x SSC, Acetabulavia chloroplast DNA melts with a Tm of 70.7°, and the melting transition is very broad. The breadth of the melting transition suggests that this DNA has a high degree of intramolecular heterogeneity. A differential plot of the thermal transition of A. meditewanea chloroplast DNA supports this conclusion. The buoyant densities of DNA from bacterial contaminants found in Acetabulavia cultures differed from the buoyant density of the chloroplast DNA. In any case, the amount of bacterial contamination was too low to account for any of the results obtained. Renaturation experiments indicate a kinetic complexity of 1.1 x 10⁹ daltons from Acetabulavia meditewanea chloroplast DNA. As a result of uncertainties in the values of alkaline sedimentation coefficients, this calculated kinetic complexity may be too low. The possible genetic information contained in the chloroplast DNA of Acetabulavia meditewanea is discussed. / Science, Faculty of / Botany, Department of / Graduate

Thesis (Ph. D.)--University of Texas at Austin, 2004. / Supervisor: Robert K. Jansen. Vita. Includes bibliographical references. Also available from UMI.

Thesis (MSc)--University of Stellenbosch, 2004. / ENGLISH ABSTRACT: A number of proteins essential for the survival of a plant are encoded by the chloroplast genome. The characterization and sequencing of a number of algal and plant chloroplast genomes has facilitated researchers understanding of cellular functions and metabolism. Chloroplast DNA (cpDNA) has also been used to determine inter- and intraspecies evolutionary relationships and this organelle offers an alternative means of expressing foreign genes. Although a number of species' chloroplast genomes have been characterized and sequenced, no previous attempts of this kind have been made for a chloroplast genome of the family Vitaceae. In this study, attempts were made to characterize and partially sequence the chloroplast genome of Vilis vinifera. Chloroplast DNA was isolated from the Sultana and Sugra 1 cultivars and digested with restriction enzymes that produced cpDNA fragments of a suitable size for cloning. The fragments were shotgun-cloned into a plasmid vector and white colonies were screened by means of PCR and colony blotting. Three EcoRI-digested clones and one PstI-digested clone were obtained in this manner. Walking outwards from a previously sequenced grapevine rrn 16 gene region by means of PCR also allowed us to sequence a further -3310 bp region of the Sultana chloroplast genome. BAC clones containing V. vinifera cv L. Cabernet Sauvignon cpDNA inserts became available later in the project. It was decided to use these clones for further library construction instead of isolated cpDNA. The 5' and 3' end sequences of seven of the 24 BAC clones were obtained. These were compared to sequences found in the NCBI database to find - homologous chloroplast regions and determine the size of each BAC insert. One clone appeared to contain the entire grapevine chloroplast genome, apart from a 500 bp region. This clone was selected for further analysis. The BAC clone DNA was isolated and restriction-digested fragments were shotgun-cloned into a plasmid vector. White colonies were screened by isolating the plasmid DNA and digesting it with appropriate restriction enzy~es. The 5' and 3' ends of putative positive clones were sequenced and mapped onto the Atropa belladonna chloroplast genome. A total of 15 clones were obtained in this project. Five of these contain cpDNA isolated from grapevine leaves and 10 contain fragments sub-cloned from the BAC clone. The biggest problem encountered with both methods used for library construction was genomic DNA contamination. Genomic DNA either originated from the plant nuclear genome or from the bacterial host cells in which the BAC clones were maintained. Many of the clones screened contained genomic DNA, and these could only be identified and removed once the clones had been sequenced. Even when a commercial kit was used for BAC clone isolation, 31% of the clones screened contained genomic DNA. This kit was specifically designed for the isolation of genomic DNA-free large constructs. The clones obtained from the two strategies provided a good representation of the grapevine chloroplast genome. The only region not represented was the Small Single Copy (SSC) region. Approximately 40% of the grapevine chloroplast genome was covered by these clones. This provides a basis for further genome characterization, physical mapping and sequencing of the grapevine chloroplast genome. / AFRIKAANSE OPSOMMING: Die chloroplasgenoom kodeer VIr 'n hele aantal proteïene wat essensieel is VIr die voortbestaan van 'n plant. Die karakterisering en volgorde bepaling van 'n aantal alg en plant chloroplasgenome het dit. vir navorsers moontlik gemaak om sellulêre funksies en metabolisme van plante te ontrafel. Chloroplas DNA (cpDNA) is ook gebruik om intra- en interspecies evolusionêre verwantskappe vas te stel. Dié organel verskaf ook 'n alternatiewe manier vir die uitdrukking van transgene. Alhoewel die chloroplasgenome van 'n hele aantal species al gekarakteriseer is en die DNA volgorde daarvan bepaal is, is daar nog geen navorsing van bogenoemde aard op die chloroplasgenoom van die Vitaceae familie gedoen rue. In hierdie studie is beoog om die chloroplasgenoom van Vitis vinifera te karakteriseer en gedeeltelike volgordebepaling daarvan te doen. Chloroplas DNA is geïsoleer vanaf Sultana en Sugra 1 kultivars en restriksie-ensiem vertering is gedoen met ensieme wat cpDNA fragmente, met geskikte grootte vir klonering, produseer. Dié fragmente is in 'n plasmiedvektor gekloneer met die haelgeweer-metode en wit kolonies is gesif deur middel van PKR en die kolonieklad metode. Op hierdie manier is drie EcoRI-verteerde klone en een PstI-verteerde kloon verkry. Deur uitwaarts te loop, deur middel van PKR, vanaf 'n druif rrnl6 geenstreek, waarvan die volgorde voorafbepaal is, was dit vir ons moontlik om ook die volgorde te bepaal van 'n verdere ~3310 bp streek van die Sultana chloroplasgenoom. BAC klone wat V. vinifera cv L. Cabernet Sauvignon cpDNA fragmente bevat, het later in die projek beskikbaar geraak. Daar is besluit om hierdie klone, i.p.v. die geïsoleerde cpDNA, te gebruik vir verdere biblioteek konstruksie. Die 5' en 3' entpuntvolgordes van sewe uit die 24 BAC ~lone is verkry. Hierdie volgordes is vergelyk met volgordes in die NCB Idatabasis om homoloë chloroplas streke te identifiseer, en die grootte van elke BAC fragment te bepaal. Die het geblyk dat die hele druif chloroplasgenoom in een van die klone vervat is, behalwe vir 'n 500 bp streek. Die BAC-kloon DNA is geïsoleer en die restriksie-verteerde fragmente is in 'n plasmiedvektor gekloon d.m.V. die haelgeweer-metode. Wit kolonies is gesif deur die isolering van plasmied DNA en die vertering daarvan met geskikte restriksie-ensieme. Die volgorde van die 5' en 3' entpunte van skynbare positiewe klone is bepaal en gekarteer op die Atropa belladonna chloroplasgenoom. In hierdie studie is 'n totaal van 15 klone verkry. Vyf hiervan bevat cpDNA wat vanaf druifblare geïsoleer is, en 10 bevat fragmente wat vanaf die BAC-klone gesubkloneer is. Genorniese DNA kontaminasie was die grootste probleem wat ondervind is tydens beide metodes wat gebruik is vir biblioteek konstruksie. Genomiese DNA was afkomstig vanaf óf die plant nukleêre genoom óf die bakteriële gasheerselle waarin die BAC-klone gehou is. Baie van die klone wat gesif is, het genomiese DNA bevat, en dit kon eers geïdentifiseer en verwyder word nadat die volgorde van die klone bepaal is. Selfs al is 'n kommersiële produk vir BAC-kloon isolasie gebruik, het 31% van die gesifde klone steeds genomiese DNA bevat. Dié kommersiële produk is spesifiek vir die isolasie van groot konstrukte, wat genomiese DNA vry is, ontwerp. Die klone wat deur die twee strategeë verkry is, het 'n goeie verteenwoordiging van die druif chloroplasgenoom gegee. Die enigste streek wat die verteenwoordig is nie, was die Klein Enkelkopie (SSC) streek. Ongeveer 40% van die druif chloroplasgenoom is deur hierdie klone gedek. Dit verskaf 'n basis vir verdere genoomkarakterisering, fisiese kartering en volgordebepaling van die druif chloroplasgenoom.

Not available / text

Thesis (M.S.)--University of Akron, Dept. of Biology, 2006. / "December, 2006." Title from electronic thesis title page (viewed 12/31/2008) Advisor, Robert Joel Duff; Committee members, Richard Londraville, Francisco B. Moore, Amy Milsted; Department Chair, Bruce Cushing; Dean of the College, Ronald F. Levant; Dean of the Graduate School, George R. Newkome. Includes bibliographical references.

Thesis (M.S.)--Brigham Young University. Dept. of Microbiology & Molecular Biology, 2004. / Includes bibliographical references (p. 58-61).

No description available.

Witsenia is a monospecific genus of the putatively basal group, the woody Iridaceae. This upright iris has extremely long black and yellow flowers ( see fig. 1) that are thought to have been pollinated by an extinct Sunbird. The role of the unusual black floral colouration is investigated as this colour is seldom associated with bird pollination. This plant typically exists in discreet and restricted populations in wet habitats in the South Western Cape (South Africa). The restricted nature of the plant is peculiar as it occurs in either low or high altitudes, yet appears to be extremely sensitive to altitude. Popular belief suggests that Witsenia maura occurs in the Peninsula only, and results from this study show the Peninsula population to be genetically separate from other populations, reflecting a long term separation. Samples from nine populations are sequenced to investigate haplotypic variation within the species, and dispersal of ancestral populations. This thesis investigates the current knowledge of Witsenia, its ecology, history and distribution. An examination of flowers under UV light reveals the first evidence of UV nectar guides in an ornithophilous flower. Conservation issues are also addressed, and it is established that although small and apparently shrinking due to global warming, populations are nonetheless viable if managed properly. A molecular study of the species and examinination of its variation revealed exceptional haplotype diversity. This diversity can best be explained by swamps acting as refugia during interglacial periods.

The mechanisms behind the high level of plant diversity and endemism observed in the Cape Floral Region (CFR) of South Africa have been the focus of many studies. Recently developed methods that employ DNA sequence data are making major contributions in reconstructing evolutionary histories of CFR species. Concurrently, palaeoenvironmental evidence is used increasingly to explain the impact of past climates on species ranges. This paper combines these two approaches by analysing the distribution of genetic diversity of the Afro-montane liverwort Jamesoniella colorata and associating its inferred evolutionary history with major palaeoclimatic trends in South Africa. Liverworts are generally well-suited for phylogeographical studies because they often have low dispersal rates, broad geographical ranges and long evolutionary persistence. In addition, the high among-population diversity observed in J colorata is conducive to the interpretation of significant historical events. The GIS-based bioclimatic envelope shows a strong correlation between potential habitat and the known distribution of J colorata and indicates that sampling in this study was sufficient to make accurate phylogeographical inferences. A combination of phylogeographical data and population genetics evidence suggests that populations of J colorata in the Western Cape Province have experienced range contractions into upper-montane refugia and range expansions into lower altitudes in response to warming and cooling climatic trends, respectively. These range shifts have probably taken place throughout the Quaternary glacial-interglacials cycles, , which are thought to have been influential in shaping modem patterns of diversity. In lV an attempt to assign approximate dates to the two expansion events inferred for J. colorata, an average chloroplast mutation rate was applied to the trnL-F cpDNA mismatch distribution. The results roughly place the expansions within the last glacial period, demonstrating the general accordance of the phylogeographical and palaeoclimatic data. The molecular work in this study also brought into question the taxonomic status of several specimens that showed distinctly divergent DNA sequences. Preliminary morphological inspection of the specimens revealed subtle but clear differences in leaf and stem anatomy that were once associated with J. oenops, a species synonymised with J. colorata in 1971.

Hierarchical sampling from populations, incipient and recognized varieties within Phacelia dubia and P. maculata has revealed high levels of intraspecific polymorphism in chloroplast DNA. Much of the variation is partitioned between populations as evidenced by population-specific variants at fixation in all three populations of P. dubia var. interior and in both populations of P. maculata. Nine of 16 populations were polymorphic for cpDNA haplotypes. A total of 16 haplotypes was found in a sample of 106 individuals; the most common occurred in eight of the 16 populations and in 31 per cent of the individuals in the entire sample. A phylogenetic analysis revealed four basic plastome types. The two major groups of plastomes were separated by four independent base-pair mutations which suggests an ancient split in the evolution of plastid genomes. Representatives from each major plastome division were found in each of five populations spanning two allopatric varieties of P. dubia. The geographical distribution of haplotypes and lack of evidence for recent admixture argue against migration as a source of the polymorphism. It is more likely that the current taxonomic varieties are descendants of a polymorphic common ancestor.