Endocytosis is an essential cellular process consisting of the internalization of extracellular cargo and its transport towards different intracellular destinations. Multiple endocytic routes are tailored for the internalization and trafficking of different types of cargo and multiple endocytic organelles provide specialized biochemical environments where different molecular events take place. Membrane receptors and cargo molecules are internalized by both Clathrin-dependent and –independent endocytosis into early endosomes. From here two main endocytic routes are followed: 1) the recycling route, mainly followed by membrane receptor and other molecules like Transferrin, brings the cargo back to the plasma membrane and 2) the degradative route, followed by molecules like Epidermal Growth Factor (EGF) and Lipoprotein particles (LDL), leads the cargo to degradation into late endosomes/lysosomes. In addition to the basic function of intracellular cargo transport, the endocytic system fulfils many other cellular and developmental functions such as transmission of proliferative and survival signals and defence against pathogens. In order for cells to properly perform their various and numerous functions in organs and tissues, the activity of the endocytic system needs to be coordinated between cells and, within individual cells, integrated with other cellular functions. Even though molecules orchestrating the endocytic sorting and transport of different types of cargo have long been investigated, our understanding of the molecular machinery underlying endocytosis and its coordination into the cellular systems remains fragmentary. The work presented in this thesis aimed at understanding how this high-order regulation and integration is achieved. This requires not only a comprehensive analysis of molecular constituents of the endocytic system but also an understanding of the general design principles underlying its function. To this end, in collaboration with several members of the Zerial group and with the HT-Technology Development Studio (TDS) at MPI-CBG, I developed a new strategy to accurately profile the activity of human genes with respect to Transferrin (Tfn) and Epidermal Growth Factor (EGF) endocytosis by combining genome-wide RNAi with several siRNA/esiRNA per gene, automated high-resolution confocal microscopy, quantitative multi-parametric image analysis and high-performance computing. This provided a rich and complex genomic dataset that was subsequently subjected to analysis with a combination of tools such as a multi-parametric correlation of oligo profiles, phenotypic clustering and pathways analysis, and a Bayesian network reconstruction of key endocytic features. Altogether, the genomic endeavour and the subsequent analyses provided a number of important results: first, they revealed a much higher extent of off-target effects from RNAi and provided novel tools to infer the specific effects of genes loss of function; second, they identified a large number of novel molecules exerting a regulatory role on the endocytic system, including uncharacterized genes and genes implicated in human diseases; third, they uncovered the regulatory activity of signalling pathways such as Wnt, Integrin, TGF-β, and Notch, and found new genes regulating the sorting of cargo to a specialized subset of early endosomes that function as intracellular signalling platforms; and fourth, a systems analysis by Bayesian networks revealed that the cell specifically regulates the number, size, concentration of cargo and intracellular position of endosomes, thus uncovering novel properties of the endocytic system. In conclusion, the work presented here not only provided a dataset extremely rich of information whose potential has just begun to be uncovered but also shows how genomic datasets can be used to reveal design principles governing the functioning of biological processes.

Chagas disease is caused by the parasite Trypanosoma cruzi and transmitted by multiple triatomine vectors across the Americas. In Central America, the predominant vector is Triatoma dimidiata, a highly adaptable and genetically diverse Hemiptera. In this research, we used a novel reduced-representation DNA sequencing approach to discover community dynamics among multiple biotic factors associated with Chagas disease in Central America, and assess the infestation patterns of T. dimidiata after seasonal and chemical disturbances in Jutiapa, Guatemala. For our first study, we used a hierarchical sampling design to obtain multi-species DNA data found in the abdomens of 32 T. dimidiata specimens from Central America. We aimed to understand (1) the prevalence of T. cruzi infection, (2) the population genetics of the vector and parasite, (3) the blood meal history of the vector, and (4) gut microbial diversity. Our results indicated the presence of nine infected vectors harboring two distinct DTUs: TcI and possibly TcIV. We found significant clusters among T. dimidiata populations in countrywide and within-country levels associated with sylvatic ecotopes and diverse domestic genotypes. There was significantly higher bacteria species richness in infected T. dimidiata abdomens than those that were not infected, with further analysis suggesting that gut bacteria diversity relates to both T. cruzi infection and the local environment. We identified vertebrate blood meals from five T. dimidiata abdomens including chicken, dog, duck and human; however, additional detection methods are necessary to confidently identify blood meal sources. In our second study, we analyzed the GBS genotypes of 440 T. dimidiata specimens collected in two towns of Jutiapa, Guatemala. Our aim was to assess (1) the domestic population patterns that aid the recovery of T. dimidiata after an insecticide treatment in El Carrizal and (2) the seasonal changes that regulate the dispersal of the vector in the untreated communities of El Chaperno. Results showed that the insecticide application was effective at reducing the population abundance immediately after the application in El Carrizal; nevertheless, 18-month post-treatment the town-wide infestation and genetic diversity were recovering. Within-house relatedness among specimens recovered 18 months post-treatment, suggesting that the insecticide treatment failed to fully eliminate domiciliated colonies. In contrast, lack of change in abundance or genetic diversity in El Chaperno implied absence of dispersers from sources beyond the town periphery, while evidence of a decrease of relatedness among individuals implied dispersal among houses. After the insecticide treatment in El Carrizal, population reduction led to lack of genetic spatial autocorrelation; nevertheless, rapid dispersal into neighboring houses lead to autocorrelation 18 months after the insecticide treatment. This pattern was also observed in El Chaperno, where an increase in spatial autocorrelation during seasonal dispersal suggests spillover to close-by households. The creation of a novel genomics pipeline allowed us to understand community and dispersal patterns of T. dimidiata and other biotic factors important for the prevalence and transmission of Chagas disease at local and regional levels. Future studies should include complementary approaches for taxa verification (e.g. bacteria 16S barcoding, PCR-base detection), as well as expand the scope of local population analyses to peridomestic and sylvatic genotypes that could suggest a broader range of vector sources and region-wide patterns of temporal and spatial dispersion.

Comprendre comment les espèces s'adaptent à leur environnement est un des buts majeurs de la biologie évolutive. Il s'agit d'identifier les gènes responsables des caractères adaptatifs, mais aussi de comprendre les mécanismes généraux de l'adaptation, et des phénomènes empêchant une adaptation optimale. Les régions non-recombinantes sont particulières pour ces aspects. En effet, elles peuvent protéger de la recombinaison des combinaisons d'allèles favorables, et inversement, la suppression de recombinaison peut entraîner une dégénérescence, comme une accumulation de mutations délétères ou des pertes de gènes. Même les organismes à reproduction sexuée possèdent cependant souvent de larges régions non-recombinantes, associées à la détermination du sexe génétique ou du type sexuel. Dans cette thèse, j’ai ainsi étudié les traces d’adaptation et de dégénérescence dans des génomes de champignons pathogènes de plantes. Les champignons du complexe d'espèces Microbotryum violaceum, qui causent la maladie du charbon des anthères chez les Caryophyllacées et comptent des dizaines d'espèces spécifiques d’hôtes différents, sont d'excellents modèles pour l'étude des processus génomiques de l'adaptation. Ils possèdent de plus des chromosomes de types sexuels non-recombinants sur une partie de leur longueur. Pour étudier l'évolution des chromosomes de types sexuels, la dégénérescence et l'adaptation à l'hôte dans le complexe M. violaceum, nous avons adopté diverses approches de génomique. En utilisant la technologie PacBio, nous avons obtenu un assemblage complet des chromosomes de types sexuels pour l'espèce M. lychnidis-dioicae. Nous avons montré que la région non-recombinante s'étend sur 90 % des chromosomes de types sexuels, présente un niveau de réarrangements exceptionnel entre les deux types sexuels, et que des centaines de gènes sont présents à l'état hémizygote et ont donc probablement été perdus dans un type sexuel. De plus, la comparaison des génomes d'une douzaine d'espèces de M. violaceum a montré une accumulation de mutations non-synonymes et d'éléments transposables dans les chromosomes de types sexuels. Nous avons aussi étudié la dégénérescence dans le contexte de l'exposition aux radiations ionisantes, en analysant des populations de M. lychnidis-dioicae exposées à différents niveaux de radiation dans la région de Tchernobyl. Nous n'avons pas détecté d'augmentation du taux de mutations non-synonymes par rapport au groupe témoin, ce qui suggère que le champignon est radio-résistant ou que la sélection est plus forte dans la région de Tchernobyl. Enfin, pour étudier l'adaptation à l’hôte, nous avons reséquencé des dizaines des génomes de deux espèces sœurs de M. violaceum. L'analyse du polymorphisme a révélé des balayages sélectifs tout le long des génomes et à des localisations différentes entre les deux espèces. Nous avons identifié un certain nombre de gènes candidats pour l'adaptation à l’hôte dans ces régions de balayages sélectifs, sur la base de leur expression in planta et de leurs annotations. Les gènes sur-exprimés dans la plante montraient d’autre part un taux de substitutions non-synonymes entre les deux espèces sœurs plus élevé que les autres gènes, ce qui suggère qu’une bonne partie pourrait être impliquée dans l'adaptation à l’hôte. Ces travaux ouvrent la voie à une comparaison des génomes de différentes espèces du complexe M. violaceum, d’une part pour reconstituer l'histoire de la suppression de recombinaison dans les chromosomes de types sexuels, et d’autre part pour étudier les bases génétiques de l'adaptation à différents hôtes dans un complexe d’espèces phylogénétiquement proches. / Understanding how species adapt to their environment is a major goal in evolutionary biology. Scientists aim to identity the genes underlying key adaptive traits, but also to understand more broadly adaptive processes and phenomena that allow or prevent optimal adaptation. Non-recombining regions are particular for these aspects. They can indeed protect adaptive combinations of alleles from recombination, and conversely, suppressed recombination can lead to degeneration, such as accumulation of deleterious mutations or genes losses. Even sexually-reproducing organisms often possess large non-recombining regions associated with sex ou mating-type determination. In this thesis, I therefore studied signatures of adaptation and degeneration in genomes of plant pathogenic fungi. Fungi of the species complex Microbotryum violaceum, with dozens of host-specific sibling species causing anther-smut disease in the Caryophyllaceae family, are particularly good models for addressing the question of the genomic processes involved in host adaptation. Moreover, they possess size-dimorphic, partly non-recombining mating-type chromosomes. To study the evolution of mating-type chromosomes, degeneration and host-adaptation in the M. violaceum species complex, we used a genomic approach. Using PacBio sequencing, we obtained a complete assembly of the mating-type chromosomes of the species M. lychnidis-dioicae. We showed that the non-recombining regions span 90 % of the mating-type chromosomes, exhibit an exceptional level of rearrangements between the two mating-types, and that hundreds of genes are in a hemizygous state and were therefore probably lost in one of the two mating-type chromosomes. Moreover, comparing a dozen of species of the M. violaceum complex revealed an accumulation of non-synonymous substitutions and of transposable elements in mating-type chromosomes. We also studied degeneration in the context of ionizing radiations, by analysing populations of M. lychnidis-dioicae exposed to different radiation levels in the Chernobyl area. We did not detect any increase in the rate of non-synonymous mutations compared to the control group or with radiation, which suggests that the fungi is radio-resistant or that selection is higher in the Chernobyl area. Lastly, we resequenced dozens of genomes of two sibling species of M. violaceum in order to study host adaptation. Analysing polymorphism patterns, we found several selective sweeps along the genome, at different locations in the two species. We identified candidate genes for host-adaptation in the regions of selective sweeps, based on their expression pattern and on their putative functions. In addition, genes up-regulated in planta exhibited a higher rate of non-synonymous substitutions than other genes, suggesting that many of them are likely involved in host adaptation. This work paves the way to a larger comparison of genomes of different species of the M. violaceum species complex, in order to reconstruct the history of recombination suppression on the mating-type chromosomes on the one hand, and to study the genetic bases of adaptation to different hosts in a complex of phylogenetically close species on the other hand.

Oenococcus oeni est une espèce de bactérie lactique adaptée à l'environnement hostile de la fermentation du vin. Elle montre un degré de spécialisation remarquable face au stress provoqué par le faible pH et la forte teneur en éthanol, ce qui lui permet de proliférer là où la plupart des bactéries ne survivent pas. Cette bactérie est très importante dans la production de vin, car elle réalise la fermentation malolactique, qui se produit après la fermentation alcoolique, et au cours de laquelle l'acide malique est métabolisé en acide lactique et où le vin est désacidifié. L'espèce accumule des mutations plus vite que les autres espèces de bactéries lactiques, ce qui a probablement accéléré le processus de domestication. Son degré de spécialisation a été démontré par la présence de populations spécifiques adaptées aux vins rouges ou aux vins blancs dans la même région. Dans cette étude, nous avons utilisé des approches de séquençage haut débit et de génomique pour élucider la diversité des souches d’O. oeni, identifier leurs caractéristiques génomiques et mesurer leur dispersion dans différents environnements ainsi que leur dynamique au cours des fermentations. En raison de son importance pour la vinification, plusieurs centaines de souches ont été isolées et séquencées. Dans ce travail, nous avons augmenté la collection de génomes en séquençant des souches de cidre et de kombucha et en effectuant des analyses phylogénétiques afin de clarifier la structure de la population de l'espèce. En calculant un pangénome à l'échelle de l'espèce, nous avons effectué une analyse génomique comparative afin d'explorer des gènes spécifiques à une ou plusieurs sous-populations. Avec le séquençage de nouvelle génération, nous avons produit des génomes entièrement circularisés à partir des principales sous-populations et analysé leurs arrangements génomiques. Ces nouveaux génomes ont été annotés avec de nouveaux pipelines automatiques et une curation manuelle pour la première fois depuis la publication du génome de référence PSU-1. L’évolution des communautés bactériennes au cours de la fermentation, du moût de raisin au vin fini, a été examinée par le séquençage de fragments 16S dans quatre exploitations du bordelais. À l’aide d’amorces universelles et spécifiques, nous avons comparé la biodiversité des espèces dans des vins issus d’agriculture biologique ou conventionnelle. De plus, en se basant sur les groupes phylogénétiques de souches d’O. oeni nouvellement définis, nous avons développé une méthode de qPCR pour analyser la dispersion des groupes de souches d’O. oeni et leur dynamique au cours des fermentations. Cette nouvelle méthode a également été utilisée pour analyser la diversité des souches d’O. oeni dans les vins de base de Cognac et au cours de la production de cidre, deux produits qui se distinguent des productions de vins traditionnels par la non-utilisation de sulfites. Les deux autres espèces du genre Oenococcus, O. kitaharae et O. alcoholitolerans, se retrouvent également dans les environnements de boissons fermentées. O. kitaharae ne possède pas de gène malolactique fonctionnel, mais O. alcoholitolerans, découvert plus récemment, serait capable de réaliser la réaction malolactique. Nous l’avons caractérisée, ainsi que sa tolérance aux facteurs de stress de l'environnement vin. Constatant qu'elle était incapable de survivre dans le vin, nous avons produit un génome entièrement circularisé d'O. alcoholitolerans et effectué une analyse de génomique comparative afin d'identifier les gènes d'O. oeni lui permettant de tolérer le pH et l'éthanol, ce qui manque à O. alcoholitolerans et à O. kitaharae. En conclusion, nous avons utilisé les nouvelles technologies de séquençage de nouvelle génération pour produire des génomes de haute qualité et effectuer des analyses comparatives approfondies à l’échelle de l’espèce qui nous ont permis d’identifier des gènes susceptibles d’expliquer l’adaptation d’O. oeni à l’environnement. / Oenococcus oeni is a lactic acid bacteria species adapted to the inhospitable environment of fermenting wine, where it shows a remarkable degree of specialization to the stress of low pH and high ethanol that allows it to proliferate where most bacteria fail to survive. The bacteria is supremely important in wine production, because it carries out malolactic fermentation, a process that occurs after alcoholic fermentation, where malic acid is metabolised into lactic acid and the pH of the wine is raised. The species has only a small genome and accumulates mutations several orders of magnitude faster than other lactic acid bacteria due to a loss of DNA mismatch repair genes. This has likely sped up the process of domestication to wine. The degree of specialization has been demonstrated by finding specific populations adapted to red or white wines in the same region. In this study, we used high throughput sequencing and genomics approaches to elucidate the diversity of O. oeni strains, to identify their genomic characteristics and measure their dispersion in different environments as well as their dynamics during fermentation. Because of its importance to wine-making, several hundred strains have been isolated and sequenced. In this work, we have expanded upon the collection of genomes by sequencing strains from cider and kombucha and performing phylogenetic analyses to clarify the population structure of the species. By calculating a species-wide pangenome, we performed comparative genomics to explore gene clusters that were specific to one or more sub-populations. With next generation sequencing, we produced fully circularized genomes from the major sub-populations and analysed their genomic arrangements. These new genomes were annotated with new, automatic pipelines and manual curation for the first time since the publication of the reference genome PSU-1. The evolution of bacterial communities over the course of fermentation, from grape must to finished wine, was examined with 16S amplicon sequencing in four Bordeaux wineries. Using a universal and a specific primer-set, we compared the biodiversity in wines resulting from organic or conventional farming practices. In addition, with the newly defined phylogenetic groups, we developed a qPCR experiment to detail the composition of O. oeni in the fermentations and cemented the dispersal of even rarely isolated strain sub-populations in grape must. This new method was also used to analyse the diversity of O. oeni strains in the base wines of Cognac and during the production of cider, two products that are distinguished from traditional wine production by not using sulfite. The two other species in the Oenococcus genus, kitaharae and alcoholitolerans, are also found in the environments of fermenting beverages. O. kitaharae does not have a functional malolactic gene, but the more recently discovered O. alcoholitolerans was thought capable of performing the malolactic reaction. We characterized this, as well as the species tolerance for the stressors of the wine environment. Finding it unable to survive in wine, we produced a fully circularized genome of O. alcoholitolerans and performed a comparative genomics analysis to identify the O. oeni genes that enable it to tolerate the pH and ethanol, which O. alcoholitolerans and O. kitaharae lacks. In conclusion, we have used the new technologies of next generation sequencing to produce high-quality genomes and performed extensive, species-wide comparative analyses that allowed us to identify patterns in gene presence that provide likely explanations for environmental adaptation.

No description available.

No description available.

The U.S. aquaculture industry has become well established in the last three decades, and channel catfish aquaculture is the most significant component of this industry. Virulent Aeromonas hydrophila has been a serious disease problem since 2009 in the U.S. catfish aquaculture, and Aeromonas veronii and Edwardsiella piscicida are emerging pathogens of catfish. Therefore, this study aims to address fundamental questions on virulence mechanisms of these three fish pathogens, which I expect to support the development of control measures for preventing these diseases. In this study, E. piscicida and virulent Aeromonas hydrophila (vAh) genomes were sequenced, and comparative analyses were conducted using the genome sequences. Average nucleotide identity (ANI) calculations showed that E. piscicida strains share high sequence identity, yet they are from diverse host species and geographic regions. vAh isolates share very high sequence identity, while the other A. hydrophila genomes are more distantly related to this clonal group. We applied several comparative genomics approaches to evaluate E. piscicida genomes and E. ictaluri genomes, providing valuable information about unique and shared features of these two important pathogens in the Edwardsiella genus. Comprehensive secretion system analysis of 55 A. hydrophila genomes and deletion of tssD and tssI core elements of T6SS from vAh isolate ML09-119 has provided new knowledge. We sequenced the genome of virulent Aeromonas veronii strain ML09-123 from catfish indicated that it was highly similar to an A. veronii strain from China. Evaluation of all 41 A. veronii genomes available in the National Center for Biotechnology Information (NCBI) provides a base platform to investigate in detail the molecular mechanism of A. veronii biology and virulence. Lastly, we constructed deletion mutants vAhΔsia, vAhΔent, vAhΔcol, vAhΔhfq1, vAhΔhfq2, and vAhΔhfq1Δhfq2 to determine roles of A. hydrophila secreted proteins and regulatory proteins on virulence in catfish. Results showed that sialidase (vAhΔsia) and enterotoxin (vAhΔent) mutants were significantly attenuated.

Multi -omics data analysis and integration facilitates hypothesis building toward an understanding of genes and pathway responses driven by environments. Methods designed to estimate and analyze gene expression, with regard to treatments or conditions, can be leveraged to understand gene-level responses in the cell. However, genes often interact and signal within larger structures such as pathways and networks. Complex studies guided toward describing dynamic genetic pathways and networks require algorithms or methods designed for inference based on gene interactions and related topologies. Classes of algorithms and methods may be integrated into generalized workflows for comparative genomics studies, as multi -omics data can be standardized between contact points in various software applications. Further, network inference or network comparison algorithmic designs may involve interchangeable operations given the structure of their implementations. Network comparison and inference methods can also guide transfer-of-knowledge between model organisms and those with less knowledge base.

tRNA genes are highly transcribed and perform one of the most fundamental cellular functions. Although a universal pattern observed across all three domains of life is that highly transcribed genes tend to evolve slowly, tRNA genes have been shown previously to evolve rapidly. This rapid sequence evolution could result from relaxed selection, increased mutation rate, or a combination of both. Here, we use mutation-accumulation line sequencing data to show that tRNA genes accumulate more mutations than other gene types. Our results indicate that this elevated mutation rate is a consequence of both elevated transcription-associated mutagenesis and a lack of transcription-coupled repair in tRNA genes. We also identify the gene MSH2 as being involved in transcription-coupled repair.

The complete genomic sequence of Rhizobium leguminosarum ATCC 14479 has been determined. Its genome size is 7,935,223 base-pairs of DNA (bp). This multipartite genome contains 5 distinct replicons: a chromosome of 4,883,137 bp and four mega-plasmids of size 1,234,209 bp, 415,988 bp, 771,583 bp, and 630,306 bp. In silico (literally: on computer) analysis was done on the complete genome to detect genes relating to iron metabolism by bacteria. Seven iron-related operons and genes were found: nodulation genes, the Tol operon, the hmuPSTUV operon, iron response regulator genes, the cycHJKL operon, genes for bacterial cyclic glucans, and vicibactin genes.