Microsatellites are strings of short DNA motifs (≤6 bp) repeated in tandem across genomes of both prokaryotes and eukaryotes. In 20 years, they became popular genetic markers, successfully employed in the field of genetic mapping and gene hunting, as well as to address various biological questions at the individual, family, population and species level. However, evolutionary and demographic inferences from microsatellite polymorphism are hampered by controversy and ambiguity in the mutational processes of microsatellite sequences. Drawing on new data from genome projects, I review in Chapter 1 the concept of a microsatellite life cycle, which hypothesizes that microsatellites follow a life cycle from birth, through expansion, contraction, death and potentially resurrection. To document and understand this integrative concept of evolution, which could help improve current models of microsatellite evolution, there is an implicit need to study the evolution of microsatellites above the species level. A prerequisite of such comparative studies is therefore to find microsatellite loci that are conserved between different species. The near or full completion of many vertebrate genomes and their alignment against one another offer the ultimate approach to find genomic elements conserved over a large evolutionary scale. In Chapter 2, I present a new comprehensive method to find conserved microsatellites in whole genomes. Using the multiple-alignment of the human genome against those of 11 mammalian and five non-mammalian vertebrates, I examine the genomewide conservation of microsatellites, and challenge the general assumption that microsatellites are too labile to be maintained in distant species. In Chapter 3, I present similar results using the alignment of the newly sequenced platypus genome against those of three mammals, the chicken and the lizard, and incorporate these data into the framework created by the 17-genome analysis. This enlarged dataset was ground for attempting to reconstruct a vertebrate phylogeny from the presence/absence of microsatellites in the different genomes. Maximum parsimony analyses resulted in a tree much similar to that of the current view of the vertebrate phylogeny, while Bayesian analyses showed some discrepancies. This work opens a way for novel theoretical developments regarding the inference of ancestral states of microsatellites. In Chapter 4, I show how knowledge on conserved microsatellite sites can help for the development of a set of comparative primers useful across the Mammalia; implementing a similar protocol, nine conserved dinucleotide repeats were genotyped in 20 unrelated individuals of 18 species (nine sister species) encompassing the mammalian phylogeny, including marsupials and monotremes, and four microsatellites were sequenced in 4 individuals per species. My results emphasize conserved microsatellites as a new resource for genetic mapping and population studies. Finally, in Chapter 5, I recount the unexpected extent of structural change among mammalian orthologous microsatellites, including change of complexity, motif replacement and overall length variability. Altogether, these findings provide a comprehensive framework that may help in many areas of research, including molecular ecology, genome mapping, population genetics, and genome and microsatellite evolution.

Master of Science / Genetics Interdepartmental Program / Sanzhen Liu / The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Genotype specific 45S rDNA sequences were discovered. The B73 and Mo17 polymorphic k-mers were used to examine allele-specific expression of 45S rDNA in the hybrids. Although Mo17 contains higher copy number than B73, equivalent levels of overall 45S rDNA expression indicates that transcriptional or post-transcriptional regulation mechanisms operate for the 45S rDNA in the hybrids. Using WGS sequences of B73xMo17 doubled haploids, genomic locations showing differential repetitive contents were genetically mapped, revealing differences in organization of highly repetitive sequences between the two genomes. In an analysis of WGS sequences of HapMap2 lines, including maize wild progenitor, landraces, and improved lines, decreases and increases in abundance of additional sets of k-mers associated with centromere, 45S rDNA, knob, and retrotransposons were found among groups, revealing global evolutionary trends of genomic repeats during maize domestication and improvement.

Small nucleolar RNAs (snoRNAs) are one of the most abundant and evolutionary ancient group of small non-coding RNAs. Their main function is to target chemical modifications of ribosomal RNAs (rRNAs) and small nuclear (snRNAs). They fall into two classes, box C/D snoRNAs and box H/ACA snoRNAs, which are clearly distinguished by conserved sequence motifs and the type of modification that they govern. The box H/ACA snoRNAs are responsible for targeting pseudouridylation sites and the box C/D snoRNAs for directing 2’-O-methylation of ribonucleotides. A subclass that localize to the Cajal bodies, termed scaRNAs, are responsible for methylation and pseudouridylation of snRNAs. In addition an amazing diversity of non-canonical functions of individual snoRNAs arose. The modification patterns in rRNAs and snRNAs are retained during evolution making it even possible to project them from yeast onto human. The stringent conservation of modification sites and the slow evolution of rRNAs and snRNAs contradicts the rapid evolution of snoRNA sequences. Recent studies that incorporate high-throughput sequencing experiments still identify undetected snoRNAs even in well studied organisms as human. The snoRNAbase, which has been the standard database for human snoRNAs has not been updated ince 2006 and misses these new data. Along with the lack of a centralized data collection across species, which incorporates also snoRNA class specific characteristics the need to integrate distributed data from literature and databases into a comprehensive snoRNA set arose. Although several snoRNA studies included pro forma target predictions in individual species and more and more studies focus on non-canonical functions of subclasses a systematic survey on the guiding function and especially functional homologies of snoRNAs was not available. To establish a sound set of snoRNAs a computational snoRNA annotation pipeline, named snoStrip that identifies homologous snoRNAs in related species was employed. For large scale investigation of the snoRNA function, state-of-the-art target pedictions were performed with our software RNAsnoop and PLEXY. Further, a new measure the Interaction Conservation Index (ICI) was developed to evaluate the conservation of snoRNA function. The snoStrip pipeline was applied to vertebrate species, where the genome sequence has been available. In addition, it was used in several ncRNA annotation studies (48 avian, spotted gar) of newly assembled genomes to contribute the snoRNA genes. Detailed target analysis of the new vertebrate snoRNA set revealed that in general functions of homologous snoRNAs are evolutionarily stable, thus, members of the same snoRNA family guide equivalent modifications. The conservation of snoRNA sequences is high at target binding regions while the remaining sequence varies significantly. In addition to elucidating principles of correlated evolution it was possible, with the help of the ICI measure, to assign functions to previously orphan snoRNAs and to associate snoRNAs as partners to known but so far unexplained chemical modifications. As further pattern redundant guiding became apparent. For many modification sites more than one snoRNA encodes the appropriate antisense element (ASE), which could ensure constant modification through snoRNAs that have different expression patterns. Furthermore, predictions of snoRNA functions in conjunction with sequence conservation could identify distant homologies. Due to the high overall entropy of snoRNA sequences, such relationships are hard to detect by means of sequence homology search methods alone. The snoRNA interaction network was further expanded through novel snoRNAs that were detected in data from high-throughput experiments in human and mouse. Through subsequent target analysis the new snoRNAs could immediately explain known modifications that had no appropriate snoRNA guide assigned before. In a further study a full catalog of expressed snoRNAs in human was provided. Beside canonical snoRNAs also recent findings like AluACAs, sno-lncRNAs and extraordinary short SNORD-like transcripts were taken into account. Again the target analysis workflow identified undetected connections between snoRNA guides and modifications. Especially some species/clade specific interactions of SNORD-like genes emerged that seem to act as bona fide snoRNA guides for rRNA and snRNA modifications. For all high confident new snoRNA genes identified during this work official gene names were requested from the HUGO Gene Nomenclature Committee (HGNC) avoiding further naming confusion.

L'augmentation du nombre de génomes totalement séquencés rend de plus en plus efficace l'étude des mécanismes évolutifs à partir de la comparaison de génomes contemporains. L'un des principaux problèmes réside dans la reconstruction d'architectures de génomes ancestraux plausibles afin d'apporter des hypothèses à la fois sur l'histoire des génomes existants et sur les mécanismes de leur formation. Toutes les méthodes de reconstruction ancestrale ne convergent pas nécessairement vers les mêmes résultats mais sont toutes basées sur les trois mêmes étapes : l'identification des marqueurs communs dans les génomes contemporains, la construction de cartes comparatives des génomes, et la réconciliation de ces cartes en utilisant le critère de parcimonie maximum. La qualité importante des données à analyser nécessite l'automatisation des traitements et résoudre ces problèmes représente de formidables challenges computationnels. Affiner le modèles et outils mathématiques existants par l'ajout de contraintes biologiques fortes rend les hypothèses établies biologiquement plus réalistes. Dans cette thèse, nous proposons une nouvelle méthode permettant d'identifier des marqueurs communs pour des espèces évolutivement distantes. Ensuite, nous appliquons sur les cartes comparatives reconstituées une nouvelle méthode pour la reconstruction d'architectures ancestrales basée sur les adjacences entre les marqueurs calculés et les distances génomiques entre les génomes contemporains. Enfin, après avoir corrigé l'algorithme existant permettant de déterminer une séquence optimale de réarrangements qui se sont produits durant l'évolution des génomes existants depuis leur ancêtre commun, nous proposons un nouvel outil appelé VIRAGE qui permet la visualisation animée des scénarios de réarrangements entre les espèces / Abstract

Yarrowia lipolytica appartient à un groupe de levures qui a divergé très tôt dans l'arbre des hémiascomycètes. Cette levure est capable d'utiliser, comme seule source de carbone, des substrats hydrophobes très variés et est capable de synthétiser de nouveaux acides gras libres à partir de composés non hydrophobes. Ces caractéristiques font de Y. lipolytica un modèle de levure hémiascomycète pour l'étude du métabolisme des lipides. Sa capacité oléagineuse est facilitée par l'expansion de familles de protéines ayant eu lieu au cours de l'évolution après la divergence du clade Yarrowia. En effet, parmi les 204 gènes impliqués dans le métabolisme des lipides dans Y. lipolytica, plus de 67% sont regroupés dans 30 familles multigéniques avec un maximum de 16 membres pour la famille de la lipase. Le récent séquençage de génomes 5 dans le clade Yarrowia a permis de comparer leur contenu génétique. L'étude des familles de gènes du métabolisme des lipides a permis de mettre en évidence les mécanismes impliqués dans l'évolution de ce clade. Toutes les fonctions nécessaires pour le métabolisme des lipides sont présentes dans toutes les espèces étudiées, avec au moins un gène par famille, même pour les espèces qui ont de 500 à 1000 moins de gènes que Y. lipolytica. Ces espèces se sont d'ailleurs révélées être toutes oléagineuses, grâce à des études physiologiques. Les familles de gènes observées proviennent de multiples duplications de gènes dont chaque exemplaire évolue indépendamment par différents processus de sub- ou neofonctionalisations, fixations, pseudogénisations ou pertes. Les contractions et expansions de familles de protéines, l'expression des gènes, la synténie et la localisation relative des gènes dans le génome ont été étudiés. Plus particulièrement, la pression de sélection agissant sur ces familles de gènes a été comparée à celles agissant sur le reste du génome. La combinaison de ces approches, physiologie, génomique et transcriptomique, a permis d'améliorer la compréhension du métabolisme lipidique, de son évolution et de la régulation des gènes dans un clade des levures oléagineuses. / Yarrowia lipolytica belongs to a group of yeasts that have diverged very early from most other hemiascomycetous yeasts. This yeast is able to use various hydrophobic substrates as unique carbon source and to synthesize new free fatty acid from non hydrophobic compounds. These characteristics make Y. lipolytica a known oleaginous model for the lipid metabolism survey of yeasts. Its oleaginous capacity is facilitated by protein family expansions that occurred across evolution after the divergence of the Yarrowia clade. Indeed, among 190 genes involved in the lipid metabolism in Y. lipolytica, more than 67% are grouped into 30 multigenic families with up to 16 members in the lipase family. The recent sequencing of 5 genomes within the Yarrowia clade enabled to compare their gene content. The study of gene families of the lipid metabolism allowed to highlight the evolutionary mechanisms involved in this clade. All the functions necessary to lipid metabolism are present in all species studied with at least one gene per family even for species that have 500 to 1,000 fewer genes than Y. lipolytica. These species are also found to be all oleaginous through physiological studies. The observed gene families derive from multiple gene duplications of which each copy evolves independently by different processes of sub- or neofunctionalisation, fixation, pseudogenization or loss. Contractions and expansions of protein families, gene expression, synteny and relative localisation of genes in the genome were investigated. More particularly, the selection pressure acting on these gene families was compared with those acting on the rest of the genome. The combination of these approaches, physiology, genomics and transcriptomics, has improved the comprehension of the lipid metabolism, its evolution and gene regulation within a clade of oleaginous yeasts.

Since the dawn of agriculture man has been genetically modifying crop plants to increase yield, quality and utility. In addition to selective breeding and hybridization we can utilize mutant populations and biotechnology to have greater control over crop plant modification than ever before. Increasing the production of plant oils such as soybean oil as a renewable resource for food and fuel is valuable. Successful breeding for higher oil levels in soybean, however, usually results in reduced protein, a second valuable seed component. We show that by manipulating a highly active acyl-CoA: diacylglycerol acyltransferase (DGAT) the hydrocarbon flux to oil in oilseeds can be increased without reducing the protein component. Compared to other plant DGATs, a DGAT from Vernonia galamensis (VgDGAT1A) produces much higher oil synthesis and accumulation activity in yeast, insect cells and soybean. Soybean lines expressing VgDGAT1A show a 4% increase in oil content without reductions in seed protein contents or yield per unit land area. Furthermore, we have screened a soybean fast neutrino population derived from M92-220 variety and found three high oil mutants that do not have reduced levels of protein. From the F2 plant populations we quantitatively pooled the high oil and low oil plants and performed comparative genomics hybridization (CGH). From the data it appears that two families have a 0.3 kb aberration in chromosome 14. We are performing further analysis to study this aberration and develop markers for molecular breeding. Mutagenic techniques are also useful for developing other traits such as early flowering varieties and adapting new high oil crops to a new region. Chia (Salvia hispanica) is an ancient crop that has experienced an agricultural resurgence in recent decades due to the high omega 3 fatty acid (ω-3) content of the seeds and good production potential. The area of cultivation has been expanded to Kentucky using mutagenized populations and the composition traits are similar to that of the original regions of cultivation in Central and South America.

Le genre Mucor appartient au phylum des Mucoromycota, un groupe issu de l’une des lignées ayant divergé très tôt dans l'évolution des espèces fongiques (early diverging lineages). Ces groupes restent encore très peu connus par rapport aux Ascomycètes et Basidiomycètes. Le genre Mucor est un genre d'espèces saprophytes, avec cependant une certaine diversité au niveau du mode de vie. Il existe en effet au sein du genre, des endophytes de plantes (comme M. endophyticus) ou encore des pathogènes opportunistes d'animaux (comme les espèces thermophiles M. circinelloides ou M. indicus). Le genre est ubiquiste mais il existe des associations à certains habitats qui semblent dénoter une certaine spécialisation. L’objectif de cette thèse était de mieux connaître les potentialités génétiques du genre Mucor lui permettant ce mode de vie ubiquiste, son potentiel d'adaptation mais également de mieux comprendre l'existence au sein du genre d'espèces semblant s'être spécialisées en colonisant préférentiellement ou exclusivement certains habitats comme le fromage. Afin d'atteindre cet objectif des études transcriptomiques et génomiques comparées ont été menées dans le cadre de cette thèse, afin de déterminer les principales caractéristiques des génomes de Mucor aussi bien structurelles que fonctionnelles, identifier les similitudes au niveau des espèces étudiées et aussi leur spécificités et en fonction des modes de vie/habitats et déterminer s'il existe chez les espèces fréquemment rencontrées dans les fromages (et notamment pour celles considérées comme technologiques) des traces d'adaptation voire de domestication. / The genus Mucor belongs to the phylum Mucoromycota; a group that derived from the lineages that diverged early in the evolution of fungal species (early diverging lineages). These groups have been less well studied and are less well understood in comparison to Ascomycetes and Basidiomycetes. The genus Mucor is composed of saprophytic species, but also encompasses species with diverse lifestyles.For example, it includes plant endophytes (such as M. endophyticus) or opportunistic animal pathogens (such as the thermophilic species M. circinelloides or M. indicus). The genus is ubiquitous but there are some associations with specific habitats which seem to indicate specialisation. The aim of this thesis is to better understand the genetic potential of the genus Mucor in particular, to decipher how it maintains this ubiquitous lifestyle, its capacity to adapt to diverses habitats and to better understand the existence within the genus of species that may have undergone specialization allowing them to preferentially or exclusively colonise certain habitats, such as cheese. In order to achieve this, we have performed comparative transcriptomic and genomic studies in order to determine the main structural and functional characteristics of the Mucor genomes, identify similarities among the species studied and also assess whether there exist specific genetic associations with lifestyle/habitat and determine whether the species frequently found in cheese (in particular those species considered as technological) harbour imprints of adaptation or even domestication.

La brucellose est une zoonose causée par le genre bactérien Brucella (B.) dont l’incidence mondiale est estimée à 500 000 cas humains par an. Le réservoir est animal, touchant principalement les espèces de rente. Les espèces les plus importantes pour l’Homme sont B. melitensis, B. abortus et B. suis qui partagent plus de 90% d’identité de séquence. Bien qu’elles soient très apparentées sur le plan génétique, elles présentent une diversité de caractéristiques phénotypiques, de préférence d’hôte et de pathogénicité. L’homogénéité génétique de ces espèces peut apparaître comme un atout pour le développement d’outils de diagnostic universels robustes. En revanche, il s’agit d’un challenge pour les distinguer, rendant difficile la caractérisation précise des isolats issus d’un même foyer. Dans le cadre de cette thèse, un outil de diagnostic moléculaire de PCR en temps réel ciblant le genre Brucella a été développé et optimisé. L’outil a été évalué sur des prélèvements de lait de ruminants, ces prélèvements peuvent être une source importante de Brucella et peuvent être utiles au dépistage de la maladie à l’échelle du troupeau. Basée sur la détection de l’élément d’insertion IS711, une séquence présente en plusieurs exemplaires dans le génome, cette méthode affiche des valeurs de sensibilité et de spécificité qui la rendent intéressante pour un schéma global de lutte contre la brucellose. D’autre part, en vue d’améliorer la compréhension de la stabilité génétique de B. melitensis, un panel original de souches isolées dans le cadre d’un foyer et impliquant 4 espèces d’hôtes différentes a été comparé. Ainsi à l’aide de différentes approches complémentaires, leurs séquences génomiques, les caractères phénotypiques ainsi que leurs comportements dans un modèle in vitro ont été comparés. Nos résultats n’ont pas mis en évidence marqueurs qui laisserait à penser que des mutations dans le génome soient indispensables pour s’adapter à un nouvel hôte / Brucellosis is a zoonotic disease caused by the bacterial genus Brucella (B.), whose global incidence is estimated at 500,000 human cases per year. The reservoir is animal, affecting mainly livestock. The most important species for humans are B. melitensis, B. abortus and B. suis, which share more than 90% sequence identity. Although highly genetically related, Brucella spp. exhibit a variety of phenotypic characteristics, host preference and pathogenicity. The genetic homogeneity of these species may appear as an asset for the development of robust universal diagnostic tools. On the other hand, it is a challenge to distinguish them, making it difficult to precisely characterize isolates from the same outbreak. As part of this thesis, a real-time PCR molecular diagnostic tool targeting the genus Brucella was developed and optimized. The method has been evaluated on ruminant milk samples; these samples may be an important source of Brucella and may be useful for herd-scale disease screening. Based on the detection of the IS711 insertion element, a sequence present in several copies within the genome, this method displays sensitivity and specificity values that make it interesting for a global scheme to fight against brucellosis. On the other hand, in order to improve the understanding of the genetic stability of B. melitensis, an original panel of strains isolated in an outbreak and involving four different host species was compared. Thus, using different complementary approaches, their genomic sequences, phenotypic characteristics and their behavior in an in vitro model were compared. Our results did not highlight markers that would suggest that mutations in the genome are essential to adapt to a new host

Orientador: Maria Elisabete Jorge Amaral / Coorientador: Nedenia Bonvino Stafuzza / Banca: Vera Fernanda Martins Hossepian de Lima / Banca: Luciane Madureira de Almeida / Resumo: No presente estudo, cinco novos genes codificantes de proteínas foram selecionados para o mapeamento do cromossomo 6 bubalino (BBU6). Os novos genes (muc1, ppp1r7, psmd4, tshb e gtf2b) foram testados com a tecnologia de PCR resultando em produtos de PCR adequados ao mapeamento utilizando-se um painel de células somáticas híbridas irradiadas, denominado BBURH5000. Os resultados obtidos mostraram uma freqüência de retenção (FR) do produto de PCR de cada gene nas diferentes linhagens do painel com variação de 13,3% (gtf2b) a 26,6% (psmd4). A análise comparativa entre os mapas RH do BBU6 e a sequência do cromossomo 3 bovino permitiu indicar a localização dos novos genes no cromossomo 6 bubalino / Abstract: In this study, five new protein coding genes were select for mapping buffalo chromosome 6. The new genes (muc1, ppp1r7, psmd4, tshb and gtf2b) were tested using PCR technology resulting in PCR products suitable for mapping using a radiation hybrid panel (BBURH5000). The retention frequency of the PCR products in each hybrid cell line of the panel showed the percentage from 13,3% (gtf2b) to 26,6% (psmd4). Comparative analysis between the buffalo chromosome 6 RH map and the sequence from bovine chromosome 3 allowed to assign the location of the new genes on buffalo chromosome 6 / Mestre

Entre espèces, les génomes présentent des différences dans leur organisation, que ce soit au niveau du caryotype ou de l'ordre des gènes. Ceci reste vrai même entre espèces relativement proches comme l'humain et la souris, et est du aux réarrangements chromosomiques. Reconstruire l'histoire évolutive d'une lignée revient donc à déterminer des scénarios de réarrangements qui transforment un génome actuel en un autre. Le génome ancestral se trouve alors être l'un des états intermédiaires atteint par l'un de ces scénarios.Les réarrangements chromosomiques sont des évènements biologiques violents pour la cellule. En effet, de nombreux mécanismes moléculaires ont pour fonction de stopper le cycle cellulaire dans le cas où le génome aurait été altéré. De plus, les réarrangements peuvent être à l'origine de phénotypes aberrants, et donc probablement désavantageux pour leur porteur. Au vu de tout cela, il paraît raisonnable de poser l'hypothèse selon laquelle les scénarios de réarrangements sont parcimonieux.Cependant, il est admis que ce seul critère ne permet pas de reconstruire efficacement l'histoire évolutive des génomes. En effet, quelque soit le modèle utilisé pour générer les scénarios, leur nombre est exponentiel en le nombre de réarrangements. Une autre contrainte biologique doit donc être ajoutée. La conservation de la structure spatiale de la chromatine pourrait être un critère manquant essentiel. Il a été montré in vitro que lors d'une cassure double-brin suivie d'une réparation non-homologue, le brin utilisé pour la réparation se situe spatialement proche de la cassure. Notre hypothèse est donc que les points de cassures qui sont proches en 3D ont plus probablement participé à des réarrangements que les autres. Cela est appuyé par des analyses génomiques sur des cellules somatiques et entre espèces. Nommons cette hypothèse: l'hypothèse de localité.Notre approche a été de proposer une méthode pour utiliser l'information structurale afin de prioriser les scénarios de réarrangements. Les données de Hi-C ont été l'information structurale qui nous a permis d'appliquer la méthode aux scénarios entre D. melanogaster et D. yakuba.Ces résultats nous ont ensuite menés à nous demander si la structure de la chromatine ne pouvait pas elle-même évoluer. Elle serait alors susceptible d'être considérée comme un caractère phylogénétique. Cette idée est appuyée par d'autres résultats montrant la conservation de domaines topologiques entre espèces.Cette question ne semble pas avoir été posée auparavant. Elle est pourtant très intéressante car elle permet d'ouvrir tout un champ d'étude. En effet, si la structure de la chromatine porte un signal phylogénétique, alors il devient possible de s'interroger sur les mécanismes en œuvre lors de la sélection, ou sur la possibilité de reconstruire l'état ancestral de cette structure. Par la suite, il serait même possible de comparer l'évolution de la séquence et celle de la structure de la chromatine.Nous avons ainsi défini une distance entre les structures des génomes, basée sur la comparaison des contacts entre loci orthologues. Nous l'avons appliquée à une ensemble de six espèces comprenant l'humain, la souris et quatre drosophiles. Ces résultats confirment la présence d'un signal phylogénétique dans la structure spatiale des génomes. Ils mettent également en lumière l'intérêt de la mise en place de méthodes permettant de comparer efficacement des données de contacts entre espèces. / Different species have different genome organization. Whether it be the karyotype or gene order, these differences are seen even with relatively close species like Human and Mouse. This is caused by the chromosomal rearrangement. Infererence of rearrangement scenarios that transform one present-day species into another can give insight into evolutionary states, the ancestral genome being one of the intermediates of the true scenario.The chromosomal rearrangements are violent biological events for the cell. Indeed, numerous mechanisms are present to stop the cell cycle when the genome sequence is altered. Moreover, rearrangements can be the source of aberrant phenotypes, which are probably unfavorable for the carrier. With all that, it seams reasonable to assume the rearrangement scenarios are parsimonious.However, it is accepted that this criterion alone is not sufficient to efficiently build the evolutionary history of the genomes. Indeed, for whatever model we choose, the number of scenario is exponential in the number of rearrangements. Another biological constraint is needed. The spatial structure of the chromatin could be an essential missing criterion. It has been shown in vitro that when a double-stranded break of the DNA is non-homologously repaired, the strand used for repairing is close in space to the breakpoint. Our hypothesis is that the closer the breakpoints are in space, the more probable they are to participate in a rearrangement. This hold on genomics analysis of somatic cells, and between species. Let's name that hypothesis the locality hypothesis.We proposed a method to use the structural information in order to prioritize the rearrangements scenarios. The Hi-C data were the structural information that allowed us to apply our method to scenarios between D. melanogaster and D. yakuba.This results led us to ask whether the chromatin structure could evolve by itself. Then, it could be used as a phylogenetic mark. This idea is related to previous results showing the conservation of topological domains between species.This question seams to be new, and could open a new line of investigation. If the chromatin structure holds a phylogenetical signal, it becomes possible to ask ourselves about the mechanisms that occur during the selection, or if it is possible for the ancestral state to be inferred. Then, it could even be possible to compare the evolution of the sequence with the one of the chromatin structure.Thus, we defined a distance between genome structures, based on the comparison of contacts between orthologous loci. We applied this distance to a set of six species, including the Human, the Mouse and four Drosophila. This result confirms the presence of a phylogenetic signal in the spatial structure of the genomes. They also showed that we're in need for efficient methods to compare contacts data between species.