Appropriate recognition of parasites is crucial for effective immune response, ensuring activation of adequate defence mechanisms. In vertebrates, it has frequently been demonstrated that genes encoding proteins involved in pathogen recognition by an adaptive immune system are often subject to intense selection pressures. On the contrary, much less information has been provided on the evolution of recognition mechanisms of innate immunity. The aim of this thesis is to describe the pattern of natural variation of innate immunity genes involved in pathogen recognition in rodents and to analyze the mechanisms of their evolution. We used murine rodents (subfamily Murinae) as a principal model group because they are potential reservoirs of various pathogens dangerous to humans. First, we studied the intraspecific variability of five bacterial sensing Toll-like receptors (TLR1, TLR2, TLR4, TLR5, and TLR6) in inbred strains derived from two subspecies of the house mouse (M. m. musculus, hereafter abbreviated as Mmm and Mus musculus domesticus, Mmd). Wild-derived inbred strains are suitable tools for studying variation of immunity genes because they provide information about alleles that occur in natural populations, and at the same time they occur at homozygous state. The most significant results include the findings of a stop codon in exon 2 of the Tlr5 gene in one Mmm strain and no variability in Tlr4 of Mmd. Following these results we decided to check whether the absence of Tlr4 polymorphism in Mmd reflects the pattern found in natural populations, or whether it is a consequence of insufficient sampling or subsequent breeding. We therefore sequenced Tlr4 in both subspecies across a large part of the Western Palearctic region (in total 39 Mmm and 62 Mmd individuals), then we compared these results with variability on mitochondrial DNA (cytochrome b). The result confirmed our prediction that observed variability in Mmd is strongly reduced also in free-living populations (compared to Mmm), probably due to strong purifying selection by pathogens with which they met during the westward colonization. However, the influence of random evolutionary processes (e.g. drift during bottlenecks) cannot be excluded based on our data. At the intraspecific level, we could not find any sign of positive selection. The last part of my dissertation is devoted to interspecific comparison of two receptors, TLR4 and TLR7. These two TLRs differ in the exposure and the ligands detection. TLR4 is an extracellular receptor detecting mainly bacterial ligands (especially lipopolysaccharides), while TLR7 is located inside the cell and detects ssRNA viruses. The aim of this part of the thesis was to describe variability of both receptors at the interspecific level and to reveal selection forces acting on TLRs in longer evolutionary time scale. In total we analyzed 23 rodent species of the subfamily Murinae in Europe, Asia and Africa. Our results suggest that purifying selection has been a dominant force in evolution of the Tlr4 and Tlr7 genes, but we also demonstrated that episodic diversifying selection has shaped the present species-specific variation in rodent Tlrs. Sites under positive selection were concentrated mainly in the extracellular domain of both receptors, which is responsible for ligand binding. The comparison between two TLRs lead us to the conclusion that the intracellular TLR7 is under much stronger negative selection pressure, presumably due to its interaction with viral nucleic acids.

MADS-box genes are important regulators of reproductive development in seed plants, including both flowering plants and conifers. In this thesis the evolution of the AGAMOUS subfamily of MADS-box genes, and what the ancestral function of this group of genes might have been in the early seed plants about 300 million years ago, was addressed by the discovery of two novel conifer genes, both basal to all previously known AGAMOUS subfamily genes. DAL20, the most basal of these genes, was exclusively expressed in roots, unlike all previously known AGAMOUS subfamily genes. I also studied the evolutionary mechanisms leading to functional diversification of duplicated genes in two different subfamilies of MADS-box genes; the AGAMOUS and AGL6 subfamilies. Focus was on studying changes in gene expression pattern, representing changes in the transcriptional regulation between the genes, and on comparing the functional properties of the gene products, representing changes in the protein-coding sequence between the genes. Duplicated genes in the AGL6 subfamily were found to have evolved by both mechanisms. In the AGAMOUS subfamily I found duplicated spruce genes; DAL2 and DAL20, that appear to have functionally diversified mainly by changes in the transcriptional regulation. Conifer AGAMOUS subfamily genes were also used in a comparative developmental-genetics approach to evaluate hypotheses, based on the morphology of fossil and extant conifer seed cones, on the identity of the female reproductive organ, the ovuliferous scale, and the evolution of seed cone morphology in the conifer families Pinaceae, Taxodiaceae and Cupressaceae. Seed cones in these families have been hypothesized to have homologous ovule-bearing organs, but I found substantial differences in the expression patterns of orthologous AGAMOUS subfamily genes in seed cones of these families that are not compatible with this hypothesis, indicating that the evolutionary history of conifer seed cones is more diverse than previously thought.

O veneno de animais contém um arsenal de toxinas que desencadeia respostas fisiológicas e bioquímicas específicas. A crotamina, um peptídio catiônico (4,4 kDa, pI 9,5), é um dos componentes mais abundantes do veneno de cascavel Sul Arrericana (Crotalus durissus terrificus). No Brasil, há populações de C. d. terrificus que expressam ou não a crotamina no veneno. Em um único espécime de C. d. terrificus crotamina-positivo, foram isolados cDNAs precursores de duas isoformas de crotamina, dentre as quais a crotamina lle-19, presente somente no veneno de C.d. ruruima. Análise por Northern blot de RNA total e mensageiro de glândulas de C.d. terrificus crotamina-positivo e -negativo, indica que a expressão é defectiva em espécimes de cascavel crotamina-negativo. O gene da crotamina (Crt-pl) foi isolado e possui três exons interrompidos por dois introns de diferentes fases e tamanhos. O exon I codifica a totalidade do peptídio sinal; o exon II codifica os três resíduos carboxi-terminais do peptídio sinal, bem como a maior parte da toxina madura; o terceiro exon codifica os resíduos terminais da toxina. Tentativa de identificar o pseudogene da crotamina, que indicaria a ausência de transcritos na glânlula de veneno, permitiu isolar um gene parálogo ao da crotamina, isto é o gene crotasin (Cts-p2). Esse gene apresenta a mesma organização estrutural do gene da crotamina, contudo, o intron I é cerca de 800 pares de base mais longo e o exon II é hipermutado. Esse gene é expresso em diferentes tecidos de cascavel, majoritariamente no pâncreas, mas insignificantemente nas glândulas de veneno. Surpreendentemente, esse gene é também detectado no genoma de C. d. terrificus crotamina-positivo, sugerindo que o gene de crotamina é o produto de uma duplicação gênica, bem como da evolução acelerada que operou restritivamente ao exon II. Buscando as funções do produto desse gene nos tecidos de cascavel, por alinhamento de domínios protéicos e outras famílias de peptídios de vertebrados, duas categorias foram encontradas: peptídios catiônicos antibióticos (β-defensinas) e domínios ricos em cisteína de receptores de fator de crescimento. Testes antibióticos indicam que o crotasin, a crotamina e oligopeptídios derivados sintéticos possuem certa atividade microbicida seletiva. Por outro lado, ensaios com células-tronco embrionárias de camundongo e crotamina de veneno mostram que a crotamina é citotóxica em concentrações milimolares, mas induz a diferenciação dos corpos embrionários, em concentrações micromolares. Esses achados demonstram a multi-funcionalidade de peptídios catiônicos, com três pontes de cisteína precisamente arranjadas, é decorrente da versatilidade dos domínios protéicos anfipáticos, que permitem interação com a membrana plasmática, modulando canais iônicos e receptores celulares. / Abstract not available.

O veneno de animais contém um arsenal de toxinas que desencadeia respostas fisiológicas e bioquímicas específicas. A crotamina, um peptídio catiônico (4,4 kDa, pI 9,5), é um dos componentes mais abundantes do veneno de cascavel Sul Arrericana (Crotalus durissus terrificus). No Brasil, há populações de C. d. terrificus que expressam ou não a crotamina no veneno. Em um único espécime de C. d. terrificus crotamina-positivo, foram isolados cDNAs precursores de duas isoformas de crotamina, dentre as quais a crotamina lle-19, presente somente no veneno de C.d. ruruima. Análise por Northern blot de RNA total e mensageiro de glândulas de C.d. terrificus crotamina-positivo e -negativo, indica que a expressão é defectiva em espécimes de cascavel crotamina-negativo. O gene da crotamina (Crt-pl) foi isolado e possui três exons interrompidos por dois introns de diferentes fases e tamanhos. O exon I codifica a totalidade do peptídio sinal; o exon II codifica os três resíduos carboxi-terminais do peptídio sinal, bem como a maior parte da toxina madura; o terceiro exon codifica os resíduos terminais da toxina. Tentativa de identificar o pseudogene da crotamina, que indicaria a ausência de transcritos na glânlula de veneno, permitiu isolar um gene parálogo ao da crotamina, isto é o gene crotasin (Cts-p2). Esse gene apresenta a mesma organização estrutural do gene da crotamina, contudo, o intron I é cerca de 800 pares de base mais longo e o exon II é hipermutado. Esse gene é expresso em diferentes tecidos de cascavel, majoritariamente no pâncreas, mas insignificantemente nas glândulas de veneno. Surpreendentemente, esse gene é também detectado no genoma de C. d. terrificus crotamina-positivo, sugerindo que o gene de crotamina é o produto de uma duplicação gênica, bem como da evolução acelerada que operou restritivamente ao exon II. Buscando as funções do produto desse gene nos tecidos de cascavel, por alinhamento de domínios protéicos e outras famílias de peptídios de vertebrados, duas categorias foram encontradas: peptídios catiônicos antibióticos (β-defensinas) e domínios ricos em cisteína de receptores de fator de crescimento. Testes antibióticos indicam que o crotasin, a crotamina e oligopeptídios derivados sintéticos possuem certa atividade microbicida seletiva. Por outro lado, ensaios com células-tronco embrionárias de camundongo e crotamina de veneno mostram que a crotamina é citotóxica em concentrações milimolares, mas induz a diferenciação dos corpos embrionários, em concentrações micromolares. Esses achados demonstram a multi-funcionalidade de peptídios catiônicos, com três pontes de cisteína precisamente arranjadas, é decorrente da versatilidade dos domínios protéicos anfipáticos, que permitem interação com a membrana plasmática, modulando canais iônicos e receptores celulares. / Abstract not available.

Cotton has been a world-wide economic staple in textiles and oil production. There has been a concerted effort for cotton improvement to increase yield and quality to compete with non-natural man-made fibers. Unfortunately, cultivated cotton has limited genetic diversity; therefore finding new marketable traits within cultivated cotton has reached a plateau. To alleviate this problem, traditional breeding programs have been attempting to incorporate practical traits from wild relatives into cultivated lines. This incorporation has presented a new problem: uncultivated cotton hampered by photoperiodism. Traditionally, due to differing floral times, wild and cultivated cotton species were unable to be bred together in many commercial production areas world-wide. This worldwide breeding problem has inhibited new trait incorporation. Before favorable traits from undomesticated cotton could be integrated into cultivated elite lines using marker-assisted selection breeding, the markers associated with photoperiod independence needed to be discovered. In order to increase information about this debilitating trait, we set out to identify informative markers associated with photoperiodism. This study was segmented into four areas. First, we reviewed the history of cotton to highlight current problems in production. Next, we explored cotton’s floral development through a study of floral transition candidate genes. The third area was an in-depth analysis of Phytochrome C (previously linked to photoperiod independence in other crops). In the final area of study, we used Genotype-By-Sequencing (GBS), in a segregating population, was used to determine photoperiod independence associated with single nucleotide polymorphisms (SNPs). In short, this research reported SNP differences in thirty-eight candidate gene homologs within the flowering time network, including photoreceptors, light dependent transcripts, circadian clock regulators, and floral integrators. Also, our research linked other discrete SNP differences, in addition to those contained within candidate genes, to photoperiodicity within cotton. In conclusion, the SNP markers that our study found may be used in future marker assisted selection (MAS) breeding schemas to incorporate desirable traits into elite lines without the introgression of photoperiod sensitivity.