Diss. (sammanfattning) Stockholm : Karol. inst., 2004. / Härtill 5 uppsatser.

PIKE, L. M., HU, A., RENZAGLIA, K. S. and MUSICH, P. R., 1992. Liverwort genomes display extensive structural variations. Analyses of the total genomic DNA of eight species of liverworts and two species of green algae by thermal denaturation and CsCl buoyant density gradient centrifugation reveal a high degree of structural complexity and interspecific heterogeneity. The hepatic taxa exhibit two or more DNA components of varying base composition. Average G4‐C contents of total cellular DNA calculated from melting profiles are similarly variable, ranging from 38% to 53% G + C. The green alga Chara, a member of the ancestral line to land plants, shows similarities with liverworts in possessing multiple DNA components of comparable complexity, whereas Hydrodiciyon DNA displays a single component. Detailed hybridization analyses of individual density gradient fractions using α‐tubulin, rRNA and ribulose 1,5‐bisphosphate carboxylase/oxygenase large subunit rbcL gene probes were performed to locate the low‐copy number and moderately repetitive nuclear genes, and the chloroplast chromosome, respectively. The location of each gene within the density gradient is highly variable among the organisms examined; a‐tubulin occurs in fractions ranging from 44–64% G + C, rDNA in 50–64% G + C fractions, and the RbcL gene is located in fractions from 30–59% G + C. For a given species, the two nuclear genes normally overlap in their distributions within the gradient. In most instances, neither gene occurs in the major DNA components, indicating that these components may contain repetitive DNAs. The observed variation in the density of the rbcL gene implies substantial reorganization of the chloroplast genome. The overall differences in the genomic components within and between taxa provide insight into the dynamics of DNA structure that have occurred during the extended evolutionary history of these organisms.

Colorimetric methods combined with color-changing chemical probes are widely used as simple yet effective tools for identifying and quantifying a wide variety of molecules in solution. For nucleic acids (DNA and RNA), perhaps the most commonly used colorimetric probe is potassium permanganate, which can be used to identify single-stranded pyrimidines (thymine and cytosine) in polymers. Unfortunately, permanganate is not an effective probe for identifying purines (adenine and guanine), especially in the presence of the more reactive pyrimidines. Therefore, robust methods for discriminating between the purines remain elusive, thereby creating a barrier toward developing more complex colorimetric applications. In this dissertation, we demonstrate that chromophores such as permanganate and bicinchoninic acid (BCA) and copper, however, when combined with nucleobase-specific chemical cleavage reactions, can be a colorimetric probe for the identification and quantification of cytosines, adenines and/or guanines in single-stranded DNA oligomers, even in the presence of thymines. Furthermore, the reactions are stoichiometric, which allows for the quantification of cytosine, adenine and/or guanine frequency in these oligomers. The BCA/copper reagent detects the reducing sugar, 2-deoxyribose, resulting from the chemical cleavage of a given nucleotide’s N-glycosidic bond. Therefore, these colorimetric assays are effectively detecting abasic sites in DNA oligomers, which are known to occur in damaged DNA. Our analytic approach termed colorimetric identification of exposed nucleic acids (CIENA) combines the use of BCA/copper, permanganate, and diphenylamine chromophores along with digital image capture to identify and quantify each nucleobase within DNA. The digital image color properties are quantified in terms of the image’s hue, saturation, and lightness using the CIELAB color space and ΔE quantification of color. CIENA is a simple, low-cost tool that could be applicable in various types of nucleic acid analyses, such as the quantification of nucleobase composition and the identification of damaged DNA.

This thesis aims to address issues relating to genome architecture and base composition. The first part of this thesis addresses questions relating to codon usage. Initially I will investigate thousands of bacterial species using a detailed analysis of strengths of selection acting upon codons usage while also investigating patterns of optimal codon changes with respect to genomic base composition and tRNA abundance. I report that selection on codon usage increases throughout the length of highly expressed genes, in particular, the first quarter of genes have significantly lower selection. Further, it is clear that factors affecting genomic base composition can eventually lead to changes in optimal codons if the change in base composition is strong enough, however these patterns differ substantially between amino acids. The debate over translational efficiency vs. accuracy was addressed by comparing sites of differing conservation. Differing conservation were defined using a phylogenetic method, allowing sites to change in their extent of conservation throughout the tree. The results show that translational accuracy acts strongly on the top 10% of conserved sites, however is relatively weak when compared to the efficiency for other sites. Also detected is a reduction in apparent selection on codon usage on the bottom 10% of conserved sites which is likely to be caused by conflicting positive selection on amino acids. Finally, although differences in patterns are observed between amino acids, the general relationship to conservation is similar. As much of the variation in codon usage is determined by variation in base composition, this aspect of base composition is investigated in the second part of the thesis. The observed variation in intragenomic base composition in bacteria was found to be far higher than expected for GC-rich bacteria. The non-core part of the genome contributes to this variation to a greater extent than the core part, suggesting that processes such as AT-rich horizontal gene transfer may be involved. Secondly, base composition is modelled under Brownian motion and as an extension, the Ornstein- Uhlenbeck process, which allows for multiple optima throughout the tree. The model including optima fits the data better than standard Brownian motion or Brownian motion with multiple diffusion coefficients. Finally, I investigate a case where a previous codon usage analysis has been seriously confounded by an unusual genome architecture of abnormal regional base composition in two species of eukaryotic parasites in the genus Theileria. In both species, the background G+C content is 37% at most, out of the four syntenic chromosomes. In many orthologous regions however, T.annulata has a decreased G+C content of 28% while T.parva has an increased G+C content of 41%. Various factors coincide with this remarkable divergence: increased divergence at all types of site, recombination hot spots in T.parva, an increased frequency of tandem repeats and DNA sequence motifs in both species. The evolutionary origins of these unusual patterns will be discussed.

<p>To shed light on forces that shape the molecular evolution of bird genomes, and in turn avian adaptations, comparative analyses of avian DNA sequences are important. Moreover, contrasting findings in birds to those of other organisms will lend a clearer view on general aspects of molecular evolution. However, few such analyses have been conducted in birds. Progress is presented in this thesis.</p><p>Theories predict a reduction in the mutation rate of the Z chromosome as the harmful effects of recessive mutations are exposed in female birds. We find no evidence for this. Instead, the substitution rates of sex chromosomes and autosomes are largely compatible with expectations from male-biased mutation. This suggests that a majority of mutations arise during DNA replication.</p><p>Substitution rates also vary across chicken autosomes. For instance, microchromosomes accumulate ~20% more substitutions than macrochromosomes. We show that a majority of the autosomal variation in substitution rate can be accounted for by GC content, mainly due to the incidence of mutable CpG-dinucleotides.</p><p>Sequence comparisons also show that the pattern of nucleotide substitution varies in the chicken genome and this reinforces regional differences in base composition. </p><p>The level of selective constraint in at least some avian lineages is higher than in mammalian lineages as indicated by low<i> d</i><i>N</i><i>/d</i><i>S</i><i> </i>– ratios. Larger historical population sizes of birds relative to mammals could explain this observation. Within the avian genome, the<i> d</i><i>N</i><i>/d</i><i>S</i> is lower for genes on micro- than macrochromosomes, potentially owing to a higher incidence of house-keeping genes in the former category.</p><p>Contrasting data on non-synonymous and synonymous substitution for divergence and polymorphism shows that positive selection has contributed more to the evolution of Z-linked than autosomal genes. This is likely explained by the full exposure of beneficial recessive mutations on Z when in female birds.</p>

To shed light on forces that shape the molecular evolution of bird genomes, and in turn avian adaptations, comparative analyses of avian DNA sequences are important. Moreover, contrasting findings in birds to those of other organisms will lend a clearer view on general aspects of molecular evolution. However, few such analyses have been conducted in birds. Progress is presented in this thesis. Theories predict a reduction in the mutation rate of the Z chromosome as the harmful effects of recessive mutations are exposed in female birds. We find no evidence for this. Instead, the substitution rates of sex chromosomes and autosomes are largely compatible with expectations from male-biased mutation. This suggests that a majority of mutations arise during DNA replication. Substitution rates also vary across chicken autosomes. For instance, microchromosomes accumulate ~20% more substitutions than macrochromosomes. We show that a majority of the autosomal variation in substitution rate can be accounted for by GC content, mainly due to the incidence of mutable CpG-dinucleotides. Sequence comparisons also show that the pattern of nucleotide substitution varies in the chicken genome and this reinforces regional differences in base composition. The level of selective constraint in at least some avian lineages is higher than in mammalian lineages as indicated by low dN/dS – ratios. Larger historical population sizes of birds relative to mammals could explain this observation. Within the avian genome, the dN/dS is lower for genes on micro- than macrochromosomes, potentially owing to a higher incidence of house-keeping genes in the former category. Contrasting data on non-synonymous and synonymous substitution for divergence and polymorphism shows that positive selection has contributed more to the evolution of Z-linked than autosomal genes. This is likely explained by the full exposure of beneficial recessive mutations on Z when in female birds.

Le paysage nucléotidique – la manière dont la composition nucléotidique varie le long du génome – est une caractéristique marquante de l'organisation des génomes et varie fortement entre espèces. Plusieurs hypothèses émergent des nombreux débats autour des mécanismes évolutifs à l'origine de ces hétérogénéités du taux de GC, parmi lesquelles la conversion génique biaisée vers G et C (BGC) et la sélection sur l'usage du code (SUC). La BGC est un processus neutre associé à la recombinaison qui favorise les allèles en G ou C au détriment des allèles en A ou T. La SUC est une force de sélection qui favorise les codons dits « préférés », ceux dont la traduction serait la plus efficace. Contrairement à ceux des vertébrés, les paysages nucléotidiques des plantes sont peu connus. La plupart des études ont été consacrées au génome d'Arabidopsis thaliana, pauvre en GC et homogène, et à celui du riz, riche en GC et hétérogène. Le contraste entre ces deux génomes a souvent été généralisé comme une dichotomie entre dicotylédones et monocotylédones, mais cette vision est clairement phylogénétiquement biaisée.Les objectifs de ce travail de thèse sont de caractériser les paysages nucléotidiques des angiospermes à une large échelle phylogénétique et de mieux comprendre quels sont les mécanismes évolutifs jouant sur l'évolution de ces paysages nucléotidiques. Comment varient les paysages nucléotidiques le long de la phylogénie des angiospermes ? SUC et BGC façonnent-elles ces paysages nucléotidiques ? Les différents taxons sont-ils affectés avec la même intensité ?Pour répondre à ces questions, j'ai utilisé une approche de génomique comparative basée sur l'analyse de données EST chez plus de 230 espèces d'angiospermes et de gymnospermes. L'exploration des paysages nucléotidiques de ce large éventail de plantes a montré que les patrons d'hétérogénéité des paysages nucléotidiques suivent un continuum le long de la phylogénie, avec des groupes particulièrement riches et hétérogènes en GC, les graminées par exemple. Mes résultats suggèrent que les paysages nucléotidiques des plantes pourraient avoir été façonnés par la BGC et, dans une moindre mesure, par la SUC. Des épisodes indépendants d'enrichissement et d'appauvrissement en GC ont vraisemblablement eu lieu au cours de l'évolution des plantes, et pourraient être expliqués par des variations d'intensité de ces mécanismes. En utilisant une prédiction du degré d'expression des EST, j'ai également mis en évidence une diversité dans les codons préférés entre espèces. Les préférences d'usage des codons se sont révélées plus labiles au cours de l'évolution pour les codons des acides aminés au code quatre et six fois dégénéré. J'ai pu lier l'évolution des préférences d'usage des codons à l'évolution de la composition nucléotidique des génomes. Mes résultats suggèrent que la composition en base des génomes, affectée en partie par la BGC, orienterait la coévolution entre préférence d'usage du code et ARNt. / The nucleotide landscape – the way base composition varies along a genome – is a striking feature of genome organization and is highly variable between species. The evolutionary causes of such heterogeneity in GC content have been much debated. Biased gene conversion towards G and C (BGC) and selection on codon usage (SCU) are thought to be main forces. BGC is a neutral process associated with recombination favouring G and C alleles over A and T ones. SCU is a selection process favouring the so-called “preferred” codons, i.e., those whose translation is the most efficient. Contrary to vertebrates, plant nucleotide landscapes are still poorly known. Most studies focused on the GC-poor and homogeneous Arabidopsis thaliana genome and on the GC-rich and heterogeneous rice genome. The contrast between these two genomes was often generalized as a dicot/monocot dichotomy but this vision is clearly phylogenetically biased.The objectives of this study are to characterize angiosperm nucleotide landscapes on a wide phylogenetic scale and to better understand the evolutionary mechanisms acting upon the evolution of nucleotide landscapes. To what extent do nucleotide landscapes vary across angiosperm phylogeny? Are nucleotide landscapes shaped by BGC and SCU? Are taxa affected with the same intensity?To tackle these issues, I used a comparative genomic approach relying on EST data analysis on over 230 angiosperm and gymnosperm species. Through the nucleotide landscape survey for such a wide range of species I found a continuum of GC-heterogeneity patterns across phylogeny, some taxa such as Poaceae being strikingly GC-rich and heterogeneous. My results suggest that nucleotide landscapes could have been shaped by BGC and, to a lesser extent, by SCU. GC-content enrichment and impoverishment are likely to have occurred several times independently during plant evolution and could be explained by intensity variations of BGC and SCU. Using a proxy for EST expression level, I also characterized the diversity of preferred codons between species. Codon usage preferences were shown to be evolutionarily more unstable for four- and six-fold degenerate codon families. Finally, I could link the evolution of codon usage preferences to the evolution of genome base composition. My results suggest that genome base composition, partially shaped by BGC, seems to drive the coevolution between codon usage preferences and tRNAs.