Yes / Aneuploidy is usually deleterious in multicellular organisms but appears to be tolerated and potentially beneficial in unicellular organisms, including pathogens. Leishmania, a major protozoan parasite, is emerging as a new model for aneuploidy, since in vitro-cultivated strains are highly aneuploid, with interstrain diversity and intrastrain mosaicism. The alternation of two life stages in different environments (extracellular promastigotes and intracellular amastigotes) offers a unique opportunity to study the impact of environment on aneuploidy and gene expression. We sequenced the whole genomes and transcriptomes of Leishmania donovani strains throughout their adaptation to in vivo conditions mimicking natural vertebrate and invertebrate host environments. The nucleotide sequences were almost unchanged within a strain, in contrast to highly variable aneuploidy. Although high in promastigotes in vitro, aneuploidy dropped significantly in hamster amastigotes, in a progressive and strain-specific manner, accompanied by the emergence of new polysomies. After a passage through a sand fly, smaller yet consistent karyotype changes were detected. Changes in chromosome copy numbers were correlated with the corresponding transcript levels, but additional aneuploidy-independent regulation of gene expression was observed. This affected stage-specific gene expression, downregulation of the entire chromosome 31, and upregulation of gene arrays on chromosomes 5 and 8. Aneuploidy changes in Leishmania are probably adaptive and exploited to modulate the dosage and expression of specific genes; they are well tolerated, but additional mechanisms may exist to regulate the transcript levels of other genes located on aneuploid chromosomes. Our model should allow studies of the impact of aneuploidy on molecular adaptations and cellular fitness. / This study was supported by Belgian Science Policy Office (TRIT, P7/41), Flemish Fund for Scientific Research (G.0.B81.12), and Department of Economy, Science and Innovation in Flanders ITM-SOFIB (SINGLE project, to J.C.D.). G.D. and B.C. were supported by the Research Foundation—Flanders (FWO) (grants 12Q8115N and 11O1614N, respectively). V.S., J.M. and P.V. were supported by Czech Science Foundation (project no. 13-07500S) and Charles University (UNCE 204017/2012). J.R.V. was supported by research grants from the KU Leuven (SymBioSys [PFV/10/016]) and the Hercules Foundation (ZW11-14). M.S., M.B., and J.A.C. were supported by the Wellcome Trust through the core support for the Wellcome Trust Sanger Institute (grant no. 098051). G.B., P.P., and G.F.S. were supported by Institut Pasteur strategic fund for the LeiSHield project (to G.F.S.).

Yes / There are more than 200 published species within the Lactobacillus genus complex (LGC), the majority of which have sequenced type strain genomes available. Although genome-based species delimitation cutoffs are accepted as the gold standard by the community, these are seldom actually checked for new or already published species. In addition, the availability of genome data is revealing inconsistencies in the species-level classification of many strains. We constructed a de novo species taxonomy for the LGC based on 2,459 publicly available genomes, using a 94% core nucleotide identity cutoff. We reconciled these de novo species with published species and subspecies names by (i) identifying genomes of type strains and (ii) comparing 16S rRNA genes of the genomes with 16S rRNA genes of type strains. We found that genomes within the LGC could be divided into 239 de novo species that were discontinuous and exclusive. Comparison of these de novo species to published species led to the identification of nine sets of published species that can be merged and one species that can be split. Further, we found at least eight de novo species that constitute new, unpublished species. Finally, we reclassified 74 genomes on the species level and identified for the first time the species of 98 genomes. Overall, the current state of LGC species taxonomy is largely consistent with genome-based species delimitation cutoffs. There are, however, exceptions that should be resolved to evolve toward a taxonomy where species share a consistent diversity in terms of sequence divergence. / This study was supported by the Research Foundation Flanders (grant 11A0618N), the Flanders Innovation and Entrepreneurship Agency (grants IWT-SB 141198 and IWT/50052), and the University of Antwerp (grant FFB150344).

In the past decade it has become increasingly clear that a biological response is rarely caused by a single gene or protein. Rather, it is a result of a myriad of biological factors, constituting a systematic network of biological variables that span multiple granularities of biology from gene transcription to cell metabolism. Therefore it has become a significant challenge in the field of bioinformatics to integrate different levels of biology and to think of biological problems from a network perspective. In my thesis, I will discuss three projects that address this challenge. First, I will introduce two novel methods that integrate quantitative and qualitative biological data in a network approach. My aim in chapters two and three is to combine high-throughput data with biological databases to identify the causal mechanisms of action (MoA), in the form of canonical biological pathways, underlying the data for a given phenotype. In the second chapter, I will introduce an algorithm called Latent Pathway Identification Analysis (LPIA). This algorithm looks for statistically significant evidence of dysregulation in a network of pathways constructed in a manner that explicitly links pathways through their common function in the cell. In chapter three, I will introduce a new method that focuses on the identification of perturbed pathways from high-throughput gene expression data, which we approach as a task in statistical modeling and inference. We develop a two-level statistical model, where (i) the first level captures the relationship between high-throughput gene expression and biological pathways, and (ii) the second level models the behavior within an underlying network of pathways induced by an unknown perturbation. In the fourth chapter, I will focus on the integration of high throughput data on two distinct levels of biology to elucidate associations and causal relationships amongst genotype, gene expression and glycemic traits relevant to Type 2 Diabetes. I use the Framingham heart study as well as its extension, the SABRe initiative, to identify genes whose expression may be causally linked to fasting glucose.

Marine organisms occupy environments spanning wide distributions of conditions across large (e.g., latitudinal gradients) and small (e.g., different depths) scales. Populations that exist across these environments might be adapted to local conditions and exhibit genetic divergence between habitats, sometimes to the point of becoming different species or lineages within a species complex. Corals are excellent organisms in which to study dynamics across large geographic ranges spanning divergent environments. They not only contain many species rich genera and exhibit local adaptation and long-range dispersal potential, but they are also the structural engineers of coral reef ecosystems that are facing serious threat from warming oceans, acidification, and other anthropogenic disturbances. Thus, investigating mechanisms of adaptation to environmental conditions in corals is critical because these processes also secondarily impact many reef-dependent marine organisms. My dissertation investigates population genomic variation across different ecological (latitudinal, local and within colony gradients) and evolutionary (populations and species) scales. First, I obtained samples of the ubiquitous pacific reef-building coral Acropora hyacinthus from its subtropical habitat in the Ryukyus Islands and temperate habitat in mainland Japan and uncovered the presence of three cryptic lineages in the region. Of these three, only one exists in temperate environments and this lineage has also recently expanded its range even further north along the coast of mainland Japan with warming oceans. I found genetic structure separating the recently expanded site and the other northernmost edge sites from core temperate sites. This divergence existed despite a model of larval dispersal suggesting higher connectivity of marginal and core sites relative to pairs of marginal sites. These findings suggest that cryptic lineages evolved to occupy different niches along a latitudinal gradient and that range expansion has been facilitated by adaptions to higher latitudes. Second, I investigated the role of the coral’s algal symbiont and bacterial communities in adaptation across smaller spatial scales by characterizing these communities in the massive scleractinian coral Porites lobata across a sedimentation gradient and across individual colonies in Guam. I found that both algal and bacterial communities varied within a single colony, but only bacteria showed clear structuring by colony position and only rare bacterial taxa were structured by the sedimentation gradient. Lastly, I investigated the contributions of host and symbiont to thermal adaptation in the facultatively symbiotic corals Astrangia and Oculina. I uncovered the existence of four genetic lineages of coral, two within each genus, with inter-lineage differences in distributions, thermal performance, and symbiotic partnerships. I also found evidence for shared genetic variation between Oculina and Astrangia when they exist sympatrically, suggesting the potential for adaptive introgression between these lineages. The findings of this dissertation shed light on the complex and dynamic nature of coral populations, highlighting the importance of considering multiple spatial scales and levels of evolutionary divergence when studying adaptation in marine organisms. Overall, this dissertation advances our understanding of the population genomics of corals and the ecological and evolutionary processes that shape their adaptation to diverse environments.

<p dir="ltr">Nitrogen (N) is a macronutrient required for plant growth and is a major constituent of nucleic acids and proteins that are essential for several life processes. Plant response to N has been well understood at a molecular level but little is known about the chromatin or epigenetic level regulation of N response. Uncovering the epigenetic level regulation essential for plant N signaling and response is essential to improving our molecular understanding of N use efficiency (NUE). To fill this knowledge gap, we first performed a meta-analysis intersecting the published transcriptomic study of N-responsive genes in <i>Arabidopsis thaliana </i>with EpiNet, an extensive epigenetic regulatory network previously constructed in our lab through machine learning approaches, to identify a list of 18 potential epigenetic regulators that are predicted to control N response in plants. Next, by adopting a reverse genetics approach, we aimed to validate the <i>in-silico</i> prediction of these essential epigenetic regulators. To do this, we grew T-DNA insertional mutants for the genes encoding these epigenetic regulators, along with wild-type controls, under high and low N conditions, and compared them in various physiological traits. Our results indicate that 8 out of 10 confirmed knock-down mutants do show altered N-responsive phenotypes in comparison to the wild type. One of the mutants, <i>ashr2-1, </i>which is mutated in a gene encoding a putative SET-domain containing group protein (SDG) of putative histone methyltransferase, displayed reduced growth of primary root compared to WT in response to N. We performed RNA-sequencing to identify the differentially expressed genes that are induced or repressed by ASHR2 in N treatments to gain further insight into the molecular underpinnings of the ASHR2-mdediated N response in roots<i>.</i> In summary, our study has revealed knowledge on important epigenetic regulators in plant N responses, which has the potential to be extended to crop species as novel targets for enhancing NUE.</p>

This PhD seeks to explore the development of a bio-molecular (i.e., genomic) map as a sovereign resource in Mexico. The basic analytical thread of the dissertation is related to the circulation of genomic variability through the policy/legal and scientific social worlds that compose the Mexican medical-population genomics arena. It follows the construction of the Mexican Institute of Genomic Medicine (INMEGEN), the notion of genomic sovereignty, and the Mexican Genome Diversity Project (MGDP).The key argument for the construction of the INMEGEN relied in a nationalist policy framing, which considered the Mexican genome as a sovereign resource, coupling Mexican “uniqueness” to the very nature of genomic science. Nevertheless, the notion of genomic sovereignty was nothing similar to a paradigm, and was not based on shared visions of causality, since the very “nature” of the policy object —Mexican Genome— was, and still is, a disputed reality. It was through the rhetoric upon independence, emancipation and biopiracy: i.e. experiences of dispossession “in archaeology, botany or zoology” (IFS 2001: 25) that the novelty of population genomics became amenable to be understood as a sovereign matter. Therefore, the strategic reification of Mexicanhood fuelled the whole policy and the legal agenda of the INMEGEN as well, which permitted cooperation without consensus and opened the process of policy innovation. Conversely, scientists considered genomic sovereignty an unfounded exaggeration, but anyhow they cooperated and even created a new policy and scientific enterprise. Genomic sovereignty exemplifies the process of cooperation without consensus on its most extreme version .So, as the notion circulated and gradually became a law to protect Mexican genomic patrimony, the initial coalition of scientists, lawyers and policy makers disaggregated. Many of the original members of the coalition now think of genomic sovereignty as a strategy of the INMEGEN to monopolise genomic research in the country. This dissertation additionally explores the way in which the MGDP is constructed in mass media, in INMEGEN´s communication and in the laboratory practices. These different dimensions of the MGDP depict the difficulties that emerge between the probabilistic, relative and multiple constructions of population genomics and the rhetorical strategies to continually assert the existence of the unique “Mexican Genome”. I argue that the Mexican case study provides an entry point to what I and others (Benjamin 2009; Schwartz-Marin 2011) have identified as a postcolonial biopolitics in which the nation state is reasserted rather than diluted. However the relation between sovereignty, race and nation is not mediated by the biological purification of the nation (Agamben 1998; Foucault 2007), or the active participation of citizens looking to increase their vitality (Rose 2008, Rose & Rabinow 2006), but on an awareness of subalternity in the genomic arena and a collective desire to compete in the biomedical global economy.

In recent years, the development of new genomic technologies has allowed for the investigation of many regulatory epigenetic marks besides expression levels, on a genome-wide scale. As the price for these technologies continues to decrease, study sizes will not only increase, but several different assays are beginning to be used for the same samples. It is therefore desirable to develop statistical methods to integrate multiple data types that can handle the increased computational burden of incorporating large data sets. Furthermore, it is important to develop sound quality control and normalization methods as technical errors can compound when integrating multiple genomic assays. DNA methylation is a commonly studied epigenetic mark, and the Infinium HumanMethylation450 BeadChip has become a popular microarray that provides genome-wide coverage and is affordable enough to scale to larger study sizes. It employs a complex array design that has complicated efforts to develop normalization methods. We propose a novel normalization method that uses a set of stable methylation sites from housekeeping genes as empirical controls to fit a local regression hypersurface to signal intensities. We demonstrate that our method performs favorably compared to other popular methods for the array. We also discuss an approach to estimating cell-type admixtures, which is a frequent biological confound in these studies. For data integration we propose a gene-centric procedure that uses canonical correlation and subsequent permutation testing to examine correlation or other measures of association and co-localization of epigenetic marks on the genome. Specifically, a likelihood ratio test for general association between data modalities is performed after an initial dimension reduction step. Canonical scores are then regressed against covariates of interest using linear mixed effects models. Lastly, permutation testing is performed on weighted correlation matrices to test for co-localization of relationships to physical locations in the genome. We demonstrate these methods on a set of developmental brain samples from the BrainSpan consortium and find substantial relationships between DNA methylation, gene expression, and alternative promoter usage primarily in genes related to axon guidance. We perform a second integrative analysis on another set of brain samples from the Stanley Medical Research Institute.

The homeobox superfamily is one of the most significant gene families in the evolution of developmental processes in animals. Within this superfamily the ANTP class has expanded exclusively in animals and, therefore, the reconstruction of its origin and diversification into the different ‘modern' families have become prominent questions in the ‘evo-devo' field. The current burgeoning availability of animal genome sequences is improving the resolution of these questions, putting them in a genome evolution context, as well as providing the field with a large, detailed and diverse catalogue of animal homeobox complements. Here I have contributed with a new hypothesis on the origin and evolution of the Hox and ParaHox loci and the new term, ghost loci, referring to homologous genome regions that have lost their homeobox genes. This hypothesis proposes that the last common ancestor of all animals had a much more complex genome (i.e. differentiated Hox, ParaHox and NK loci) that underwent a simplification in the early animal lineages of sponges and placozoans. In collaboration with the Adamska group I resolved the orthology of the first ever ParaHox genes reported in calcareous sponges. This finding serves as an independent confirmation of the ghost loci hypothesis and further resolves the events of secondary simplification within the sponge lineage. Finally, I have catalogued the homeobox complement of the newly sequenced arthropod, the myriapod Strigamia maritima, and examined the linkage and clustering of these genes. This has furthered our understanding of the evolution of the ANTP class. The diversity of the homeobox complement and the retention in this myriapod and the retention of some homeobox genes not previously described within arthropods, in combination with the interesting phylogenetic position that this lineage occupies relative to other arthropods, makes this complement an important point of reference for comparison within the arthropods and in a broader perspective in the ecdyzosoans. These findings have provided significant further insights into the origin and evolution of the homeobox superfamily, with important implications for animal evolution and the evolution of development.

Le genre Rickettsia, sont des petites bactéries Gram-négatives et symbiotes intracellulaires obligatoires des eucaryotes. Les Rickettsia sont surtout connus pour leur pathogénicité et pour provoquer des maladies graves chez l'homme et les autres animaux. À ce jour, 26 espèces valides de Rickettsies ont été identifiées dans le monde entier, dont 20 sont des agents pathogènes éprouvées. Toutes les espèces de Rickettsies validées sont associées à des arthropodes. Les phylogénies basées sur divers marqueurs moléculaires ont présenté des topologies discordantes, avec seulement R. bellii et R. canadensis qui ne sont classées ni parmi la fièvre boutonneuse groupe rickettsies, ni parmi le typhus groupe rickettsies. En utilisant les méthodes avancées de séquençage de génomes entiers, nous avons obtenu et analysé quatre séquences génomiques de Rickettsies : R. helvetica, R. honei, R. australis et R. japonica. Via la phylogénomique qui constitue une nouvelle stratégie permettant de mieux comprendre leur évolution, l'on remarque que ces micro-organismes ont subi une évolution génomique réduite au cours de spécialisation en intracellulaire. Plusieurs caractéristiques évolutives, comme le réarrangement des gènes, la réduction génomique, le transfert horizontal de gènes et l'acquisition d'ADN égoïste, ont formé les génomes Rickettsia d'aujourd'hui. Ces processus peuvent jouer un rôle important pour équilibrer la taille du génome afin de l'adapter au mode de vie intracellulaire. En outre, la pathogénicité des rickettsies peut être associée à la réduction génomique. / The Rickettsia genus is composed of small, Gram-negative, bacteria that are obligate intracellular eukaryotic symbionts. Members of the genus Rickettsia are best known for infecting and causing severe diseases in humans and other animals. To date, 26 valid Rickettsia species have been identified worldwide, including 20 that are proven pathogens. All validated Rickettsia species are associated to arthropods that act as vectors and/or reservoirs. The phylogenies based on various molecular markers have resulted in discrepant topologies, with R. bellii and R. canadensis being classified neither among spotted fever nor typhus group rickettsiae. In this thesis, using the advanced whole genomic sequencing methods, we have and analyzed the genomic sequences from four Rickettsia species, including R. helvetica, R. honei, R. australis and R. japonica. Phylogenomics constitute a new strategy to better understand their evolution. These microorganisms underwent a reductive genomic evolution during their specialization to their intracellular lifestyle. Several evolutive characteristics, such as gene rearrangement, reduction, horizontal gene transfer and aquisition of selfish DNA, have shaped Rickettsia genomes. These processes may play an important role in free-living bacteria for balancing the size of genome in order to adapt the intracellular life style. In addition, in contrast with the concept of bacteria becoming pathogens by acquisition of virulence factors, rickettsial pathogenecity may be linked to genomic reduction of metabolism and regulation pathways.

A major challenge to evolutionary developmental biology is to understand the how modifications to gene regulatory networks can lead to biological diversity. Heliconius butterfly wing patterns provide an excellent example of this diversity. In particular, the species H. melpomene and H. erato display wide variation in wing pattern across their ranges in Central and South America, but wherever they co-occur, they have converged on remarkably similar wing patterns due to Müllerian mimicry. Linkage analysis of wing pattern genes has shown that in both species, there are three genomic loci that are responsible for most of the pattern variation, and that these loci are homologous. One locus, containing the transcription factor optix, is responsible for red pattern elements. A set of non-coding sequences linked to some of the red pattern elements have been identified. Another locus, containing the gene WntA, has been linked to the shape of the forewing band elements and is responsible for variation in wing pattern development in several species of lepidoptera. A third locus, responsible for yellow pattern elements, contains multiple candidate genes that may affect wing pattern development, including the gene cortex, which is also linked to the industrial melanism phenotype in the moth Biston betularia, as well as the genes domeless and washout, linked to the Bigeye mutant in Bicyclus anynana. I first investigated modifications to regulatory sequence near the transcription factor optix, detecting a module associated with the band pattern element. I also found that for some pattern regulatory modules at optix, the same sequence has independently evolved the same function in H. melpomene and H. erato, in association with non-coding sequences conserved throughout the Lepidoptera. I then investigated gene expression differences in two morphs from either side of a hybrid zone that vary only in the presence or absence of a yellow pattern element, in order to determine a role for candidate genes at the yellow pattern locus. In H. melpomene the gene cortex was upregulated in the larval wing discs of the black morph, whereas in H. erato it was upregulated in the larval wing discs of the yellow morph. In pupal wings, washout was differentially expressed, again in the opposite pattern in the two species, suggesting the same locus is responsible for convergent pattern modification, but by a different mechanism. Finally, I investigated the spatial transcriptomic landscape across the wings of three different heliconiine butterflies. I identified candidate factors for regulating the expression of wing patterning genes, including genes with a conserved expression profile in all three species, and others, including genes in the Wnt pathway, with markedly different profiles in each of the three species. Each of these studies contributes to our understanding of how gene regulatory networks can be modified to create diversity: first, at the level of cis-regulation, second at the level of gene interaction and expression, and lastly at the level of developmental bias and constraint.