Thesis advisor: Tim van Opijnen / Thesis advisor: Welkin Johnson / Pathogenic bacteria can experience various stress factors during an infection including antibiotics and the host immune system. Whether a pathogen will establish an infection largely depends on its survival-success while enduring these stress factors. We reasoned that the ability to predict whether a pathogen will survive under and/or adapt to a stressful condition will provide great diagnostic and prognostic value. However, it is unknown what information is needed to enable such predictions. We hypothesized that under a stressful condition, a bacterium triggers responses that indicate how the stress is experienced in the genome, thereby correctly identifying a stress response holds the key to enabling such predictions. Bacterial stress responses have long been studied by determining how small groups of individual genes or pathways respond to certain environmental triggers. However, the conservation of these genes and the manner in which they respond to a stress can vary widely across species. Thus, this thesis sought to achieve a genome-wide and systems-level understanding of a bacterial stress response with the goal to identify signatures that enable predictions of survival and adaptation outcomes in a pathogen- and stress-independent manner. Here, we first set up a multi-omics framework that maps out a stress response on a genome-wide level using the human respiratory pathogen Streptococcus pneumoniae as a model organism. Under an environmental stress, gene fitness changes are determined by transposon insertion sequencing (Tn-Seq) which represents the phenotypic response. Differential expression is profiled by RNA-Seq which represents as the transcriptional response. Much to our surprise, the phenotypic response and transcriptional response are separated on different genes, meaning that differentially expressed genes are poor indicators of genes that contribute to the fitness of the bacterium. By devising and performing topological network analysis, we show that phenotypic and transcriptional responses are coordinated under evolutionary familiar stress, such as nutrient depletion and host infection, in both Gram-positive and -negative pathogens. However, such coordination is lost under the relatively unfamiliar stress of antibiotic treatment. We reasoned that this could mean that a generalizable stress response signature might exist that indicates the level to which a bacterium is adapted to a stress. By extending stress response profiling to 9 antibiotics and 3 nutrient depletion conditions, we found that such a signature indeed exists and can be captured by the level of transcriptomic disruption, defined by us as transcriptomic entropy. Centered on entropy, we constructed predictive models that perform with high accuracy for both survival outcomes and antibiotic sensitivity across 7 species. To further develop these models with the goal to eventually enable predictions on disease progression, we developed a dual RNA-Seq technique that maps out the transcriptomic responses of both S. pneumoniae and its murine host during lung infection. Preliminary data show that a high entropy is observed in the pathogen’s transcriptome during clearance (a failed infection) compared to a successful/severe infection, while the host transcriptome exhibits a pro-inflammatory and active immune response under the severe infection. Lastly, we characterized evolutionary trajectories that lead to long-term survival success of S. pneumoniae, for instance this means that the bacterium successfully adapts to the presence of an antibiotic and becomes resistant or can grow successfully in the absence of a formerly critical nutrient. These trajectories show that adaptive mutations tend to occur in genes closely related to the adapted stress. Additionally, independent of the stress, adaptation triggers rewiring of transcriptional responses resulting in a change in entropy from high to low. Most importantly, we demonstrate that by combining multi-omics profiles with additional genomic data including gene conservation and expression plasticity, and feeding this into machine learning models, that adaptive evolution can become (at least partially) predictable. Additionally, the genetic diversity in bacterial genomes across different strains and species can indeed influence a bacterium’s adaptation trajectory. In conclusion, this thesis presents a substantial collection of multi-omics stress response profiles of S. pneumoniae and other pathogenic bacteria under various environmental and clinically-relevant stresses. By demonstrating the feasibility of predictions on bacterial survival and adaptive outcomes, this thesis paves the way towards future improvements on infectious disease prognostics and forecasting the emergence of antibiotic resistance. / Thesis (PhD) — Boston College, 2020. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

Major fraction of eukaryotic genomes is composed of transposons. Mobilization of these transposons leads to mutations and genomic instability. In animals, these selfish genetic elements are regulated by a class of small RNAs called PIWI interacting RNAs (piRNAs). Thus host piRNA pathway acts as a defense against pathogenic transposons. Many piRNA pathway genes are rapidly evolving indicating that they are involved in a host-pathogen arms race. In my thesis, I investigated the nature of this arms race by checking functional consequences of the sequence diversity in piRNA pathway genes. In order to study the functional consequences of the divergence in piRNA pathway genes, we swapped piRNA pathway genes between two sibling Drosophila species, Drosophila melanogaster and Drosophila simulans. We focused on RDC complex, composed of Rhino, Deadlock and Cutoff, which specifies piRNA clusters and regulates transcription from clusters. None of the D. simulans RDC complex proteins function in D. melanogaster. Rhino and Deadlock interact and colocalize in D. simulans and D. melanogaster, but D. simulans Rhino does not bind D. melanogaster Deadlock, due to substitutions in the rapidly evolving Shadow domain. Cutoff from D. simulans stably binds and traps D. melanogaster Deadlock. Adaptive evolution has thus generated cross-species incompatibilities in the piRNA pathway which may contribute in reproductive isolation.

<p>Extensive use of the sulphonamide drugs against the bacterium <i>Neisseria meningitidis</i> has resulted in drug resistance development. Sulphonamide resistance in <i>N. meningitidis</i> is caused by alterations in the chromosomal <i>folP</i> gene, coding for DHPS (dihydropteroate synthase). One type of resistant DHPS has high sequence divergence compared to DHPS from susceptible strains. This divergent DHPS has a duplication of two amino acids, crucial for resistance, and an altered amino acid in position 68, important for both resistance and substrate binding. When introduced into a susceptible DHPS, these two alterations did not incur resistance and resulted in abnormal substrate binding properties. This indicated that the divergent DHPS was not directly developed by mutations, but rather had been acquired by horizontal transfer of <i>folP</i> from another species.</p><p>Commensal <i>Neisseria</i> species are implied as the origin of the horizontally transferred resistance. Sulphonamide-resistant commensal <i>Neisseria</i> isolates were detected in throat swabs from healthy individuals not exposed to these drugs; however, transformation of resistance from these commensals to <i>N. meningitidis</i> was restricted in the laboratory. A comparison of the genomic region surrounding <i>folP</i> revealed differences in gene organisation and in the DNA uptake sequence between <i>N. meningitidis</i> and distantly related commensals. These differences are likely to restrict transformation between distantly related <i>Neisseria</i> species.</p><p>DHPS participates in the folate biosynthesis pathway. The enzyme preceding DHPS in the pathway, HPPK (hydroxymethyl-dihydropterin pyrophosphokinase), from <i>N. meningitidis</i> was characterised and a method for studying substrate channelling from HPPK to DHPS was developed. The information gained could be exploited in the search for new antibiotics.</p><p>In conclusion, well-adapted sulphonamide-resistant strains of <i>N. meningitidis</i> and commensal <i>Neisseria</i> are established in the bacterial population and resistance can be horizontally spread by natural transformation. This may explain the abundance of sulphonamide-resistant <i>N. meningitidis</i>, although these drugs are no longer used against this bacterium.</p>

Extensive use of the sulphonamide drugs against the bacterium Neisseria meningitidis has resulted in drug resistance development. Sulphonamide resistance in N. meningitidis is caused by alterations in the chromosomal folP gene, coding for DHPS (dihydropteroate synthase). One type of resistant DHPS has high sequence divergence compared to DHPS from susceptible strains. This divergent DHPS has a duplication of two amino acids, crucial for resistance, and an altered amino acid in position 68, important for both resistance and substrate binding. When introduced into a susceptible DHPS, these two alterations did not incur resistance and resulted in abnormal substrate binding properties. This indicated that the divergent DHPS was not directly developed by mutations, but rather had been acquired by horizontal transfer of folP from another species. Commensal Neisseria species are implied as the origin of the horizontally transferred resistance. Sulphonamide-resistant commensal Neisseria isolates were detected in throat swabs from healthy individuals not exposed to these drugs; however, transformation of resistance from these commensals to N. meningitidis was restricted in the laboratory. A comparison of the genomic region surrounding folP revealed differences in gene organisation and in the DNA uptake sequence between N. meningitidis and distantly related commensals. These differences are likely to restrict transformation between distantly related Neisseria species. DHPS participates in the folate biosynthesis pathway. The enzyme preceding DHPS in the pathway, HPPK (hydroxymethyl-dihydropterin pyrophosphokinase), from N. meningitidis was characterised and a method for studying substrate channelling from HPPK to DHPS was developed. The information gained could be exploited in the search for new antibiotics. In conclusion, well-adapted sulphonamide-resistant strains of N. meningitidis and commensal Neisseria are established in the bacterial population and resistance can be horizontally spread by natural transformation. This may explain the abundance of sulphonamide-resistant N. meningitidis, although these drugs are no longer used against this bacterium.

Submitted by Alison Vanceto (alison-vanceto@hotmail.com) on 2017-01-24T10:55:13Z No. of bitstreams: 1 DissLPMoc.pdf: 5018835 bytes, checksum: 6e118e7b00ba50c95eaca8d0df293f3a (MD5) / Approved for entry into archive by Camila Passos (camilapassos@ufscar.br) on 2017-02-08T10:50:35Z (GMT) No. of bitstreams: 1 DissLPMoc.pdf: 5018835 bytes, checksum: 6e118e7b00ba50c95eaca8d0df293f3a (MD5) / Approved for entry into archive by Camila Passos (camilapassos@ufscar.br) on 2017-02-08T10:51:51Z (GMT) No. of bitstreams: 1 DissLPMoc.pdf: 5018835 bytes, checksum: 6e118e7b00ba50c95eaca8d0df293f3a (MD5) / Made available in DSpace on 2017-02-08T10:51:59Z (GMT). No. of bitstreams: 1 DissLPMoc.pdf: 5018835 bytes, checksum: 6e118e7b00ba50c95eaca8d0df293f3a (MD5) Previous issue date: 2016-03-31 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Biodiesel is a renewable fuel and its production generate raw glycerol (RG) as main byproduct. The use of RG as carbon source in microorganism cultivations poses as an alternative to add value and reduce the environmental impact of this residue. However, RG impurities (salts, esters, alcohol and soap) can inhibit cell growth. Techniques that aims adapting microorganisms to environments containing contaminants by adaptive evolution have been employed to overcome inhibition problems. Adaptation strategies allows imposing a certain selective pressure upon the population, favoring the appearance of mutants and selection of most beneficial mutations, which will make the cell more suited to develop itself in a hostile environment. This work employed Adaptive Evolution methodology to obtain an E. coli K12 strain adapted to RG concentrated by rotary evaporation (RGRota). Cultivations were carried out in plates (E. coli – USP strain) incubated at 37 ºC, as well as shaken flasks (E. coli – UMinho strain), kept at 37 ºC and 300 rpm, involving transfers to defined media gradually enriched with RGRota. Obtained evolved strain as well as the wild-type strain E. coli – UMinho were characterized in cultivations using 2 L, bench-scale bioreactor, equipped with monitoring and control system. During shaken flask experiments, growth was followed by optical density (OD) readings. In bioreactor cultures, samples were withdrawal to analyze cell concentration of the suspension (OD and dry cell weight), concentrations of glycerol, ethanol and organic acids (liquid chromatography), concentration of viable cells (colony forming units counting) and morphology. Cultures characterization were carried out with E. coli – USP in shaken flasks, the values of maximum specific growth rate (μmax) remained between 0.40 e 0.45 h-1 and they showed little influence of strain or media composition. These results suggest that the selected strain did not have differentiated characteristics from the wild-type strain. For E. coli – UMinho, two adaptation strategies were evaluated: successive transfer during exponential growth phase (OD = ~2.5) and during stationary growth phase (OD = ~10). In both cases cells evolved, showing increased μmax values, with more homogeneous populations being observed for adaptation conducted under the first strategy. After 26 days of adaptation, corresponding to 534 generations, an evolved strain, exhibiting μmax of 0.60 h-1 and capable of growing in medium containing 29 g/L of glycerol from RGRota was selected by the methodology of successive transfers in exponential phase. This growth rate was 27.6 % superior to that achieved by the wild-type strain (0.47 h-1). Evolved and wild-type strains were cultivated in bioreactor, containing defined medium prepared with GBRota to have 40 g/L of glycerol. The evolved one maintained μmáx of 0.61 h-1. Acetate formation was observed, with yield of 0.19 g acetate/g glycerol, which caused growth inhibition and limited biomass yield to 0.26 gbiomass/gglycerol. When the wild-type strain was cultivated in bioreactor, exponential growth started after 24 h of lag phase and it presented μmax of 0.28 h-1, biomass yield of 0,39 gbiomass/gglycerol and acetate yield of 0.19 gacetate/gglycerol. The evolved strain obtained, capable of growing in the biodiesel production residue, showed a μmax value similar to the best results reported in the literature for E. coli adaptation in pure glycerol (0.7 h-1), what demonstrates the successful application of the adaptive evolution methodology. Acetate accumulation can be reduced by Genetic Engineering techniques to manipulate metabolic pathways and this will lead to development of an industrial strain which can be employed as a platform of high value products using unrefined glycerol as substrate. / O biodiesel é um combustível renovável cuja produção gera o glicerol bruto (GB) como principal subproduto. O aproveitamento de GB como fonte de carbono em cultivos de microrganismos se apresenta como uma alternativa para agregar valor e reduzir o impacto ambiental deste resíduo. Contudo, as impurezas do GB (sais, ésteres, álcool e sabão) podem inibir o crescimento das células. Técnicas que visam adaptar os microrganismos via evolução adaptativa a ambientes contendo contaminantes vêm sendo empregadas para contornar problemas de inibição. As estratégias de adaptação permitem impor uma certa pressão seletiva sobre a população, favorecendo o aparecimento de mutantes e a seleção de mutações benéficas, que tornam a célula mais apta a se desenvolver em um ambiente hostil. O trabalho empregou a metodologia de Evolução Adaptativa para obter uma linhagem de E. coli K12 adaptada ao GB concentrado por rotaevaporação (GBRota). Os cultivos foram realizados tanto em placas (linhagem E. coli – USP) incubadas a 37ºC, como em frascos agitados (linhagem E. coli – UMinho), mantidos a 37ºC e 300 rpm, envolvendo transferências para meios definidos gradualmente enriquecidos com GBRota. A linhagem evoluída obtida assim como a linhagem selvagem E. coli – UMinho foram caracterizadas em cultivos em biorreator de bancada de 2 L, dotado de sistema de monitoramento e controle. Durante os experimentos em frascos agitados, o crescimento foi acompanhado por leitura de densidade ótica (DO). Nos cultivos em biorreator, amostras foram coletadas para análises de concentração celular da suspensão (DO e massa seca), da concentração de glicerol, etanol e ácidos orgânicos (por cromatografia líquida), da concentração de células viáveis (por contagem de unidades formadoras de colônia) e de morfologia. Para os cultivos de caracterização da E. coli – USP realizados em frascos agitados, os valores da velocidade máxima específica de crescimento (max) permaneceram entre 0,40 e 0,45 h-1, sendo pouco influenciados pela linhagem ou pela composição dos meios, sugerindo que a metodologia adotada para adaptação em placa não foi eficiente, já que a linhagem selecionada não possuía características diferenciadas em relação à linhagem selvagem. Para a E. coli – UMinho foram avaliadas duas estratégias de adaptação: transferências sucessivas na fase exponencial do cultivo (DO = ~2,5) e na fase estacionária (DO = ~10). Em ambos os casos, as células evoluíram, apresentando aumento nos valores de max., sendo que populações mais homogêneas foram observadas na adaptação realizada pela primeira estratégia. Após 26 dias de adaptação, correspondendo a 534 gerações, foi selecionada pela metodologia de transferências sucessivas na fase exponencial, uma linhagem evoluída apresentando velocidade máxima específica de 0,60 h-1, resultado superior em 27,6% ao da linhagem selvagem (0,47h-1), capaz de crescer em meio contendo ~30 g/L de glicerol proveniente do GBRota. As linhagens selvagem e evoluída foram cultivadas em biorreator contendo meio preparado com GBRota na concentração de 40 g/L de glicerol. A linhagem evoluída manteve o μmáx de 0,61 h-1. Foi observada formação de acetato, com rendimento de 0,19 gacetato/gglicerol, o que causou inibição do crescimento e limitou o rendimento em biomassa a 0,26 gbiomassa/gglicerol. Enquanto que, para a linhagem selvagem o cultivo em biorreator apresentou uma fase lag de 24 h, um max de 0,28 h-1, rendimento em biomassa de 0,39 gacetato/gglicerol e rendimento em acetato 0,19 gacetato/gglicerol. A linhagem evoluída obtida no presente trabalho, capaz de crescer no resíduo da produção de biodiesel, apresenta max semelhante aos melhores resultados relatados na literatura para adaptação de E. coli em glicerol puro (0,7 h-1), demonstrando o sucesso da aplicação da metodologia de evolução adaptativa. O acúmulo de acetato pode ser amenizado utilizando técnicas de Engenharia Genética para manipulação das vias metabólicas e permitindo o desenvolvimento de uma linhagem industrial que poderá ser empregada como plataforma para obtenção de produtos de alto valor agregado usando o glicerol não refinado como substrato.

Submitted by (ana.araujo@ufrpe.br) on 2016-07-05T12:45:54Z No. of bitstreams: 1 Edilson de Araujo Goncalves.pdf: 586732 bytes, checksum: a681dd9d8537af4fa4a8e2cd099b6bb3 (MD5) / Made available in DSpace on 2016-07-05T12:45:54Z (GMT). No. of bitstreams: 1 Edilson de Araujo Goncalves.pdf: 586732 bytes, checksum: a681dd9d8537af4fa4a8e2cd099b6bb3 (MD5) Previous issue date: 2007-06-13 / Adaptation of populations takes place with the occurrence and subsequent fixation of mutations that confer some selective advantage to the individuals that acquire it. For that reason, the study of the process of advantageous mutations fixation has a long history in the population genetics literature. Particularly, the previous investigations aimed to find out the main evolutionary forces affecting the strength of natural selection in the populations. In the current work, we investigate the dynamics of fixation of bene cial mutations in a subdivided population. The subpopulations (demes) can exchange migrants among their neighbors. The migration network is assumed to have either a random graph or a scale-free topology. We have seen that the migration rate drastically affect the dynamics of mutation fixation, despite of the fact that the probability of fixation is invariant on the migration rate, accordingly to Maruyama's conjecture.In addition, we have observed that a topological dependence of the adaptive evolution of the population exists when clonal interference becomes effective. / A adaptação de populações decorre do surgimento e posterior fixação de mutações benéficas que conferem alguma vantagem seletiva aos indivíduos que as adquirem. Por esta razão, o estudo do processo de fixação de mutações benéficas tem uma longa história na literatura de genética de populações. Particularmente, tais investigações objetivaram encontrar as principais forças evolucionárias que afetam a atuação da seleção natural nas populações. No presente trabalho, nós investigamos a dinâmica de fixação de mutações benéficas em uma população subdividida. As subpopulações, denominadas de demes, podem permutar migrantes entre seus vizinhos. Consideramos duas topologias para a rede de migração, uma tipo grafo aleatório e uma outra para rede livre de escala. Nós verificamos que a taxa de migração afeta drasticamente a dinâmica de fixação de mutações, apesar do fato da probabilidade de fixação ser independente da taxa de migração de acordo com a conjectura de Maruyama. Além disso, observamos uma influência da topologia da rede migratória na evolução adaptativa quando a interferência clonalse torna relevante.

La fermentation œnologique et le vieillissement oxydatif des vins sous voile représentent des modes de vie très contrastés qui sont effectués par deux lignées différentes de souches de levures de l'espèce Saccharomyces cerevisiae. Dans cette thèse, nous avons comparé le génome de souches de levures de voile à celui de levures de vin afin de détecter leurs spécificités. Nous tout d'abord sélectionné 16 souches (8 levures de vin et 8 levures de voile) isolées en France, Hongrie, Italie et Espagne, pour séquencer leur génome sur une plateforme Illumina (HiSeq2000). Nous avons également développé un ensemble de souches de vin et de voile haploïdes pour l'évaluation moléculaire de différentes cibles. Nous avons également mis au point un milieu synthétique mimant le vin à cette fin. A partir de la comparaison des séquences du génome nous avons établi une phylogénie qui montre que les levures de voile représentent un groupe spécifique de levure, différentes des levures de vin, puis à partir de différentes méthodes (analyse en composantes principale, diversité nucléotidique et D de Tajima) nous avons identifié des régions divergentes. Ces régions variantes comprennent des gènes remplissant plusieurs fonctions clé associées à la croissance en voile. En particulier, des variations alléliques ont été rencontrées chez les levures de voile pour plusieurs gènes impliqués dans la régulation de l'expression de FLO11 tels que les voies MAP kinase, ou des voies Ras/cAMP/PKA, ainsi que pour plusieurs gènes impliqués dans l'homéostasie des cations divalents de métaux de transition tels que le zinc, le cuivre ou le fer. La comparaison des transcriptomes d'une levure de voile et d'une levure de vin sur notre milieu synthétique a révélé des différences d'expression pour les floculines (FLO1, 5, 8, 11) ainsi que pour le transport des hexoses, mais a également suggéré que la levure de voile P3-D5 était en situation de carence en zinc et en inositol par rapport à la levure de vin, tandis que la levure de vin K1 exprimait certains gènes suggérant des défauts mitochondriaux. L'impact de la variation allélique de plusieurs gènes a été évalué dans le phénotype de voile: le transporteur de zinc à haute affinité Zrt1 ainsi que la pyruvate décarboxylase majeure Pdc1. / Wine fermentation and flor ageing are performed by two groups of the yeast Saccharomyces cerevisiae, with very different lifestyles. In this thesis we have studied the genome of flor yeast in comparison to wine yeast in order to unravel their specificities. We have first selected 16 strains (8 wine and 8 flor) from France, Hungary, Italy and Spain in order to sequence their genome sequence on an Illumina HiSeq2000 platform. Three flor strains and two wine strains were haploidized in order to obtain a set of haploid flor strains for the molecular evaluation of different targets. We developed as well a synthetic media mimicking wine for that purpose. From the genome sequence we have drawn a phylogeny that showed that flor yeasts represent a specific lineage of yeast, different from the wine strains lineage, and identified divergent regions. These regions contain genes involved in key functions and several associated with velum growth. Remarkably, many genes involved in FLO11 regulation such as MAP kinase, or Ras/PKA pathways were mutated among flor strains and many variations were encountered in genes involved in metal homeostasis such as zinc and divalent metal transporters. A transcriptome analysis comparing one flor and one wine yeast on our wine synthetic media revealed expression differences associated to floculins and hexose transport, but also suggested that flor yeast P3-D5 face a zinc and inositol deficiency, whereas wine yeast K1 presented mitochondrial defects. The impact of allelic variation of several genes coding for the high affinity zinc transporter (ZRT1), and the major pyruvate decarboxylase (PDC1) has been evaluated in order to assess their role in the flor phenotype.

Rhodopsin, a visual pigment protein found in retinal photoreceptors, mediates vision at low-light levels. Recent studies focusing primarily in human and mouse have challenged the assumption of neutral evolution of synonymous substitutions in mammals. Using recently developed likelihood-based codon models accounting for mutational bias and selection, we find significant evidence for selective constraint on synonymous substitutions in mammalian rhodopsins, and a preference for cytosine at 3rd codon positions. A second project investigated adaptive evolution in rhodopsin, in view of theories of nocturnality in early mammals. We detected a significant acceleration of non-synonymous substitution rates at the origins of therian mammals, and a tendency of synonymous substitutions towards C-ending codons prior to that. These findings suggest an evolutionary scenario in which synonymous substitutions that increase mRNA stability and/or translation efficiency may have preceded adaptive non-synonymous evolution in early mammalian rhodopsins. These findings have important implications for theories of early mammalian nocturnality.

Ce travail a contribué à la compréhension des bases moléculaires de l'immunité de l'huître creuse par la caractérisation la diversité de trois effecteurs antimicrobiens de C. gigas et par l'appréhension du rôle de cette diversité dans les mécanismes de défense. Des analyses phylogénétiques de deux peptides antimicrobiens (AMPs), Cg-Défensines (Cg-Defs) et Cg-Proline rich peptide (Cg-Prp), et d'une protéine de type Bactericidal Permeability Increasing protein, Cg-BPI, nous a permis montrer la grande diversité pour les 2 AMPs, qui est générée par plusieurs mécanismes génétiques et par des pressions de sélection directionnelles, suggèrant une diversité fonctionnelle des variants. L'importance biologique de cette diversité a été étudiée pour trois variants de Cg-Defs. Une forte activité antimicrobienne a été mise en évidence contre les bactéries à Gram positive, mais celle-ci diffère selon les variants. De plus, nous avons démontré que le mécanisme d'action des Cg-Defs contre S. aureus repose sur l'inhibition de la biosynthèse du peptidoglycane par le piegeage de son précurseur, le lipide II. Finalement, l'expression des transcrits et la localisation de ces effecteurs en réponse à une infection par un Vibrio pathogène ont montré un réseau complexe des profils d'expression des différents antimicrobiens, au niveau des populations hémocytaires et des tissus d'huître, suggérant une interaction entre les antimicrobiens du fait de leur colocalization. La combinaison entre les familles ou entre les variants d'une même famille produit de fortes activités synergiques qui élargissent les spectres d'activité. Ainsi, la diversité produit par la coévolution entre hôte et pathogènes pourrait améliorer l'activité des AMPs d'huître, lui conférant une plus grande protection contre les pathogènes de son environnement. / This work contributed to the knowledge of the molecular bases of oyster immunity by the characterization of the diversity of three antimicrobials of C. gigas and the understanding of the role played by their diversity in the oyster antimicrobial response. Phylogenetic analyses of two antimicrobial peptides (AMPs), Cg-Defensins (Cg-Defs) and Cg-Proline rich peptide (Cg-Prp), and one Bactericidal Permeability Increasing protein, Cg-BPI, led us to the identification of a high diversity for both AMPs. Further analyses showed that this diversity is generated by gene duplication, allelic recombination and directional selection pressures, suggesting their functional diversification. The biological meaning of AMP diversity was investigated for the three major variants of Cg-Defs, which revealed a strong but variable potency against Gram-positive bacteria. We evidenced that oyster defensins kill S. aureus through binding to the cell wall precursor lipid II, resulting in the inhibition of peptidoglycan biosynthesis. Finally, transcript expression and localization of oyster antimicrobials after a pathogenic infection evidenced a complex network in their expression profiles in hemocyte populations and oyster tissues, suggesting a potential interplay between antimicrobials as a result of their colocalization. Indeed, the combination of oyster antimicrobials produced strong synergistic activities that enlarged their antimicrobial spectra. Thus, the diversity of oyster antimicrobials may provide significant means in acquiring functional divergence, probably concerned in the evolutionary arms race between hosts and their pathogens.From our data, it would provide oysters with a higher protection against the potential pathogens from their environment.

Many previous studies in evolutionary genetics have been based on few model organisms that can be reared at ease in the laboratory. In contrast, genetic studies of non-model, natural populations are desirable as they provide a wider range of adaptive phenotypes throughout evolutionary timescales and allow a more realistic understanding of how natural selection drives adaptive evolution. This thesis represents an example of how modern genomic tools can be effectively used to study adaptation in natural populations. Atlantic herring is one of the world’s most numerous fish having multiple populations with phenotypic differences adapted to strikingly different environments. Our study demonstrated insignificant level of genetic drift in herring that resulted in minute genetic differences in the majority of the genome among these populations. In contrast, a small percentage of the loci showed striking genetic differentiation that were potentially under natural selection. We identified loci associated with adaptation to the Baltic Sea and with seasonal reproduction (spring- and autumn-spawning) and demonstrated that ecological adaptation in Atlantic herring is highly polygenic but controlled by a finite number of loci. The study of Darwin’s finches constitutes a breakthrough in characterizing their evolution. We identified two loci, ALX1 and HMGA2, which most likely are the two most prominent loci that contributed to beak diversification and thereby to expanded food utilization. These loci have played a key role in adaptive evolution of Darwin’s finches. Our study also demonstrated that interspecies gene flow played a significant role in the radiation of Darwin’s finches and some species have a mixed ancestry. This thesis also explored the genetic basis for the remarkable phenotypic differences between three male morphs in the ruff. Identification of two different versions of a 4.5 MB inversion in Satellites and Faeders that occurred about 4 million years ago revealed clues about the genetic foundation of male mating strategies in ruff. We highlighted two genes in the inverted region; HSD17B2 that affects metabolism of testosterone and MC1R that has a key role in regulating pigmentation, as the major loci associated with this adaptation.