Dans le côlon humain, le genre Faecalibacterium est le membre principal du groupe Clostridium leptum et comprend le deuxième genre représentatif le plus commun dans les échantillons fécaux, après Clostridium coccoides. Il a été reconnu comme une bactérie importante favorisant la santé intestinale et est aujourd'hui considéré comme un probiotique de prochaine génération. Jusqu'à récemment, on croyait qu'il n'y avait qu'une seule espèce dans ce genre, mais depuis 2012, certaines études ont commencé à suggérer l'existence de deux phylogroupes dans le genre. Cette nouvelle proposition de reclassification dans ce genre augmente l'importance de nouvelles études, toutes souches confondues, pour mieux comprendre la diversité, les interactions avec l'hôte et les aspects sécuritaires dans son utilisation comme probiotique. Brièvement, dans ce travail, nous introduisons les analyses de génomique comparative au genre Faecalibacterium en effectuant une étude phylogénétique profonde et en évaluant les aspects de sécurité pour son utilisation comme probiotique. Les analyses phylogénétiques comprenaient non seulement l'utilisation classique du gène de l'ARNr 16S, mais aussi l'utilisation de 17 génomes et techniques complets comme le typage de séquence multi-locus (wgMLST), l'identité nucléotidique moyenne (ANI), le synténie génique et le pangénome. C'est aussi le premier travail à combiner une analyse du développement du pangénome avec l'analyse ANI afin de corroborer l'attribution de souches à de nouvelles espèces. Les analyses phylogénétiques ont confirmé l'existence de plus d'une espèce dans le genre Faecalibacterium. De plus, l'évaluation de la sécurité impliquait (1) la prédiction des régions acquises horizontalement (îlots de résistance aux antibiotiques, îlots métaboliques et régions phagiques), (2) la prédiction des voies métaboliques, (3) la recherche de gènes liés à la résistance aux antibiotiques et des bactériocines. Ces analyses ont identifié des îlots génomiques dans tous les génomes, mais aucun d'entre eux n'est exclusif à une souche ou à une génospécie. En outre, ont été identifiés 8 gènes liés aux mécanismes de résistance aux antibiotiques répartis entre les génomes. 126 voies métaboliques ont été prédites et parmi certaines ont été mises en évidence: la dégradation du bisphénol A, le métabolisme du butanoate et la biosynthèse de la streptomycine. En outre, nous avons étudié le contexte génomique d'une protéine (molécule anti-inflammatoire microbienne - MAM) décrite pour la première fois par notre groupe. Cette recherche montre que la MAM apparaît proche des gènes liés au processus de sporulation et, dans certaines souches, proche d'un transporteur ABC. / Within the human colon, the genus Faecalibacterium is the main member of the Clostridium leptum cluster and comprises the second-most common representative genus in fecal samples, after Clostridium coccoides. It has been recognized as an important bacterium promoting the intestinal health and today is considered as a potential next generation probiotic. Until recently, it was believed that there was only one species in this genus, but since 2012, some studies have begun to suggest the existence of two phylogroups into the genus. This new proposition of reclassification into this genus increases the importance of new studies, with all strains, to better understand the diversity, the interactions with the host and the safety aspects in its use as probiotic. Briefly, in this work we introduce the comparative genomics analyzes to the genus Faecalibacterium performing a deep phylogenetic study and evaluating the safety aspects for its use as a probiotic. The phylogenetic analyzes included not only the classical use of 16S rRNA gene, but also the utilization of 17 complete genomes and techniques like whole genome Multi-Locus Sequence Typing (wgMLST), Average Nucleotide Identity (ANI), gene synteny, and pangenome. Also, this is the first work to combine an analysis of pangenome development with ANI analysis in order to corroborate the assignment of strains to new species. The phylogenetic analyzes confirmed the existence of more than one species into the genus Faecalibacterium. Moreover, the safety assessment involved the (1) prediction of horizontally acquired regions (Antibiotic resistance islands, Metabolic islands and phage regions), (2) prediction of metabolic pathways, (3) search of genes related to antibiotic resistance and (4) search of bacteriocins. These analyzes identified genomic islands in all genomes, but none of than are exclusive to one strain or genospecies. Also, were identified 8 genes related to antibiotic resistance mechanisms distributed among the genomes. 126 metabolic pathways were predicted and among than some were highlighted: Bisphenol A degradation, Butanoate metabolism and Streptomycin biosynthesis. In addition, we studied the genomic context of one protein (Microbial Anti-inflammatory Molecule - MAM) first described by our group. This investigation shows that MAM appears close to genes related to sporulation process and, in some strains, close to an ABC-transporter.

Les bactéries magnétotactiques (MTB) appartiennent à différents phyla procaryotes et ont la capacité de synthétiser des magnetosomes (cristaux de magnétite entourés par une membrane). Durant la thèse, nous avons procédé à l’analyse génomique de 2 bactéries magnétotactiques: Magnetospira sp. QH-2 et Magnetococcus MO-1. La synthénie et la correlation génique des gènes impliqués dans la formation des magnétosomes montrent que l'insertion de cet îlot chez QH-2 a eu lieu après la divergence entre les Magnetospirillum sp et Magnetospira sp. L'analyse comparative a mis en évidence trois groupes distincts de MTB : Groupe I, comprenant les souches Magnetospirillum spp. et Magnetospira; Groupe II avec MO-1 et M. marinus MC-1 et le Groupe III, avec D. magneticus RS-1. QH-2 montre aussi une évolution adaptative distincte par comparaison aux souches marines ou d'eau douce. L'analyse comparative des réseaux métaboliques révèle une très grande similitude intra-Groupe et une importante variabilité inter-Groupe. Cela est probablement dû aux enzymes impliqués dans les voies métaboliques anoxiques, qui représentent ainsi la contrainte à une distribution taxonomique large des MTB. Ces enzymes permettent ainsi de prédire le phénotype métabolique nécessaire à la production des magnétosomes. Différentes analyses (des protéines ribosomales au genome entier) indiquent une composition taxonomique chimérique des gènes de MO-1 et MC-1, et peut représenter une nouvelle lignée taxonomique chez les Protéobactéries. J’ai aussi participé à l'analyse des génomes de deux bactéries piezophiles, d’une bactérie photosynthétique pourpre et l’analyse phylogénomique des tyrosine-Kinases bactériennes. / Magnetotactic bacteria (MTB) are a diverse group of aquatic prokaryotes, which synthesize membrane-Enclosed magnetic crystals known as magnetosomes. In this thesis, the genome sequences of two marine MTB strains, Magnetospira sp. QH-2 and magneto-Ovoid strain MO-1 were analyzed. The magnetosome gene cluster synteny and mam gene correlation indicate that the insertion of the magnetosome island into QH-2 chromosome occurred after divergence between freshwater and marine magnetospirilla. Comparative genomic analysis revealed three distinct groups of sequenced MTB strains: Group I with Magnetospirillum spp. strains and Magnetospira strain, Group II with MO-1 strain and M. marinus MC-1, and Group III including Desulfovibrio magneticus RS-1. In addition, it shows an adaptive evolution of two marine MTB strains to marine sediments in comparison with closely related freshwater species. Moreover, comparative metabolic network analysis reveals high level of intra-Group similarity and inter-Group variety in MTB. With anoxic network enzymes, potential “MTB” strains are predicted, and are consistent with recently isolated MTB strains. It suggested that the anoxic metabolic network might be one restricted constraint for MTB distribution in bacterial lineages. Interestingly, analyses from ribosomal proteins to the whole MTB genome strongly support a taxonomic chimeric nature of MO-1 and MC-1 genes, and may represent a novel Proteobacteria lineage. Additionally, I also participate to genome analyses of piezophilic Desulfovibrio and Phaeospirillum molischianum strains as well as genome-Wide analysis of bacterial tyrosine kinases.

Du fait de la complexité des processus de spéciation, l'étude des relations évolutives entre espèces nécessite une approche intégrative. Nous avons combiné croisements expérimentaux et études moléculaires (séquençage mitochondrial et RAD-seq) pour étudier les relations évolutives entre espèces indigènes et introduites du genre Ciona, en Europe. Nous avons examiné deux mécanismes post-zygotiques restant à explorer pour expliquer l'absence d'introgression de C. robusta et C. intestinalis dans leur zone de sympatrie en Manche : 1) la contre-sélection des hybrides par l'environnement (température et salinité) et 2) des incompatibilités de type Dobzhansky-Muller (DMIs). L'absence de dépression hybride (étudiée chez 725 hybrides F1) nous a conduit à rejeter le premier mécanisme. Le second a été exploré grâce à l'étude de sept familles double-hybrides ou issues de rétrocroisements, analysées par RAD-seq. Une stérilité sur la fonction mâle des hybrides F1 et d'importantes distorsions de ségrégation sont en faveur de la présence de DMIs. Nous avons étendu notre étude à d'autres espèces du genre Ciona. Les principaux résultats, notamment soutenus par une approche phylogénomique (7 taxons - 89 individus), sont : 1) la remise en cause du statut d'espèce de C. roulei par rapport à C. intestinalis (probablement deux lignées allopatriques), 2) les premières données montrant la forte divergence évolutive de C. edwardsi avec les autres Ciona spp. et 3) la présence de variabilité génétique et/ou d'introgression chez C. intestinalis type C et type D. Ces résultats ouvrent d'intéressantes perspectives de recherches dont des études populationnelles des espèces présentes en Méditerranée. / Speciation is a complex process. Evolutionary relationships between close species thus required an integrative approach. We combined experimental crosses and molecular data (mitochondrial and RAD-tag sequencing) to investigate evolutionary relationships between native and non-indigenous species of the genus Ciona nowadays found in Europe. We studied two post-zygotic mechanisms, still to be examined, to explain the lack of introgression between C. robusta and C. intestinalis in their sympatric range –i.e. the English Channel: i) selection against hybrids, by the environment (here temperature and salinity) and ii) Dobzhansky-Muller incompatibilities (DMIs). The absence of outbreeding depression (over 725 F1-hybrids) makes unlikely the first mechanism. The second has been investigated with seven families of F2-hybrids and backcrosses, all studied with RAD-tag sequences. Male sterility on F1-hybrids and many segregation distortions are in favor of presence of DMIs. We then expanded our study to other Ciona species. The main outcomes, supported by a phylogenomic approach (7 taxa - 89 individuals) are: 1) a needed reappraisal of the species status of C. roulei and C. intestinalis, which are most likely two allopatric lineages of a same species (as defined by biological and phylogenetic species concepts), 2) the first data showing that C. edwardsi is strongly evolutionary divergent from the other Ciona species and 3) the presence of unexpected genetic variability and/or introgression in C. intestinalis type C and D. All together these results open new research perspectives, in particular based on population studies of the species nowadays found in the Mediterranean Sea.

Submitted by Ana Damasceno (ana.damasceno@unipampa.edu.br) on 2016-11-07T16:30:36Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Dissertação - Evelise Carvalho.pdf: 2321912 bytes, checksum: 3957e800afc8b54ee2d2bc427c9dffd6 (MD5) / Made available in DSpace on 2016-11-07T16:30:36Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Dissertação - Evelise Carvalho.pdf: 2321912 bytes, checksum: 3957e800afc8b54ee2d2bc427c9dffd6 (MD5) Previous issue date: 2015-05-19 / Algas verdes da classe Trebouxiphyceae estão entre os organismos presentes no continente Antártico, onde a espécie mais relatada é a macroalga verde Prasiola crispa (Lightfoot) Kützing. Considerada um organismo extremófilo, pois se desenvolve com muito sucesso no habitat extremo da Antártica, ainda são raros na literatura dados moleculares sobre esta espécie, o que impede uma avaliação sobre sua taxonomia e posição filogenética. Com o advento das tecnologias de sequenciamento de nova geração, os genomas de organelas tornaram-se uma grande ferramenta para estudos de filogenia, pois fornecem inúmeros dados filogenéticos, sequências de proteínas e nucleotídeos e também informações sobre conteúdo gênico e arquitetura. Neste trabalho, foi determinada a sequência dos genomas do cloroplasto (cpDNA) e mitocondrial (mtDNA) de P. crispa, com o intuito de inferir as relações evolutivas deste organismos com outras espécies de plantas verdes, bem como uma análise estrutural. Os genomas plastidial e mitocondrial foram sequenciados por Macrogen Service (SolexaIllumina Hi-Seq 2500). A montagem, anotação, alinhamento, construção da filogenia e análise sintênica foram realizados in silico com softwares específicos. O cpDNA e mtDNA P. crispa apresentam 196.502 pb e 89.819 pb, respectivamente. Estes genomas acessórios apresentam 21 genes putativos relacionados com a fotossíntese e 18 genes relacionados com o metabolismo oxidativo. A análise filogenômica baseada no cpDNA demonstrou que P. crispa agrupou com alga trebouxiophyceae Prasiolopsis sp. formando o clado Prasiola juntamente com Stichococcus bacilaris. Nossos resultados para filogenômica embasada no mtDNA revelam que P. crispa agrupa com as outras espécies da classe Trebouxiphyceae. A análise de sintenia do cpDNA e mtDNA de P. crispa com a espécies de plantas verdes relacionadas evolutivamente demonstram que estes organismos apresentam poucos blocos gênicos sintênicos. Este trabalho pioneiro com a alga P. crispa, demonstra que os genomas acessórios suprem uma gama de dados moleculares que podem ser utilizados para estudos filogenômicos. Além disto, as informações geradas a partir do sequenciamento do cpDNA e mtDNA de P. crispa fornecem um aporte para estudos futuros mais aprofundados / Green algae from Trebouxiophyceae class are among the organisms in the Antarctic continent, where the most reported species is the green macroalga Prasiola crispa (Lightfoot) Kützing. This algae is considered an extremophile organism because develops successfully in the harsh Antarctic habitat, however studies reporting molecular data of this species are still lacking in the literature, which prevents an assessment of their correct taxonomy and phylogenetic position. With the advent of next generation sequencing technologies, it because easier to obtain molecular information as for example from organelle genomes making them a great tool for taxonomic studies because they provide a great number of, phylogenetic data, nucleotides, protein sequences, gene content and architecture information. In this study, we determined the sequence of the chloroplast (cpDNA) and mitochondrial (mtDNA) genome of P. crispa in order to infer the evolutionary relationships of the organisms with other species of green plants, as well as a structural analysis. Plastid and mitochondrial genome was sequenced by Macrogen Service (Illumina Solexa Hi-Seq 2500). The genome assembly, annotation, sequences alignment, phylogeny construction, and structural analyses were performed in silico with specific softwares. Plastid and Mitochondrial genomes have a total length of 196,502 bp and 89,819 bp, respectively. These genomes presented 21 putative photosynthesis related genes and 18 oxidative metabolism related genes, respectively. Phylogenetic analysis based on the cpDNA demonstrated that P. crispa grouped with Trebouxiophyceae algae Prasiolopsis sp. forming the Prasiola clade along with Stichococcus bacilaris. Our results for phylogenetic analysis grounded in mtDNA show that P. crispa groups with other species of Trebouxiphyceaen alga. Synteny analysis of P. crispa cpDNA and mtDNA with evolutionarily related species of green plants shows that these organisms have few syntenic gene blocks. This pioneering work with P. crispa provided the accessories genomes which suppled a range of molecular data that can be employed to taxonomic studies. In addition, the information generated from the sequencing of cpDNA and mtDNA of P. crispa provide a contribution for further studies.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal

Made available in DSpace on 2014-08-20T13:42:05Z (GMT). No. of bitstreams: 1 Tese_Elen_Silveira_Nalerio.pdf: 599740 bytes, checksum: f430564f38cd6d98d1788d137e38ed1e (MD5) Previous issue date: 2009-11-17 / Listeria monocytogenes is the causative agent of listeriosis which may cause a range of diseases from gastroenteritis, meningitis and death. In fact, disease outcome can be related to strain serotype/lineage thus molecular analyses has demonstrated that L. monocytogenes is a highly diverse species which can be grouped into three lineages. Whole-genome microarray can be employed to study phylogenetic relationships among Listeria strains either species or serotype level, in addition to demonstrate differences on their virulence potential and/or environmental adaptation. The aim of this study was the whole genome comparison of L. monocytogenes strains from different origins. Ninety-nine L. monocytogenes strains from different geographical origins (Brazil, Denmark, Austria, Ireland, USA and unknown), including clinical strains (humans and animals), food and food industries strains were analysed. DNA from all strains were competitively hybridized on to a L. monocytogenes DNA microarray based on the whole-genome sequence L. monocytogenes EGD-e. DNA labeling and hybridization protocol were followed according to Dorrell et al., (2001). Data acquisition, processing and comparative phylogenomics were performed as previously described by Stabler et al. (2006). Comparative phylogenomics clustered the L. monocytogenes strains into two central clades which is representative of the two main lineages of this species. In addition each of these clades were divided into two further subclades. Clade formation was independent of the geographical origin of strains with the exception of the clade containing persistent strains (strains that persist in food-processing environment), where none of the Brazilian strains were present. It was found 18 specific genes for lineage I strains (1/2a and 1/2c serotypes). These genes are related to carbohydrate metabolism, two component regulatory system, ABC transporter complex and bvrB and bvrC genes. Significantly all persistent strains clustered together in the same lineage I clade. We achieved a set of unique genes belonging exclusively to L. monocytogenes persistent strains pointing to be responsible for its adaptation profile. The genes are involved in stress resistance and are related to carbohydrate transport and metabolism, environmental information processing, signal transduction mechanisms, cell surface protein, amino acid transport and metabolism, nucleotide transport and metabolism, translation, cell wall biogenesis, replication, recombination and repair, transport of small molecules similar to ABC transporter, metabolism of lipids and unknown function. Interestingly from 14 virulence listed genes most of them were present in all studied L. monocytogenes strains with exception of inlE and inlG genes. These findings indicate that genetic variability of L. monocytogenes strains point to niche adaptation instead virulence differentiation despite of different origins. Persistent strains clustered suggesting genetic origin to survival in this environment. / Listeria monocytogenes é o agente causador da listeriose, uma infecção severa que pode cursar com sintomas que variam desde gastroenterites, meningites e até mesmo a morte. De fato, o desenvolvimento da doença pode ser relacionado a determinados sorotipos/linhagens das cepas de Listeria. Análises moleculares dos diferentes sorotipos/linhagens de L. monocytogenes, demonstraram que esta espécie é amplamente diversa, a qual pode ser agrupada em três linhagens. O estudo completo de genomas, baseado na técnica de microarray, pode ser empregado para estudar a relação filogenética entre cepas de Listeria tanto em nível de espécie, quanto em nível de sorotipo. Não obstante, a técnica de microarray visa evidenciar as diferenças no potencial patogênico e/ou adaptativo das cepas. O objetivo deste estudo foi a comparação filogenética entre cepas de L. monocytogenes isoladas de diferentes fontes. Foram analisadas 99 cepas de L. monocytogenes de diferentes origens geográficas (Brasil, Dinamarca, Áustria, Irlanda, Estados Unidos da América e fontes desconhecidas), incluindo cepas clínicas (humanas e animais), de alimentos e de indústrias alimentícias. O DNA das cepas teste foi hibridizado em DNA microarrays de L. monocytogenes baseado em seqüências do genoma de L. monocytogenes EGD-e. Os protocolos para marcação e hibridização do DNA seguiram as recomendações de Dorrell et al., (2001). A aquisição de dados, o processamento e as comparações filogenômicas foram realizadas conforme previamente descrito por Stabler et al. (2006). Comparações filogenômicas agruparam as cepas de L. monocytogenes em dois clades centrais, os quais são representativos das duas principais linhagens desta espécie. Além disso, cada um destes clades foram subdivididos em mais dois sub-clades. A formação dos clades foi independente da origem geográfica das cepas, com exceção do clade contendo cepas persistentes (cepas que persistem no ambiente de processamento de alimentos), onde nenhuma cepa Brasileira esteve presente. Foram identificados 18 genes específicos para as cepas da linhagem I (sorotipos 1/2a e 1/2c). Esses genes são relacionados ao metabolismo de carboidratos, sistema regulatório two component, complexo de transporte ABC e aos genes bvrB e bvrC. A grande maioria das cepas persistentes se agrupou no mesmo clade pertencente à linhagem I. Foi obtido um conjunto de genes únicos pertencentes exclusivamente às cepas persistentes de L. monocytogenes, os quais sugerem serem os responsáveis pelo perfil adaptativo destas cepas. Os genes são envolvidos em resistência ao estresse e são relacionados ao transporte e metabolismo de carboidratos, processamento de informação ambiental, mecanismos de transdução de sinais, proteína de superfície celular, transporte e metabolismo de aminoácidos, transporte e metabolismo de nucleotídeos, tradução, biogênese de parede celular, replicação, recombinação e reparo, transporte de pequenas moléculas similar ao transportador ABC, metabolismo de lipídios e de função desconhecida. Dos 14 genes de virulência listados a maioria deles esteve presente em todas as cepas de L. monocytogenes estudadas, com exceção dos genes inlE e inlG. Estes dados sugerem que, apesar das distintas origens de isolamento, a variabilidade genética das cepas de L. monocytogenes é direcionada para adaptação ambiental, ao invés da diferenciação visando virulência.

Le cycle cellulaire chez les bactéries est un processus très étudié mais il apparait que les modèles actuels ne rendent pas compte de la complexité et surtout de la diversité des machineries et des mécanismes de régulation impliqués. En fait, notre connaissance du cycle cellulaire repose sur l'étude de quelques organismes modèles. Or les analyses comparatives ont montré que certains systèmes et mécanismes décrits sont peu conservés et donc difficilement transposables d'un taxon à l'autre. Des approches évolutives telles que la phylogénomique peuvent être utilisées pour l'étude fonctionnelle de tels systèmes biologiques à l'échelle des bactéries. Ces approches permettent notamment de déterminer les évènements évolutifs clés qui ont conduit à une telle diversité mais également d'identifier des liens fonctionnels potentiels entre protéines. De plus, le développement des méthodes de séquençage à très haut débit a conduit à une accumulation de données génomiques sans précèdent, notamment chez les procaryotes. Dans ce contexte, j'ai réalisé une analyse phylogénomique à très large échelle des protéines impliquées dans le cycle cellulaire et sa régulation chez les Firmicutes. Mon objectif était de rechercher des patrons de coévolution entre familles protéiques pouvant refléter des liens fonctionnels. L'application des méthodes développées dans le cadre cette thèse aux protéines impliquées dans le cycle cellulaire chez les Firmicutes a permis de reconstruire l'histoire évolutive de ce processus cellulaire fondamental à l'échelle de ce phylum bactérien majeur. En particulier, j'ai pu mettre en évidence l'existence de quelques points chauds correspondant par exemple à l émergence des Bacilli ou des Streptococcaceae. L'émergence de ces taxa s'est accompagnée de nombreuses acquisitions et/ou de pertes de gènes ainsi que de nombreux réarrangements dans l'organisation des clusters de gènes codant pour ces protéines, suggérant que des changements majeurs se sont produits au niveau du cycle cellulaire et de sa régulation. J'ai également pu mettre en évidence de possibles liens fonctionnels qui n'ont jamais été décrits jusqu'à présent entre des gènes impliqués dans différentes machineries du cycle cellulaire. L'application de ces approches à l'ensemble des protéomes de Firmicutes a également permis d'identifier des protéines présentant des patrons de coévolution communs avec les protéines impliquées dans la division cellulaire et sa régulation, suggérant de possibles liens fonctionnels qu'il serait nécessaire de tester expérimentalement / The bacterial cell cycle is a very well studied process but current models don't reflect the complexity and diversity of involved molecular machineries and associated regulation mechanisms. In fact, our knowledge of cell cycle is based on study of a few model organisms. Yet, comparative analyses showed that some described systems and mechanisms are not conserved and not transposable from a taxon to another. Evolutionary approach such as phylogenomic can be used for functional studies of such systems at the bacterial scale. Those approaches allow to determine the key evolutionary events that lead to a such diversity but also to identify potential functional links between proteins. Furthermore, the development of high throughput sequencing methods leads to a big amount of genomic data, particularly for prokaryotes. In this context, I realized a very large scale phylogenomic analysis of proteins involved in cell cycle and its regulation in Firmicutes. My goal was to search some coevolution patterns between protein families reflecting potentially functional links. The application of methods that I developed during my PhD to cell cycle proteins allowed to reconstruct the evolutionary history of this cell process in Firmicutes. Notably, I highlighted some hot-spots corresponding for example to the emergence of Bacilli or Streptococcaceae. The emergence of such taxa has been accompanied by many acquisitions/losses of cell cycle genes but also many genomic rearrangements in gene clusters suggesting that major changes have occurred at the level of the cell cycle and its regulation. I also highlighted some potential functional links between genes involved in different machineries of cell cycle that have never been described. The application of these approaches to the entire proteomes of Firmicutes allowed to identify proteins presenting same evolution patterns than cell cycle proteins suggesting potential functional links that have to be experimentally tested

<p>  </p> <p>Rapid climate change on a global scale is posing a considerable threat to forest biodiversity. Assessing physiological and genomic backgrounds of each tree is crucial for informing conservation and mitigation strategies to evaluate species or populations' vulnerability and adaptive capacity under climate change. The goal of my dissertation research was to use morpho-physiological and molecular approaches in combination with genomic background, as a backbone knowledge for enhancing the restoration and conservation of different hardwood tree species. The same approaches also led to a better understanding of mitigation strategies of tree species to evaluate their vulnerability and adaptability under climate change. To do so, the native <em>Juglans</em> species (<em>J. cinerea</em> and <em>J. nigra</em>), local species (Arizona walnut<em>; J. major, </em>California walnut; <em>J. hindsii</em>), exotic species (Persian walnut, <em>J. regia</em>) and its F1 interspecific hybrids were used as a case study to evaluate the level of cold hardiness in <em>Juglans</em>. Hybridization can integrate biotic and abiotic tolerance in plants and could be a potential forest restoration and conservation tool. Evidence from past studies in some F1 interspecific hybrids indicates that naturalized hybrids of Persian walnut with black walnut or butternut have higher level of tolerance to lower temperature than Persian walnut. The potential cold tolerance of native, local, exotic <em>Juglans</em> species and F1 interspecific hybrid using field, electrolyte leakage, qPCR, and genome analysis was investigated, and results presented in chapter 2. Differences in cold hardiness were observed in tested <em>Juglans</em> species, <em>J. regia</em> as an exotic species and <em>J. major</em> from Arizona maladapted in West Lafayette, Indiana. No sign of cold damage was observed in F1 interspecific hybrids or native species. Using morpho-physiological, molecular, and genome data, we confirmed that molecular and morpho-physiological data were highly correlated and thus can be used to characterize cold hardy trait in <em>Juglans</em> species. </p> <p>Although the native <em>Juglans</em> species are cold tolerant, with current trend of climate change and rapid tree migration to the northern range, it is not easy to predict how <em>Juglans</em> species may adapt to new environments and response to other biotic and abiotic stresses in future. A reference-genome assembly for nuclear and chloroplast genomes and cold hardy genes is presented in chapter 3. We used re-sequence genomes of 170 individuals collected from 20 <em>Juglans</em> species and <em>Carya</em> (as an outgroup) of the Juglandaceae family distributed in temperate-tropical forests of America and Asia. We integrate genome and temperature variables to identify a set of associated single-nucleotide polymorphisms (SNP), structural variations, and the geographical distribution of the variants in the genes related to local adaptation of <em>Juglans</em> across latitudes. Phylogeny analyses revealed that <em>Juglans</em> species were sorted based on their origin using the nuclear genome, cold-hardy genes, and organellar genome. <em>Juglans regia</em>, a native species of Asia and Europe, was distinct from other species and exhibited less genetic diversity than <em>Juglans</em> spp. of North America, based on whole genome and cold-hardy gene analysis. We identified the black walnut as a more diverse species and the California walnut and Persian walnut (<em>J. regia</em>) as less diverse species using selective sweep and heterozygosity analysis. Within <em>Juglans </em>species, those from colder areas exhibited higher diversity of cold hardy genes compared to the ones from warmer regions. Differences in genetic diversity among continents and latitudes did not follow a clear trend. Still, the level of gene diversity of <em>Juglans</em> from North America is higher than the species that originated in eastern Asia. We can use 65,000 nuclear SNPs variants in an ecological modeling system to predict genetic diversity and spatiotemporal shift of <em>Juglans</em> species in response to future climate change. These SNPs variants are helpful for forest tree breeding programs with aims such as marker-assisted selection (MAS), conservation or assisted migration in future.  </p> <p>Based on the findings of chapter 2 and 3, black walnut is the most diverse species with high genetic diversity in comparison with other <em>Juglans</em> species distributing across eastern forest of the USA. However, deeper knowledge of how this genetically diverse species will be affected by climate change is crucial. In chapter 3, we projected black walnut's current and future basal area. Utilizing machine learning, we tested different models using more than 1.4 million tree records from 10,162 Forest Inventory and Analysis (FIA) sample plots and 42 spatially explicit bioclimate and other environmental attributes. Ultimately, we used random forests (RF) model to estimate the basal area of black walnut under climate change. The mean of annual temperature and precipitation, potential evapotranspiration, topology, and human footprint were the most significant variables in prediction of basal area. Under two emission scenarios (Representative Concentration Pathway 4.5 and 8.5), the RF model projected that black walnut stocking will increase in the northern part of the current range in the USA by 2080, with a potential shift of species distribution range. However, uncertainty remains due to unpredictable events, including extreme abiotic (heat, drought) and biotic (pests, disease) occurrences. Our models can be adapted to other hardwood tree species to predict tree changes in the basal area based on future climate scenarios.  </p> <p>A similar approach of chapter 2, with a slightly different freeze test (whole plant freezing test) and use of cold-acclimated seedling was used in chapter 4. For cold acclimation, seedlings exposed to air temperatures progressively lowered for eight weeks (from 25.6/22.2 ºC to 8/4 ºC, day/night) and non-acclimated seedlings from sea level to 2,300 m, in tropical Hawaiʻi, USA to evaluate cold tolerance of koa. We also investigated gene expression using qPCR and wideseq sequencing in this study. Freezing tolerance varied significantly in non-acclimated versus cold-acclimated treatments across the elevation cline using the whole plant physiology-freezing test and gene expression. The level of freezing tolerance and the elevation at which seeds were collected were consistent with the frequency of freezing tolerance genes to facilitate variation interpretation in cold-hardy phenotypes. Findings of physiology and molecular data analysis for freezing tolerance of koa across the elevation gradient of the Hawaiian Islands provides insight into natural selection processes and will help to support forest restoration efforts. </p> <p>  </p>

Des souris aux baleines en passant par les humains, la diversité écologique des mammifères placentaires est des plus fascinantes. Bien qu'il s'agisse là d'un des groupes les plus étudiés, leur origine fait pourtant l'objet de bien des mystères. Leurs relations de parenté les plus basales restent en effet incertaines, et l'on ignore encore beaucoup du mode de vie qu'avaient nos ancêtres du Crétacé, ces mammifères placentaires qui auraient côtoyé les dinosaures pendant plus de 30 millions d'années.Afin d'aborder ces questions, cette thèse a utilisé l'outil de la génomique comparative. L'une de ses principales originalités est la prise en compte d'un distorteur majeur de notre évolution moléculaire: la conversion génique biaisée. Truquant la loterie génétique, ce mécanisme associé à la recombinaison méiotique avantage les nucléotides G et C au détriment des nucléotides A et T. Façonnés par son influence, nos paysages nucléotidiques présentent ainsi ponctuellement des taux de GC anormalement élevés.Jusque là, ce phénomène n'avait été étudié que chez une poignée d'organismes modèles. Son analyse chez plus d'une trentaine de génomes mammaliens a mis en évidence une série de résultats clés. En particulier, l'évolution du contenu en GC des gènes s'est avéré dépendre de la masse corporelle et la longévité des espèces. E nreliant ainsi évolution moléculaire et traits d'histoire de vie, des reconstructions de séquences ancestrales ont permis d'estimer la durée de vie des premiers mammifères placentaires à plus de 25 ans. Cette longévité va bien au delà de ce que peuvent espérer atteindre les souris ou musaraignes actuelles, des animaux au mode de vie pourtant jusqu'ici supposé comme étant proche de celui de nos ancêtres.Parallèlement à ces résultats, une tendance à produire des phylogénies inexactes a été détectée chez les gènes les plus GC-riches. Moins soumis à la conversion génique biaisée, les gènes AT-riches se sont montrés plus fiables, tout en soutenant que les espèces originaires d'Afrique sont situés à la base de l'arbre des placentaires. Ce résultat suggère ainsi la possible résolution d'un des noeuds les plus controversés de notre histoire évolutive.Du simple nucléotide à la naissance d'une infraclasse de plus de 4000espèces, ce travail révèle comment l'évolution moléculaire peut porter un nouveau regard sur nos origines les plus profondes. / From mice to whales through humans, placental mammals present astunning diversity. Despite being one of the most studied group ever,mysteries persist about their origin. Indeed, their most basalrelationships still remain uncertain, and nothing is really knownabout the lifestyle of our cretaceous ancestors, these placentalmammals which lived side by side with non-avian dinosaurs during 30My.To answer these evolutionnary questions, comparative genomic studiesof placental mammals have been conducted. One of its originalities isto take into account biased gene conversion. Rigging the geneticlottery, this recombination-associated mechanism involves a reparationbias favouring the G and C nucleotides over the A and T ones, whichmark the mammalian genomic landscapes by inducing localized peaks ofGC-content.This phenomenon has been so far studied in few model species. Theexploration of biased gene conversion in more than 30 mammal genomesled to several key results. In particular, GC content evolution hasproved to be correlated to the longevity and the body mass of species.By linking together molecular evolution and life history traits, thereconstruction of ancestral sequences allowed us to estimate alife-span above 25 years for early placental mammals. This value ismarkedly different from that of mice or shrews, although our mammalianancestors have often been represented as such. In addition to these results, GC-rich genes were found to be prone toproduce false phylogenies. Less affected by recombination associatedartifacts, AT-rich genes are shown to be more reliable, and to supportspecies of African origin as the sister group of all other placentalmammals - perhaps resolving one of the most controversial nodes of themammalian tree.From nucleotide to the birth of a 4,000 species infraclass, this workreveals how molecular evolution can shed new light onour deepest origins.