Arcella Ehrenberg 1832 is one of the most numerous testacean genera. Arcellinids are an aerobic lineage of testate amoeba that live in a wide variety of environments. Probably their ability to survive in such divergent conditions is related to some de- gree of metabolic flexibility. Anaerobic organisms have gained and lost a number of genes related to energetic metabolism. These processes modify classic mitochondria until loss of function and transformation in mitochondrial related organelles (mitosomes and hydrogenosomes). Here I propose that Arcella intermedia adaptation to microarophilic environments is related to the acquisition of new genes. There are two main modes of acquisition of new genes. The traditional view, where duplication is followed by mutations and neo-functionality of the duplicate. Or genes can be acquired from other species (lateral gene transfers). The second process has a major importance in prokaryotic evolution and is probably under considered in eukaryotic evolution. I also propose in this work that genes related to anaerobic metabolism in Arcella are acquired by lateral gene transfer. However, analysis of genomic and transcriptomic data are absent for A.intermedia. Characterizing genome-scale data from eukaryotes is essential for gene discovery and for inferring transitions over the tree of life. The transcriptome dataset from this work provides the first effort of characterization of expressed sequences in A.intermedia. We used single cell from different moments of growth and whole culture RNA extraction in order to increase the diversity of metabolic moments of the cells. Mapped sequences allowed us to identify functional pathways in A.intermedia cells. In general, it seems that metabolic processes are showing up more, followed by signaling and responses to stimuli. We describe functioning of carbohydrate and energy metabolism including even an anaerobic pathway to produce energy. We found ACS-ADP and PFO genes in A.intermedia. We describe amino acid metabolism, with at least 12 amino acids metabolizing pathways described and catabolism mainly related to TCA cycle intermediates. Calcium, Ras GTPases, PI3K-AK and AMPK-mTOR are the main signaling pathways represented in transcriptomes. We described important pathways for amoeba: endocytosis and phagocytosis and it seems to be similar with the ones already described for other amoeba with a dependence on F-actin and small GTPases of Rho subfamily. We couldn\'t find lots of information about programmed cell death in A.intermedia, however cell growth are similar to pathways described for dinoflagellates. We expect that upcoming genomes will finish the description of functioning of those organisms, but we believe our work already is a good starting point. In order to gain a clearer picture of the presence of anaerobic metabolism genes in Amoebozoa, we conducted BLAST searches in Amoebozoa and Arcellinida data bases for the presence/absence of ACS-ADP, PFO and [FeFe]-H2ase. Other Arcellinida species also presented these genes, Difflugia sp., Difflugia compressa and Cyclopyxis lobostoma. Besides these, the already known Mastigamoeba balamuthi, Entamoeba histolytica and Acanthamoeba castelanii. Amoebozoa sequences don\'t form a monophyletic group in any of the three genes. However, Arcellinida sequences always grouped together. As such distinct amoeba groups have those anaerobic metabolism genes, however, most of the Amoebozoa do not. It is more likely to think of lateral transfers occurring independently among these amoeba groups, generating the possibility of occupying a new niche. The main objective of this work was to start generating tools to understand the ability of some testate amoeba to resist environmental harsh conditions. We found lots of interesting questions but the one we focused on this dissertation was (1) the evolution of anaerobic related genes in testate amoeba lineages. The assembled and annotated sequence data will be available as reference sequences, making the work with this group easier. The results can also potentially be applied as biomonitoring markers for the management of water resources. This work will improve the general knowledge on the evolution and function of freshwater organisms. We expect also to make a contribution on the understanding of the impact of lateral gene transfers in Arcellinida diversity / Arcella Ehrenberg 1832 é um dos gêneros de tecamebas mais numerosos, perten- cente aos Arcellinida. Estas são uma linhagem aeróbia de amebas tecadas que vivem em uma grande variedade de ambientes. Provavelmente, sua capacidade de sobreviver em condições tão divergentes está relacionada a algum grau de flexibilidade metabólica. Os organismos anaeróbicos ganharam e perderam vários genes relacionados ao metabolismo energético. Este processo modifica mitocôndrias clássicas até a perda da função e transformação em organelas relacionadas (mitossomos e hidrogenossomos). Aqui proponho que a adaptação de Arcella intermedia a ambientes microaerófilos está relacionada à aquisição de novos genes. Existem dois modos principais de aquisição de genes. Na visão tradicional, a duplicação gênica é responsável por gerar diversidade, seguida por mutações e neofuncionalidade da duplicata. Alternativamente, os genes podem ser adquiridos de outras espécies (transferências laterais de genes). O segundo processo tem uma grande importância evolutiva e é ainda pouco considerado na evolução eucariótica. Por isso, também proponho neste trabalho que genes relacionados ao metabolismo anaeróbico em Arcella sejam adquiridos por transferência lateral de genes. Entretanto, a análise de dados genômicos e transcriptômicos é inexistente para A.intermedia. A caracterização de dados em escala genômica de eucariotos é essencial para a descoberta de genes e para a inferência transições sobre a árvore da vida. O conjunto de dados de transcriptoma deste trabalho fornece um primeiro esforço de caracterização de sequências expressas em A. intermedia. Utilizamos extrações de célula-única em diferentes momentos de crescimento e extração de RNA de cultura inteira, a fim de aumentar a diversidade de momentos metabólicos das células. Sequências mapeadas permitiram identificar vias funcionais em células de A. intermedia. Em geral, parece que genes relacionados a processos metabo?licos são os que aparecem mais frequentemente, seguidos dos de sinalização e respostas a estímulos. Nós descrevemos a função do metabolismo de carboidratos e energia, incluindo uma via anaeróbica. Encontramos em A.intermedia os genes ACS-ADP e PFO. Descrevemos o metabolismo de aminoácidos, com pelo menos 12 vias metabólicas de aminoácidos descritas e catabolismo relacionado a intermediários do ciclo de TCA. Cálcio, Ras GTPases, PI3K-AK e AMPK-mTOR são as principais vias de sinalização representadas nos transcriptomas. Descrevemos importantes vias para amebas, que são endocitose e fagocitose. Parecem ser vias semelhantes àquelas já descritas para outras amebas, com dependência de F-actina e pequenas GTPases da subfamília Rho. Não conseguimos encontrar muitas informações sobre a morte celular programada em A. intermedia, mas o crescimento celular é semelhante com as vias descritas para os dinoflagelados. Esperamos que os próximos genomas terminem a descrição da função desses organismos, mas acreditamos que nosso trabalho já é um bom ponto de partida. A fim de obter uma visão mais clara da presença de genes de metabolismo anaeróbico em Amoebozoa, realizamos buscas no BLAST em bancos de dados de Amoebozoa e Arcellinida, para a presença/ausência de ACS-ADP, PFO e [FeFe] -H2ase. Outras espécies de Arcellinida também apresentaram estes genes, Difflugia sp, Difflugia compressa e Cyclopyxis lobostoma. Além destes, os já conhecidos Mastigamoeba balamuthi, Entamoeba histolytica e Acanthamoeba castelanii. Sequências de amebozoários não formam um grupo monofilético em nenhum dos três genes. No entanto, as sequencias de Arcellinida sempre se agrupam. Como são grupos de Amoebozoa de tal maneira distintos que possuem estes genes de metabolismo anaeróbico, e sendo que a maioria não possui, é mais provável que sejam transferências laterais independentes entre esses grupos de ameba, gerando a possibilidade de ocupar um novo nicho. O objetivo principal deste trabalho foi gerar ferramentas para entender a capacidade de algumas amebas tecadas em resistir a condições adversas do meio ambiente. Encontramos muitas questões interessantes, mas a que teve nosso foco nesta dissertação foi (1) a evolução de genes relacionados ao metabolismo anaeró?bio em linhagens de amebas tecadas. Os dados da sequência reunidos e anotados estarão disponíveis como sequências de referência, facilitando o trabalho com esse grupo. Os resultados também podem ser aplicados aos marcadores de biomonitoramento para o gerenciamento dos recursos hídricos. Este trabalho irá melhorar o conhecimento geral sobre a evolução e função de organismos de água doce. Esperamos tambem contribuir para a compreensão do impacto das transferências laterais na diversidade de Arcellinida

Les génomes des eucaryotes et des procaryotes évoluent de temps en temps par un processus complexe, impliquant entre autres, des événements évolutifs tels que les spéciations, les duplications, les transferts horizontaux, et les pertes de gènes. Nous étudions ici les méthodes de réconciliation, une technique bien connue pour inférer de tels événements et retrouver leur localisation dans l'histoire d'espèces. En effet, ces méthodes construisent une correspondance entre l'histoire d'une famille de gènes (l'arbre de gènes) et l'histoire des espèces contenant ces gènes (l'arbre d'espèces) pour expliquer leurs discordances sur la base d'événements évolutifs qu'elles infèrent et positionnent sur l'arbre de gènes et l'arbre d'espèces. Les méthodes de réconciliation sont appliquées dans plusieurs domaines tels que l'étude de l'évolution du génome; l'inférence des relations d'orthologies en évolution moléculaire; l'étude de la coévolution entre hôtes et parasites en écologie, ou encore l'étude des zones de population en biogéographie. Les trois principales contributions de cette thèse sont les suivantes : premièrement, un outil nommé SEAS est proposé pour simuler l'évolution des familles de gènes dans une phylogénie d'espèces donnée. Cela permet d'obtenir des arbres de gènes synthétiques dont la réconciliation est connue et qui permettent donc d'évaluer la précision des méthodes de réconciliation. Deuxièmement, une méthode heuristique, appelée MowgliNNI, est proposée pour corriger les arbres de gènes partiellement erronés au regard des réconciliations. Cette méthode itérative réarrange les branches faiblement supportées pour rechercher une nouvelle topologie de l'arbre de gènes, dont le coût de réconciliation est moindre. Troisièmement, nous proposons une approche pour estimer la fiabilité des événements évolutifs prédits par les méthodes de réconciliation. Contrairement aux approches existantes qui ne considèrent qu'une des réconciliations optimales possible entre l'arbre de gènes et l'arbre d'espèces, notre approche prend en compte un ensemble de solutions optimales voire sous-optimales. En outre, nous introduisons le concept de réconciliations médianes symétriques et asymétriques qui servent d'éléments centraux pour représenter un ensemble de réconciliations. Nous présentons un algorithme pour calculer ces réconciliations médianes qui est en temps polynomial bien que l'ensemble de toutes les réconciliations optimales est potentiellement exponentiel. Des expériences ont été réalisées pour montrer l'exactitude, la signification et l'efficacité de nos méthodes proposées. / The genomes of eukaryotes and prokaryotes evolve over time through a complex process involving, among other things, evolutionary events such as speciations, duplications, horizontal transfers, and losses of genes. We study here reconciliation methods, a well-known technique for recovering such events as well as locating them along the species history. Indeed, reconciliation methods construct a mapping between a gene family history (a gene tree) and a species history (a species tree) to explain their incongruence thanks to the inferred evolutionary events located on both the gene and species trees. Reconciliation methods can be applied to various areas such as the study of genome evolution, the inference of orthology relationships in molecular evolution, the study of host-parasite coevolution in ecology, or the study of population areas in biogeography. The three main contributions of this thesis are as follows: First, we provide a tool, named SEAS, for simulating the evolution of gene families along a given species phylogeny. This provides synthetic gene trees along with their known reconciliations that are helpful to evaluate the accuracy of reconciliation methods. Second, we propose a heuristic method, called MowgliNNI, to correct partly erroneous gene trees based on reconciliation scores. This method iteratively rearranges the weakly supported parts of a gene tree as long as it improves the reconciliation score. Third, we propose effective solutions for estimating the reliability of the predicted evolutionary events. Unlike the currently existing approaches considering only the optimal solutions for reconciling a pair of species-gene trees, our approach additionally takes into account the nearly optimal solutions. Furthermore, we introduce the concept of symmetric and asymmetric median reconciliations, which serve as central elements to represent a set of reconciliations. We present a polynomial time algorithm computing such median reconciliations from the potentially exponential set of all optimal reconciliations for a given pair of species-gene trees. Experiments have been carried on to show the correctness, meaningfulness and effectiveness of our proposed methods.

À différentes échelles de temps, le but de ma thèse a été de comprendre l'évolution des virus entomopathogènes à travers l’étude de la diversification et de l’adaptation génomique de grands virus à ADN d’insectes. Dans un premier temps, j’ai pu estimer les âges de diversifications des baculovirus et des nudivirus, et proposer un scénario de coévolution à long terme entre ces virus et leurs hôtes insectes. Puis, me plaçant sur une échelle de temps moindre, j’ai montré que les hôtes insectes sont le facteur principal de la diversification des baculovirus, et de façon surprenante, j’ai également observé que l'environnement biotique de ces virus, c’est-à-dire les plantes hôtes des insectes, joue un rôle central dans leur évolution. Dans un second temps, des mutations ponctuelles ont pu être reliées à l’adaptation locale de populations différentiées du baculovirus SeMNPV. Enfin, l’étude de l'adaptation génomique convergente entre les entomopoxvirus et les baculovirus a mis en évidence que les transferts horizontaux de gènes sont une source importante de variabilité pour les grands virus à ADN, pour l'adaptation aux mêmes niches écologiques. Les gènes et les mécanismes identifiés dans ce travail de thèse apportent des éléments nouveaux pour comprendre comment les génomes sont façonnés par l’écologie. / At different timescales, the purpose of my PhD was to understand insect virus evolution through the study of the genomic diversification and adaptation of insect large DNA viruses. Firstly, I was able to estimate the ages of baculovirus and nudivirus diversifications, and to propose a long-term coevolutionary scenario between these viruses and their insect hosts. Then, on a narrower timescale, I showed that insect hosts are the major factor in baculovirus diversification, and surprisingly, I also observed that the virus biotic environment, i.e. insect host plants, plays a central role in their evolution. Secondly, punctual mutations have been linked to the local adaptation of differentiated populations of the baculovirus SeMNPV. Finally, the study of convergent genomic adaptation between entomopoxviruses and baculoviruses highlighted that horizontal gene transfers are an important source of variability for large DNA viruses, for the adaption to the same ecological niches. Genes and mechanisms identified in this PhD work provide new insights to understand how genomes are shaped by ecology.