Les régions centromériques reposent, chez les Primates, sur une famille de séquences répétées en tandem appelée l'ADN alpha satellite. Les monomères de cet ADN (≈170 pb) se sont diversifiés au cours de l'évolution, formant des familles de séquences aux profils d'organisation et distribution variés. La diversité des alphas satellites chez les primates non-humains reste cependant peu caractérisée, et la compréhension de la dynamique évolutive de cet ADN nécessite son intégration dans de plus larges analyses comparatives. Les Cercopithèques, qui présentent une évolution chromosomique originale par fissions et émergences de nouveaux centromères, apparaissent comme des modèles d'étude prometteurs.Nous avons appliqué une nouvelle technologie de séquençage à des monomères et dimères d'alpha satellites, isolés à partir des génomes de Cercopithecus solatus (2n = 60) et C. pogonias (2n = 72). Ces deux espèces appartiennent à des lignées primaires distinctes au sein des Cercopithèques, et ont divergé l'une de l'autre il y a plusieurs millions d'années. L'analyse computationnelle des séquences collectées a permis la caractérisation de six familles d'alpha satellites, dont quatre sont partagées entre espèces et deux ne sont retrouvées que chez C. pogonias. Au moins trois familles seraient impliquées dans des répétitions d'ordre supérieur, profil d'organisation jusque-là inconnu dans l'ADN alpha satellite des Cercopithèques. L'hybridation in situ en fluorescence des familles identifiées, réalisée grâce à des sondes oligonucléotidiques hautement discriminantes, a permis de visualiser leur distribution sur les chromosomes de C. solatus et C. pogonias. Certaines de ces familles se distribuent différentiellement entre chromosomes, révélant l'existence d'une diversité interchromosomique de l'ADN alpha satellite chez les singes de l'Ancien Monde. Leurs positions sur les régions centromériques vont en faveur de l'hypothèse du gradient d'âge des alphas satellites, selon laquelle les familles se forment aux centromères en déplaçant les familles préexistantes vers les péricentromères. L'extension de cette analyse cytogénétique à quinze espèces et l'interprétation de ses résultats à la lumière d'une phylogénie moléculaire, nouvellement reconstruite, nous ont permis de proposer un scénario évolutif pour l'ADN alpha satellite chez les Cercopithèques. Celui-ci apparaît évoluer de manière concertée avec les chromosomes, se diversifiant et se déplaçant sur les régions centromériques à mesure que ces derniers se fissionnent et voient l'émergence de nouveaux centromères. Ces travaux ont enfin apporté des informations nouvelles quant aux relations de parenté entre Cercopithèques, invitant à une intégration de l'ADN alpha satellite dans l'étude de l'histoire évolutive des Primates. L'approche méthodologique mise au point a permis de caractériser la diversité et de comprendre l'évolution de l'ADN alpha satellite chez les Cercopithèques. Elle pourra être appliquée à l'étude de ces séquences particulières chez d'autres primates, ainsi qu'à l'étude de différents satellites chez des espèces primates comme non-primates. / Alpha satellite DNA is the main family of tandemly repeated sequences lying in primate centromere regions. Alpha satellite monomers (≈170 bp) diversified during the course of evolution, forming distinct families of alpha satellite sequences that exhibit specific organizational and distribution patterns. The limited amount of studies concerning non-human primates is a restriction to the understanding of alpha satellite evolutionary dynamics, which calls for the integration of this element into comparative studies. Cercopithecini, which display an unusual chromosomal evolution by multiple fissions and new centromere formations, constitute a promising study model.We carried out next generation sequencing of alpha satellite monomers and dimers isolated from the Cercopithecus solatus (2n = 60) and C. pogonias (2n = 72) genomes. These species belong to different primary lineages within the Cercopithecini tribe and diverged from each other several million years ago. Computational tools were used to analyze the collected sequences and characterize six alpha satellite families, four of them being shared between species and two being limited to C. pogonias. At least three families belong to higher order repeats, an organizational pattern that had never been observed in Cercopithecini. The fluorescence in situ hybridization of each family, performed with highly discriminant oligonucleotide probes, showed their distribution on C. solatus and C. pogonias chromosomes. Some of them distribute on distinct sets of chromosomes, disclosing the existence of alpha satellite interchromosomal diversity in Old World monkeys. Their position along centromeric regions is largely in accordance with the age-gradient hypothesis, according to which new families expand at centromere, thereby splitting and displacing older families toward pericentromeres. The extension of this analysis to fifteen species, combined to a newly reconstructed molecular phylogeny, allowed us to propose an evolutionary scenario for alpha satellite DNA in Cercopithecini. Alpha satellite DNA diversification and displacement on centromere regions appear intimately connected to chromosome rearrangement dynamics, including new centromere formations, which suggests that centromeres and chromosomes evolve in a concerted manner. Finally, this work provided information about Cercopithecini relationships and thus encourages the integration of alpha satellite DNA into the study of primate evolutionary history.Our new methodological approach allowed deciphering alpha satellite diversity and dynamics in Cercopithecini. This framework could be used to study alpha satellite DNA in other primates, and be applied to different satellites in primates as in non-primate species.

Os elementos de transposição (TEs) se movimentam de um locus para outro no genoma afetando a estrutura e evolução destes. A superfamília de transposases hAT é definida pelos elementos que compartilham os domínios de dimerização e ligação ao DNA com os transposons previamente descritos: hobo, Activator e Tam3. Análises prévias encontraram algumas evidencias da presença genômica e ativação transcricional de TEs relacionados à superfamília hAT em cana-de-açúcar (denominados de família SChAT) e pelo menos três linhagens evolutivas foram postuladas. O objetivo deste trabalho é caracterizar versões genômicas das linhagens de transposons (191 e 257) e linhagem possivelmente domesticada (074). Pretende-se estudar as relações evolutivas, distribuição em gramíneas, identificar os padrões de expressão e propriedades funcionais. Regiões de sintenia foram estabelecidas para estes BACs em Arabidopsis thaliana, Brachypodium distachyon, Sorghum bicolor, Oryza sativa e Zea mays. Elementos relacionados com as três linhagens foram procurados nestes genomas. / Transposable elements (TEs) are able to move from one locus to another within a genome. TE mobilization affects genome structure and evolution. The hAT transposase superfamily is defined as elements that share the dimerization and DNA ligation domains with the previously described hobo, Activator and Tam3 transposon elements. Previous analyses found some genomic and transcriptional evidences of TEs related to hAT superfamily in sugarcane (named SChAT family) and at least three evolutionary lineages were proposed. The aim of this work is to characterize full-length genomic versions of the transposons lineages (191 and 257) and from the domesticated lineage (074). It is proposed to study the evolutionary relationship, distribution along grasses genomes, identify expression patterns and functional capacities of the SChAT elements. Syntenic regions for the BACs containing elements from the three lineages were mapped in Arabidopsis thaliana, Brachypodium distachyon, Sorghum bicolor, Oryza sativa and Zea mays. Related elements were search on the same genomes.

No description available.

Selon une vision populaire, l’évolution serait un processus de « progrès » qui s’accompagnerait d’un accroissement de la complexité moléculaire des êtres vivants. Cependant, les programmes de séquençage des génomes ont révélé l’existence d’espèces dont les lignées ont, au contraire, subi une réduction massive de leur génome. Ainsi, chez les cyanobactéries Prochlorococcus et Pelagibacter ubique, certaines lignées ont subi une réduction de 30% de leur génome. Une telle évolution « à rebours », dite évolution réductive, avait déjà été observée pour des bactéries endosymbiotiques, pour lesquelles la sélection naturelle n’est pas assez efficace pour éliminer les mutations délétères comme les pertes de gènes. Cela vient notamment du fait que ces bactéries endosymbiotiques subissent, à chaque reproduction de leur hôte, une réduction drastique de leur taille de population. Cette explication semble peu plausible pour des cyanobactéries marines comme Prochlorococcus et Pelagibacter, qui ont un mode de vie libre et qui font partie des bactéries les plus abondantes des océans. D’autres hypothèses ont ainsi été proposées pour expliquer l’évolution réductive comme l’adaptation à un environnement stable et pauvre en nutriments, des forts taux de mutation, mais aucun de ces hypothèses ne semble capable d’expliquer toutes les caractéristiques génomiques observées. Dans cette thèse, nous nous intéressons au cas de l’évolution réductive chez Prochlorococcus, pour laquelle de nombreuses séquences et données sont disponibles. Deux approches sont utilisées pour cette étude : une analyse phylogénétique des génomes de Prochlorococcus, et une approche théorique de simulation où nous testons différents scénarios évolutifs pouvant conduire à une évolution réductive. La combinaison de ces deux approches permet finalement de proposer un scénario plausible pour expliquer l'évolution réductive chez Prochlorococcus. / Given a popular view, evolution is an incremental process based on an increase of molecular complexity of organisms. However, some organisms have undergo massive genome reduction like the endosymbionts. In this case the reduction can be explained by the Muller’s ratchet due to the endosymbiont lifestyle with small population and lack of recombination. However, in some marine bacteria, like Prochlorococcus et Pelagibacter, lineage have undergo up to 30% of genome reduction. Their lifestyle is almost the opposite to the one of the endosymbionts and reductive genome evolution can not be easily explicable by the Muller’s ratchet. Some other hypothesis has been proposed but none can explain all the observed genomic characteristics. In the thesis, I am interested in the reductive evolution of Prochlorococcus. I used two approaches: a theoretical one using simulation where different scenarios are tested and an analysis of Prochlorococcus genomes in a phylogenetic framework to determine the causes and characteristics of genome reduction. The combination of these two approaches allows to propose an hypothetical evolutive history for the reductive genome evolution of Prochlorococcus.

Unraveling soil microbial ecology is essential for improving sustainable agricultural productivity. Community-based studies revolutionized this field in the last decades, but much is yet to be disclosed. This thesis proposed an approach to increase the resolution of such studies by combining 16S rDNA high-throughput sequencing and population genomics, aiming to further explore the differences pointed by community analyses, as well as to overcome the limitations of using operational taxonomic units (OTUs) as ecological entities, and to introduce the evolutionary thinking in microbial ecology. Our main goal was to understand the features that make bacteria able to colonize sugarcane rhizosphere or live saprophytically in bulk soil. Rhizosphere and bulk soil are contrasting habitats for microbial life as they are highly distinct in its physical, chemical and consequently biological characteristics. Our results indicated that sugarcane shapes the rhizosphere microbiome and metabolism of D-galacturonic acid is a key function for colonizing this niche. Among the taxa prevailing in the rhizosphere, Pseudomonas genus was targeted for a more detailed study considering its known attributes for plant growth promotion. Seventy-six fluorescent Pseudomonas spp. were isolated and submitted to whole genome sequencing (WGS). A comparative genomic analysis was performed between populations from rhizosphere and bulk soil. Phylogenetic analyses classified the isolates in the P. fluorescens (57) or P. putida (19) groups. Twelve putative new species and two new proposed P. fluorescens subgroups were found in the prospected tropical soil. Comparative genomics revealed that phosphatases or xylose-utilization genes were significantly enriched in the rhizosphere and bulk soil populations of the P. fluorescens group, respectively. D-galactonate catabolism was higher in the rhizosphere population of the P. putida group based on both genotypic and phenotypic results. Growth in D-xylose was further explored using genetic modified strains and confirmed that this sugar is more used by members of the bulk soil than the rhizosphere population of the P. fluorescens group, a pattern also observed in the bulk soil microbiome. In summary, these findings constitute a step forward in understanding the ecology of rhizosphere and bulk soil bacteria, by overcoming some limitations of community-based analyses and showing genomic differences between bacterial populations of these habitats. / Desvendar a ecologia microbiana do solo é essencial para aumentar a produtividade agrícola sustentável. Estudos baseados em comunidades revolucionaram esse campo nas últimas décadas, mas ainda há muito a ser revelado. Esta tese propôs uma abordagem para aumentar a resolução desses estudos, combinando sequenciamento em larga escala de rDNA 16S e genômica populacional, com o objetivo de explorar mais a fundo as diferenças apontadas por análises de comunidades, assim como superar as limitações do uso de unidades taxonômicas operacionais (UTOs) como entidades ecológicas e introduzir o pensamento evolutivo na ecologia microbiana. Nossa principal meta foi entender as características que tornam as bactérias hábeis em colonizar a rizosfera de cana-de-açúcar ou viver no solo saprofiticamente. Rizosfera e solo são hábitats contrastantes para a vida microbiana, já que são altamente distintos em suas características físicas, químicas e, consequentemente, biológicas. Nossos resultados indicaram que a cana-de-açúcar modifica o microbioma da rizosfera e o metabolismo do ácido D-galacturônico é uma função chave para colonizar este nicho. Dentre os táxons que prevalecem na rizosfera, o gênero Pseudomonas foi escolhido para um estudo mais detalhado, considerando os seus atributos de promoção de crescimento de plantas. Setenta e seis Pseudomonas spp. fluorescentes foram isoladas e submetidas ao sequenciamento do genoma. Uma análise de genômica comparativa foi realizada entre as populações obtidas do solo e rizosfera. As análises filogenéticas classificaram os isolados nos grupos P. fluorescens (57) ou P. putida (19). Doze prováveis novas espécies e dois novos subgrupos propostos de P. fluorescens foram encontrados no solo tropical prospectado. A genômica comparativa revelou que genes de fosfatases e de uso de xilose foram significativamente enriquecidos nas populações da rizosfera e solo do grupo P. fluorescens, respectivamente. O catabolismo do ácido D-galactônico foi maior na população da rizosfera do grupo P. putida, baseado tanto em resultados genotípicos quanto fenotípicos. O crescimento em D-xilose foi mais explorado usando linhagens geneticamente modificadas e confirmou que este açúcar é mais utilizado por membros da população do solo do que da rizosfera no grupo P. fluorescens, um padrão também observado no microbioma do solo. Em resumo, essas descobertas constituem um passo adiante no entendimento da ecologia bacteriana do solo e rizosfera, por superar algumas limitações de análises de comunidades e mostrar diferenças genômicas entre populações bacterianas destes hábitats.

Unraveling soil microbial ecology is essential for improving sustainable agricultural productivity. Community-based studies revolutionized this field in the last decades, but much is yet to be disclosed. This thesis proposed an approach to increase the resolution of such studies by combining 16S rDNA high-throughput sequencing and population genomics, aiming to further explore the differences pointed by community analyses, as well as to overcome the limitations of using operational taxonomic units (OTUs) as ecological entities, and to introduce the evolutionary thinking in microbial ecology. Our main goal was to understand the features that make bacteria able to colonize sugarcane rhizosphere or live saprophytically in bulk soil. Rhizosphere and bulk soil are contrasting habitats for microbial life as they are highly distinct in its physical, chemical and consequently biological characteristics. Our results indicated that sugarcane shapes the rhizosphere microbiome and metabolism of D-galacturonic acid is a key function for colonizing this niche. Among the taxa prevailing in the rhizosphere, Pseudomonas genus was targeted for a more detailed study considering its known attributes for plant growth promotion. Seventy-six fluorescent Pseudomonas spp. were isolated and submitted to whole genome sequencing (WGS). A comparative genomic analysis was performed between populations from rhizosphere and bulk soil. Phylogenetic analyses classified the isolates in the P. fluorescens (57) or P. putida (19) groups. Twelve putative new species and two new proposed P. fluorescens subgroups were found in the prospected tropical soil. Comparative genomics revealed that phosphatases or xylose-utilization genes were significantly enriched in the rhizosphere and bulk soil populations of the P. fluorescens group, respectively. D-galactonate catabolism was higher in the rhizosphere population of the P. putida group based on both genotypic and phenotypic results. Growth in D-xylose was further explored using genetic modified strains and confirmed that this sugar is more used by members of the bulk soil than the rhizosphere population of the P. fluorescens group, a pattern also observed in the bulk soil microbiome. In summary, these findings constitute a step forward in understanding the ecology of rhizosphere and bulk soil bacteria, by overcoming some limitations of community-based analyses and showing genomic differences between bacterial populations of these habitats. / Desvendar a ecologia microbiana do solo é essencial para aumentar a produtividade agrícola sustentável. Estudos baseados em comunidades revolucionaram esse campo nas últimas décadas, mas ainda há muito a ser revelado. Esta tese propôs uma abordagem para aumentar a resolução desses estudos, combinando sequenciamento em larga escala de rDNA 16S e genômica populacional, com o objetivo de explorar mais a fundo as diferenças apontadas por análises de comunidades, assim como superar as limitações do uso de unidades taxonômicas operacionais (UTOs) como entidades ecológicas e introduzir o pensamento evolutivo na ecologia microbiana. Nossa principal meta foi entender as características que tornam as bactérias hábeis em colonizar a rizosfera de cana-de-açúcar ou viver no solo saprofiticamente. Rizosfera e solo são hábitats contrastantes para a vida microbiana, já que são altamente distintos em suas características físicas, químicas e, consequentemente, biológicas. Nossos resultados indicaram que a cana-de-açúcar modifica o microbioma da rizosfera e o metabolismo do ácido D-galacturônico é uma função chave para colonizar este nicho. Dentre os táxons que prevalecem na rizosfera, o gênero Pseudomonas foi escolhido para um estudo mais detalhado, considerando os seus atributos de promoção de crescimento de plantas. Setenta e seis Pseudomonas spp. fluorescentes foram isoladas e submetidas ao sequenciamento do genoma. Uma análise de genômica comparativa foi realizada entre as populações obtidas do solo e rizosfera. As análises filogenéticas classificaram os isolados nos grupos P. fluorescens (57) ou P. putida (19). Doze prováveis novas espécies e dois novos subgrupos propostos de P. fluorescens foram encontrados no solo tropical prospectado. A genômica comparativa revelou que genes de fosfatases e de uso de xilose foram significativamente enriquecidos nas populações da rizosfera e solo do grupo P. fluorescens, respectivamente. O catabolismo do ácido D-galactônico foi maior na população da rizosfera do grupo P. putida, baseado tanto em resultados genotípicos quanto fenotípicos. O crescimento em D-xilose foi mais explorado usando linhagens geneticamente modificadas e confirmou que este açúcar é mais utilizado por membros da população do solo do que da rizosfera no grupo P. fluorescens, um padrão também observado no microbioma do solo. Em resumo, essas descobertas constituem um passo adiante no entendimento da ecologia bacteriana do solo e rizosfera, por superar algumas limitações de análises de comunidades e mostrar diferenças genômicas entre populações bacterianas destes hábitats.

A phylogenetic tree based on ITS1, Adh1 and ndhF grouped the species of the genus Sorghum into one distinct monophyletic group, but including two sister lineages, one with x=5, the other with x=10 as basic chromosome numbers. The goal of this study was to elucidate major patterns in Sorghum genome evolution, particularly n=5 vs. n=10 genomes. A very recent molecular cytogenetic study in our laboratory revealed striking structural karyotypic rearrangements between S. bicolor (x=10) and an x=5 Sorghum species, S. angustum; so an immediate objective here was to determine if identical or similar rearrangements exist in other wild Sorghum species. Our approach was [1] to extend similar methods to additional species, i.e., fluorescent in situ hybridization (FISH) analyses of sorghum genomic bacterial artificial chromosome clones and multi-BAC cocktail probes to mitotic chromosomes of S. angustum, S. versicolor, S. brachypodum and S. intrans; and [2] to augment the BAC-FISH findings by comparing telomeric and ribosomal DNA FISH signal distributions to x=5 and x=10 Sorghum species. Signals from in situ hybridizations of BAC-based probes were insufficiently robust and insufficiently localized to delineate FISH signal patterns akin to those discovered previously in S. angustum. Southern blots of the same BACs to restricted DNA of these species revealed relatively moderate affinity to smeared DNA, suggesting homology to non-tandemized sequences. FISH of the A-type TRS (Arabidopsis-like telomeric repeat sequence) revealed its presence is limited to terminal chromosomal regions of the Sorghum species tested, except S. brachypodum, which displayed intercalary signal on one chromosome and no detachable signal at its termini region. The hybridization of 45S and 5S rDNA revealed that the respective sites of tandemized clusters differ among species in terms of size, number and location, except S. angustum versus S. versicolor. Well localized BAC-FISH signals normally occur when signals from low-copy sequences discernibly exceed background signal, including those from hybridization of dispersed repetitive elements. The low level of signal intensity from BAC low-copy sequences relative to the background signal "noise" seems most likely due to low homology and(or) technical constraints. Extensive dispersal of low-copy sequences that are syntenic in S. bicolor seems unlikely, but possible. In conclusion, the result was a lack of clear experimental success with BAC-FISH and an inability to effectively screen for S. angustum-like rearrangements using BAC-FISH. The telomeric and rDNA FISH indicated that the x=5 genomes vary extensively. One can surmise that although the arrangements seen in S. angustum might extend to S. versicolor, they certainly do not extend to S. versicolor, they certainly do not extend to S. intrans or S. brachypodum. It is clear that S. brachypodum has telomeric repeats that are either very short or rely on some sequence other than the A-type TRS.

Extreme haustorial parasites have long captured the interest of naturalists and scientists with their greatly reduced and highly specialized morphology. Along with the reduction or loss of photosynthesis, the plastid genome often decays as photosynthetic genes are released from selective constraint. This makes it challenging to use traditional plastid genes for parasitic plant phylogenetics, and has driven the search for alternative phylogenetic and molecular evolutionary markers. Thus, evolutionary studies, such as molecular clock-based age estimates, are not yet available for all parasitic lineages. In the present study, we extracted 14 nuclear single copy genes (nSCG) from Illumina transcriptome data from one of the “strangest plants in the world”, Hydnora visseri (Hydnoraceae). A ~15,000 character molecular dataset, based on all three genomic compartments, shows the utility of nSCG for reconstructing phylogenetic relationships in parasitic lineages. A relaxed molecular clock approach with the same multi-locus dataset, revealed an ancient age of ~91 MYA for Hydnoraceae. We then estimated the stem ages of all independently originated parasitic angiosperm lineages using a published dataset, which also revealed a Cretaceous origin for Balanophoraceae, Cynomoriaceae and Apodanthaceae. With the exception of Santalales, older parasite lineages tend to be more specialized with respect to trophic level and have lower species diversity. We thus propose the “temporal specialization hypothesis” (TSH) implementing multiple independent specialization processes over time during parasitic angiosperm evolution.

Le fait d'avoir une généalogie datée des organismes vivants est l'un des principaux objectifs de la biologie évolutive. Cette entreprise est confrontée à deux défis majeurs. Le premier est la rareté et l'incomplétude des enregistrements fossiles, pratiquement inexistants pour les microbes et essentiels pour fournir une échelle temporelle de l'histoire de la vie. Le second est la difficulté intrinsèque d'obtenir des phylogénies d'organismes dont le génome a été largement façonné par transfert latéral de gène (TLG). L'acquisition par transfert de nouveaux gènes d'origine éloignée perturbe des arbres de gènes et rend beaucoup plus complexe la reconstruction de l'histoire des espèces. Dans ce travail de thèse, je montre comment nous pouvons utiliser ces différences entre arbres de gènes et arbres d'espèces à notre avantage pour inférer les événements anciens de TLG et comment ils peuvent fournir une nouvelle échelle de temps pour l'évolution des organismes vivants. Les transferts étant particulièrement fréquents chez les espèces dont les fossiles sont rares, ils peuvent servir de nouvelle source de datation indépendante du registre géologique pour reconstruire une phylogénie datée de la vie. Dans la première partie, je réalise une analyse à l'échelle génomique pour montrer comment les méthodes de réconciliations phylogénétiques peuvent être utilisées pour détecter les lignées correspondant aux donneurs et aux receveurs des événements de TLG. En outre, ces méthodes fournissent également une vue détaillée de la façon dont les familles de gènes évoluent le long des arbres de l'espèce. En utilisant ALE, un logiciel de réconciliation probabiliste qui prend en compte l'incertitude dans les arbres de gènes, nous sommes en mesure de cartographier les événements de duplication, de perte et de transfert dans les phylogénies des cyanobactéries et des champignons. Nous montrons également comment les méthodes qui ignorent l'information contenue dans les arbres de gènes sous-estiment la fréquence réelle des TLG. Dans la deuxième partie, je présente en détail comment le TLG porte un signal temporel et comment ce signal peut être utilisé pour inférer des arbres datés. J'introduis une nouvelle méthode appelée MaxTiC qui permet de trouver un ordonnancement des noeuds dans l'arbre des espèces qui maximise la cohérence temporelle entre les transferts. Par des simulations, nous montrons la robustesse de la méthode aux erreurs présentes dans l'arbre des espèces et le nombre de familles de gènes nécessaires pour obtenir des arbres datés fiables. Enfin, pour confirmer nos résultats, je présente différentes approches permettant de comparer les temps de divergence découlant des transferts avec ceux estimés en utilisant des horloges moléculaires. Nous effectuons une analyse phylogénomique pour détecter des milliers d'événements de TLG dans quatres groupes: les cyanobactéries, les Deltaproteobactéries, les Archées et les Champignons. Nous trouvons un large accord entre les deux méthodes de datation, ce résultat étant robuste à l'utilisation de différentes prior sur les temps de divergence et différents modèles d'horloges moléculaires relâchées. Nous montrons également que certaines des dates indiquées par l'utilisation de TLG sont en désaccord avec les horloges moléculaires tout en étant soutenues par un grand nombre de TLG. Ces résultats suggèrent que l'utilisation des TLG pourrait permettre d'améliorer les méthodes de datation, notamment pour les phylogénies anciennes et ainsi conduire à d'importants changements de notre point de vue sur l'histoire de la vie / Having a dated genealogy of living organisms is one of the major goals of evolutionary biology. This enterprise faces two major challenges. The first one is the scarcity and incompleteness of the fossil record, virtually nonexistent for microbes and essential to provide a time scale of life history. The second one is the intrinsic difficulty of obtaining phylogenies in organisms whose genome has been extensively shaped by Lateral Gene Transfer (LGT). The acquisition of new genes from distant organisms creates important differences among genes trees and complicates the reconstruction of the species history. In this thesis work I show how we can use those differences to our advantage to infer ancient events of LGT and how they provide a temporal scale of evolution. Transfers can supply an important amount of information on divergence times in organisms whose fossils are very scarce, acting as a new dating source independent of the geological record and taking us a step closer to building a whole dated phylogeny of Life. In the first part, I perform genomic-scale analyses to show how phylogenetic reconciliations can be used to detect donor and recipient lineages of LGT events. Moreover, they also provide a detailed view of how gene families evolve along species trees. Using ALE, a probabilistic reconciliation software that accounts for the uncertainty in gene trees, we are able to map events of duplication, loss and transfer in phylogenies of cyanobacteria and fungi. We also show how methods that ignore the information contained in gene trees underestimate the real frequency of LGT. In the second part, I present in detail how LGT carries a temporal signal and how this signal can be used to infer dated trees. I explain a new method called MaxTiC, that finds the best dated tree by maximizing the number of transfers that are time-compatible with a phylogeny. By simulations we show how robust the method is to errors in the species tree and how many gene families are required to obtain reliable dated trees. Finally, to confirm our results I present different metrics to compare the divergence times inferred by transfers with those inferred by molecular clocks. We perform a phylogenomic analysis to detect thousands of LGT events in cyanobacteria, Deltaproteobacteria, Archaea and fungi and obtain their dated phylogenies. We find a broad agreement between both dating methods, a result robust to the use of different priors on divergence times and different models of relaxed molecular clock. We also show that some of the dates inferred by using LGT are not recovered by molecular clocks. These results altogether suggest that the use of LGT in future dating studies may have a big impact on the inferred dates of major evolutionary events and can lead to an important change of our view of the History of Life

Abstract Species of Lactobacillus (L.) are important starter and probiotic lactic acid bacteria used in the dairy industry. Industrial fermentation processes are prone to phage infections, which can cause severe economic losses. The main objective of this thesis was to examine in more depth the genetic variation and evolution of L. delbrueckii and L. rhamnosus phages. Aspects of interactions and co-evolution of a phage and its host have also been included in this study. In this study, the complete genomic DNA sequences of four Lactobacillus phages were determined and analyzed in detail. Specific phage genes and genetic elements were identified and studied in more depth. The L. delbrueckii phage JCL1032 was found to be a temperate phage which is able to integrate into two distinct genes of L. delbrueckii, but with exceptionally low frequency. The isolated JCL1032-lysogenic bacteria expressed a complex phage resistance against several L. delbrueckii phages. The rarely reported coexistence of phage adsorption resistance and immunity could not be explained by lysogenic conversion. Instead, the spontaneously induced JCL1032 may have provided a selective advantage to adsorption resistant lysogens. The biological activity of two group I introns residing within the terminase large subunit and tape measure genes of the JCL1032 genome (49,433 bp) was demonstrated. The diversification of L. delbrueckii phages is mainly due to insertions, deletions and recombination, as was demonstrated by comparative analyses of the LL-Ku and c5 genomes of 31,080 bp and 31,841 bp, respectively. Interestingly, both phages have possible autonomous transcription units of genes within their genomes. It seemed that evolution of the 36,366-bp genome of the L. casei phage Lc-Nu has been fuelled by deletions as well. The lytic phage Lc-Nu has an imperfect lysogeny module and the phage is genetically closely related to L. casei prophages. This clearly demonstrated that Lc-Nu has a recent temperate origin. This study provides genetic tools, genes, and regulatory elements for biotechnological applications and for developing starter strains with enhanced phage resistance properties. / Tiivistelmä Hapatteina ja probiootteina käytetyt Lactobacillus-maitohappobakteerit (L. ) ovat merkittävässä asemassa meijeriteollisuudessa. Teolliset käymisprosessit ovat alttiita faagi-infektioille, jotka voivat aiheuttaa tuotantolaitoksille huomattavia taloudellisia tappioita. Tämän tutkimuksen päätavoitteena oli syventää tietoa L. delbrueckii ja L. rhamnosus -bakteereita infektoivien faagien geneettisestä muuntelusta ja evoluutiosta. Tutkimuksessa käsitellään myös faagin ja isäntäbakteerin välistä vuorovaikutusta sekä yhteisevoluutiota. Tutkimuksessa määritettiin neljän Lactobacillus-faagin genominen DNA-sekvenssi, identifioitiin faagigeenejä ja muita geneettisiä elementtejä sekä tutkittiin niiden toimintaa. L. delbrueckiin JCL1032-faagi osoittautui tutkimuksessa temperaatiksi. JCL1032-genomi voi integroitua kahteen eri geeniin isäntäbakteerin kromosomissa, joskin lysogeniafrekvenssi on hyvin alhainen. Tutkimuksessa eristetyt JCL1032-lysogeeniset bakteerikannat olivat resistenttejä useille Lactobacillus-faageille. Osassa lysogeenisia bakteereita resistenssi ilmeni jo faagin adsorptiovaiheessa. Vastaavanlainen ilmiö on kuvattu vain harvoin aiemmin. Havaittua kompleksista resistenssiä ei voitu selittää lysogeenisella konversiolla. Sen sijaan ilmiön taustalla voi olla JCL1032-profaagien spontaani indusoituminen bakteerin kromosomista, mikä voi antaa valintaetua adsorptioresistenteille lysogeenisille bakteereille. JCL1032-genomissa (49 433 emäsparia) osoitettiin olevan kaksi biologisesti aktiivista intronia terminaasin suurta alayksikköa ja hännän mittaproteiinia koodaavissa geeneissä. LL Ku- ja c5-faagien genomien (31 080 ja 31 841 emäsparia) vertailu osoitti L. delbrueckii -faagien evoluution olevan pääasiassa seurausta insertioista, deleetioista ja rekombinaatiosta. Kummassakin genomissa oli mahdollisesti päällekkäisiä ja itsenäisesti transkriptoituvia geenialueita. Deleetiot ovat muokanneet myös L. casein lyyttisen Lc- Nu-faagin genomia (36 466 emäsparia). Faagin lysogeniamoduuli sisälsi vain osan lysogeeniseen elinkiertoon tarvittavista geeneistä. Lc-Nu on geneettisesti läheistä sukua L. casei -profaageille, mikä myös viittaa siihen, että Lc-Nu on kehittynyt temperaatista faagista. Tutkimustuloksia faagien geeneistä ja säätelyelementeistä voidaan hyödyntää hapatebakteerien faagiresistenssiominaisuuksien kehittämisessä sekä erilaisissa bioteknologisissa sovelluksissa.