1,721,072 research outputs found
Early events in the evolution of spider silk genes.
Full text linkSilk spinning is essential to spider ecology and has had a key role in the expansive diversification of spiders. Silk is composed primarily of proteins called spidroins, which are encoded by a multi-gene family. Spidroins have been studied extensively in the derived clade, Orbiculariae (orb-weavers), from the suborder Araneomorphae ('true spiders'). Orbicularians produce a suite of different silks, and underlying this repertoire is a history of duplication and spidroin gene divergence. A second class of silk proteins, Egg Case Proteins (ECPs), is known only from the orbicularian species, Lactrodectus hesperus (Western black widow). In L. hesperus, ECPs bond with tubuliform spidroins to form egg case silk fibers. Because most of the phylogenetic diversity of spiders has not been sampled for their silk genes, there is limited understanding of spidroin gene family history and the prevalence of ECPs. Silk genes have not been reported from the suborder Mesothelae (segmented spiders), which diverged from all other spiders >380 million years ago, and sampling from Mygalomorphae (tarantulas, trapdoor spiders) and basal araneomorph lineages is sparse. In comparison to orbicularians, mesotheles and mygalomorphs have a simpler silk biology and thus are hypothesized to have less diversity of silk genes. Here, we present cDNAs synthesized from the silk glands of six mygalomorph species, a mesothele, and a non-orbicularian araneomorph, and uncover a surprisingly rich silk gene diversity. In particular, we find ECP homologs in the mesothele, suggesting that ECPs were present in the common ancestor of extant spiders, and originally were not specialized to complex with tubuliform spidroins. Furthermore, gene-tree/species-tree reconciliation analysis reveals that numerous spidroin gene duplications occurred after the split between Mesothelae and Opisthothelae (Mygalomorphae plus Araneomorphae). We use the spidroin gene tree to reconstruct the evolution of amino acid compositions of spidroins that perform different ecological functions
Gene expression variability and evolutionary outcomes after whole-genome duplication in fishes
No full textVariation within natural populations is fundamental to evolution, as it provides the raw material for natural selection. However, despite its central role, the study of variation and variability (the tendency of a trait to vary) has often been overlooked in evolutionary biology. Gene expression, a dynamic process that determines where, when, and how much of a gene product is formed, is a crucial intermediary between genotype and phenotype, making its variability a key yet understudied aspect of evolutionary processes. This thesis explores the evolutionary implications of gene expression variability in two main studies. Using bulk organ transcriptomic data from outbred individuals of three ray-finned fishes, I investigate (1) how variability reflects constraints on regulatory evolution, and (2) how variability reflects evolvability, based on patterns of duplication gene retention and functional divergence after whole-genome duplication (WGD).
The first study examines inter-individual gene expression variability measured in multiple organs in spotted gar (Lepisosteus oculatus), zebrafish (Danio rerio), and Northern pike (Esox lucius). I find that highly variable genes evolve under weaker purifying selection at the coding sequence, showing that intra-species variability in gene expression is linked to inter-species protein sequence divergence. The key finding is that the variability of a gene is largely determined by its primary organ of expression rather than being independently regulated in each organ. Notably, genes that are most expressed in the brain (brain-biased) are lowly variable across non-nervous organs, suggesting stabilizing selection on regulatory evolution. This suggests that organ-specific selective pressures shape gene regulatory evolution and thus variability.
The second study focuses on how gene expression variability influences the retention and functional divergence of WGD paralogs (ohnologs). Here, I use spotted gar and Northern pike as outgroups to the teleost and salmonid WGDs, respectively, to approximate the ancestral expression pattern pre-duplication. First, results suggest that genes retained in duplicate post-WGD tend to have higher variability preceding duplication, particularly organ-biased genes which evolve under weaker selective constraints relative to broadly expressed genes. Second, by characterizing the expression divergence patterns of teleost ohnolog pairs in zebrafish and relating it to variability in spotted gar, I show that variability is linked to functional divergence of lowly constrained ohnolog pairs. This suggests that variability can facilitate the evolution of gene function post-duplication. These results highlight the interplay between selective constraints and expression evolvability in shaping the evolutionary fates of ohnologs.
Lastly, I provide a perspective on approaches to classify the evolutionary outcomes of duplicate genes using transcriptomic data. This is a challenging task which involves translating conceptual models of post-duplication fates (e.g., subfunctionalization and neofunctionalization, among others) into appropriate empirical tests with suitable metrics and inclusion criteria. I discuss simplifying assumptions (heuristics) in using gene expression as a proxy for function, differences in the verbal and graphical descriptions of conceptual models (semantics), metrics, and other methodological considerations. I also highlight important factors to consider to improve comparability across studies and to advance our knowledge of gene function evolution
Penalised regression improves imputation of cell-type specific expression using RNA-seq data from mixed cell populations compared to domain-specific methods
Full text linkGene expression studies often use bulk RNA sequencing of mixed cell populations because single cell or sorted cell sequencing may be prohibitively expensive. However, mixed cell studies may miss expression patterns that are restricted to specific cell populations. Computational deconvolution can be used to estimate cell fractions from bulk expression data and infer average cell-type expression in a set of samples (e.g., cases or controls), but imputing sample-level cell-type expression is required for more detailed analyses, such as relating expression to quantitative traits, and is less commonly addressed. Here, we assessed the accuracy of imputing sample-level cell-type expression using a real dataset where mixed peripheral blood mononuclear cells (PBMC) and sorted (CD4, CD8, CD14, CD19) RNA sequencing data were generated from the same subjects (N=158), and pseudobulk datasets synthesised from eQTLgen single cell RNA-seq data. We compared three domain-specific methods, CIBERSORTx, bMIND and debCAM/ swCAM, and two cross-domain machine learning methods, multiple response LASSO and ridge, that had not been used for this task before. We also assessed the methods according to their ability to recover differential gene expression (DGE) results. LASSO/ ridge showed higher sensitivity but lower specificity for recovering DGE signals seen in observed data compared to deconvolution methods, although LASSO/ridge had higher area under curves than deconvolution methods. Machine learning methods have the potential to outperform domain-specific methods when suitable training data are available
Characterization and Evolution of Conserved MicroRNA through Duplication Events in Date Palm (Phoenix dactylifera)
No full textMicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species. Highly conserved miRNAs regulate ancestral transcription factors common to all plants, and control important basic processes such as cell division and meristem function. We selected 21 conserved miRNA families to analyze the distribution and maintenance of miRNAs. Recently, the first genome sequence in Palmaceae was released: date palm (Phoenix dactylifera). We conducted a systematic miRNA analysis in date palm, computationally identifying and characterizing the distribution and duplication of conserved miRNAs in this species compared to other published plant genomes. A total of 81 miRNAs belonging to 18 miRNA families were identified in date palm. The majority of miRNAs in date palm and seven other well-studied plant species were located in intergenic regions and located 4 to 5 kb away from the nearest protein-coding genes. Sequence comparison showed that 67% of date palm miRNA members were present in duplicated segments, and that 135 pairs of miRNA-containing segments were duplicated in Arabidopsis, tomato, orange, rice, apple, poplar and soybean with a high similarity of non coding sequences between duplicated segments, indicating genomic duplication was a major force for expansion of conserved miRNAs. Duplicated miRNA pairs in date palm showed divergence in pre-miRNA sequence and in number of promoters, implying that these duplicated pairs may have undergone divergent evolution. Comparisons between date palm and the seven other plant species for the gain/loss of miR167 loci in an ancient segment shared between monocots and dicots suggested that these conserved miRNAs were highly influenced by and diverged as a result of genomic duplication events
Developmental constraints, innovations and robustness
No full textDuring my PhD, I have been working on Evo-Devo patterns (especially the debate around the
hourglass model) in transcriptomes, with an emphasis on adaptation. I have characterized
patterns in model organisms in terms of constraints and especially in terms of positive selection.
I found that the phylotypic stage (a stage in mid-embryonic development) is an evolutionary
lockdown, with stronger purifying selection and less positive selection than other stages in
terms of the evolution of protein sequences and of regulatory elements. To study the adaptive
evolution of gene regulation during development, I have developed a machine leaning based
in silico mutagenesis approach to detect positive selection on regulatory elements.
In addition to transcriptome evolution, I have been working on the tension between precision
and stochasticity of gene expression during development. More precisely, I have shown that
expression noise follows an hourglass pattern, with lower noise at the phylotypic stage. This
pattern can be explained by stronger histone modification mediated noise control at this stage.
In addition, I propose that histone modifications contribute to mutational robustness in
regulatory elements, and thus to conserved expression levels. These results provide insight into
the role of robustness in the phenotypic and genetic patterns of evolutionary conservation in
animal developmen
Investigating relationships between sequence conservation and function using multispecies whole genome alignments
No full textThe main goal driving the work presented in this thesis is to investigate the relationship between sequence conservation and biological function in Arthropods. Indeed, the increasingly comprehensive sampling of all kingdoms of life enabled by developments in large-scale DNA sequencing and driven by large-scale sequencing initiatives brings powerful opportunities to explore patterns of genome evolution and characterise novel functional genomic elements using multi-species comparative genomics approaches. The basic premise of such approaches is that sequences that remain conserved or recognisably similar across many species over millions of years of evolution are constrained to do so because of evolutionary pressures to maintain some biologically functional role. Consequently, furthering our understanding of the relationship between these evolutionary constraints on genomic sequence and the biological function of the related genomic elements will facilitate the large-scale identification of functional elements in new genome assemblies, as well as generally strengthen our knowledge of how genomes encode biological function. A powerful method of detecting genomic sequences conserved across genomes relies on the computation of Multispecies Whole-Genome Alignments (MWGAs), which form the basic resource required to interrogate patterns of sequence changes and evolutionary constraints in relation to the functional spectra of genomic elements. Pioneering studies using signatures of evolutionary conservation to characterise functional elements first looked at the relatively small genomes of yeasts and Drosophila; following advances in sequencing technologies, further work investigated these patterns in mammals and angiosperms. However, despite the success of these studies, computing MWGAs remains a challenging task to this day, and at the start of this thesis project, there was no reliable implementation of the computational workflow required to do so. Furthermore, while the ever accelerating accumulation of available genome sequences enables increasingly powerful studies of evolutionary constraints on genomic sequence for more and more clades, the quality of these assemblies as well as the taxonomic coverage of sequence species remains heterogeneous even today.
In light of these observations, the first challenge addressed by this thesis work was to accurately assess both the quality and taxonomic distribution of genomic resources available for arthropods, in order to select genome assemblies to include in MWGAs. Our solution to this problem resulted in the release of an online resource powered by a computational workflow, the Arthropoda Assembly Assessment Catalogue (A3Cat), which regroups all available information on released and upcoming arthropod assemblies along with estimates of assembly quality computed by the workflow. This resource and the associated data was the focus of two publications, which are summarised in Chapter 1. The second task undertaken in this work was the development of bioinformatics tools and workflows necessary to build whole-genome alignment resources for arthropods as well as downstream analyses of sequence conservation and visualisation tools. In order to be useful to the general scientific community, these tools had to follow modern requirements for computational science by being portable, scalable, documented, and enabling fully reproducible computational analyses. This work resulted in two computational workflows implemented using a modern workflow management engine: one to compute MWGAs, presented in Chapter 2, and a second to perform analyses and generate powerful visualisation from MWGAs, described in Chapter 3; furthermore, additional work to develop specific missing blocks in the workflows and efforts to ensure reproducibility are covered in Chapter 5.
Because of the considerable challenges encountered during the development of the A3Cat and the two computational workflows to generate and analyse MWGAs, amplified by the need for a reproducible implementation following modern practices, these technical advances comprise the main outcome of this thesis work. However, we were able to leverage this work to compute several MWGAs, which are described as part of Chapter 2, including a MWGA of 22 mosquito species which was used for a preliminary analysis of sequence conservation at the genome level presented in the results of Chapter 3. We expanded on the results of this analysis in Chapter 4, exploring how patterns of sequence conservation relate to biological function in protein-coding genes in mosquitoes using both long-term evolutionary conservation computed from the MWGA as well population-level genetic polymorphism. We focused particularly on genes whose products are involved in the immune system, as mosquitoes are vectors of some of the deadliest diseases to humans, identifying a link between specific functions in the immune system and sequence conservation for multiple gene families. Finally, we summarise additional work contributing to collaborative projects in multiple areas of genomics in Chapter 6.
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L'objectif principal des travaux présentés dans cette thèse est d'étudier le lien entre la conservation des séquences génomiques et la fonction biologique chez les arthropodes. En effet, l'échantillonnage de plus en plus complet des espèces vivantes, rendu possible par les progrès du séquençage de l'ADN et par les initiatives de séquençage à grande échelle, offre de puissantes opportunités d'explorer les schémas d'évolution du génome et de caractériser de nouveaux éléments génomiques fonctionnels à l'aide d'approches de génomique comparative multi-espèces. Le principe de base de ces approches est que les séquences qui restent conservées ou qui présentent des similitudes reconnaissables chez de nombreuses espèces au cours de millions d'années d'évolution sont contraintes de le faire en raison de pressions évolutives visant à maintenir un certain rôle biologiquement fonctionnel. Par conséquent, une meilleure compréhension de la relation entre ces contraintes évolutives sur la séquence génomique et la fonction biologique des éléments génomiques apparentés facilitera l'identification à grande échelle des éléments fonctionnels dans les nouveaux assemblages de génomes, et renforcera d'une manière générale notre connaissance de la manière dont les génomes codent pour une fonction biologique. Un outil puissant de détection des séquences génomiques conservées à travers les génomes repose sur l'élaboration d'alignements de génomes entiers multi-espèces (MWGA), qui constituent la ressource de base nécessaire pour interroger les modèles de changements de séquence et les contraintes évolutives en lien avec les catégories fonctionnelles d’éléments génomiques. Des études pionnières utilisant les signatures évolutives de la conservation de séquences pour caractériser les éléments fonctionnels ont d'abord porté sur les génomes relativement petits de la levure et de la drosophile ; d'autres travaux ont ensuite étudié ces modèles chez les mammifères et les angiospermes. Cependant, malgré le succès de ces études, la génération de MWGA reste à ce jour une tâche difficile, et au début de ce projet de thèse, il n'existait pas d'implémentation fiable du workflow nécessaire pour y parvenir. De plus, alors que l'accumulation toujours plus rapide de séquences génomiques permet des études de plus en plus étendues des contraintes évolutives sur le génome pour un nombre croissant de clades, la qualité de ces assemblages ainsi que la couverture taxonomique des espèces séquencées restent encore aujourd'hui hétérogènes.
À la lumière de ces observations, le premier défi relevé par ce travail de thèse a été d'évaluer avec précision la qualité et la distribution taxonomique des ressources génomiques disponibles pour les arthropodes, afin de sélectionner les assemblages de génomes à inclure dans les MWGA. Notre solution à ce problème a abouti à la publication d'une ressource en ligne, l'Arthropoda Assembly Assessment Catalogue (A3Cat), qui regroupe toutes les informations disponibles sur les assemblages d'arthropodes publiés et à venir, ainsi que les estimations de la qualité des assemblages calculées par le workflow générant cette ressource. Le catalogue et les données associées ont fait l'objet de deux publications, qui sont résumées dans le Chapitre
1. La deuxième tâche entreprise dans le cadre de ce travail a été le développement d'outils bioinformatiques et de workflows nécessaires pour créer des ressources d'alignement de génomes entiers d'arthropodes ainsi que des analyses en aval de la conservation des séquences et des outils de visualisation. Afin d'être utiles à la communauté scientifique, ces outils devaient répondre aux exigences modernes de la science informatique en étant portables, scalables, documentés et en permettant des analyses informatiques entièrement reproductibles. Ce travail a abouti à deux workflows mis en œuvre à l'aide d'un moteur moderne de gestion des workflows : l'un pour générer les MWGA, présenté dans le Chapitre 2, et l'autre pour effectuer des analyses et générer des visualisations à partir des MWGA, décrit dans le Chapitre 3 ; en outre, des travaux supplémentaires visant à développer des blocs spécifiques manquants aux workflows et des efforts pour assurer la reproductibilité sont couverts dans le Chapitre 5.
En raison des défis considérables rencontrés lors du développement de l'A3Cat et des deux workflows pour générer et analyser les MWGA, amplifiés par la nécessité d'une implémentation reproductible adhérant aux pratiques modernes, ces avancées techniques constituent le principal résultat de ce travail de thèse. Cependant, nous avons pu tirer parti de ce travail pour générer plusieurs MWGA, qui sont décrits dans le cadre du Chapitre 2, y compris un MWGA de 22 espèces de moustiques qui a été utilisé pour une analyse préliminaire de la conservation des séquences au niveau du génome, présentée dans les résultats du Chapitre 3. Nous avons développé les résultats de cette analyse au Chapitre 4, en explorant la manière dont les schémas de conservation des séquences sont liés à la fonction biologique des gènes chez les moustiques, en utilisant à la fois la conservation de séquence à l'échelle évolutive calculée à partir de ce MWGA et le polymorphisme génétique au niveau des populations. Nous nous sommes particulièrement intéressés aux gènes dont les produits sont impliqués dans le système immunitaire, car les moustiques sont les vecteurs de certaines des maladies les plus mortelles pour l'homme, et nous avons identifié un lien entre des fonctions spécifiques du système immunitaire et la conservation des séquences pour plusieurs familles de gènes. Enfin, nous résumons au Chapitre 6 les travaux supplémentaires contribuant à des projets de collaboration dans de multiples domaines de la génomique
Intra-genomic variation in the ribosomal repeats of nematodes.
No full textRibosomal loci represent a major tool for investigating environmental diversity and community structure via high-throughput marker gene studies of eukaryotes (e.g. 18S rRNA). Since the estimation of species' abundance is a major goal of environmental studies (by counting numbers of sequences), understanding the patterns of rRNA copy number across species will be critical for informing such high-throughput approaches. Such knowledge is critical, given that ribosomal RNA genes exist within multi-copy repeated arrays in a genome. Here we measured the repeat copy number for six nematode species by mapping the sequences from whole genome shotgun libraries against reference sequences for their rRNA repeat. This revealed a 6-fold variation in repeat copy number amongst taxa investigated, with levels of intragenomic variation ranging from 56 to 323 copies of the rRNA array. By applying the same approach to four C. elegans mutation accumulation lines propagated by repeated bottlenecking for an average of ~400 generations, we find on average a 2-fold increase in repeat copy number (rate of increase in rRNA estimated at 0.0285-0.3414 copies per generation), suggesting that rRNA repeat copy number is subject to selection. Within each Caenorhabditis species, the majority of intragenomic variation found across the rRNA repeat was observed within gene regions (18S, 28S, 5.8S), suggesting that such intragenomic variation is not a product of selection for rRNA coding function. We find that the dramatic variation in repeat copy number among these six nematode genomes would limit the use of rRNA in estimates of organismal abundance. In addition, the unique pattern of variation within a single genome was uncorrelated with patterns of divergence between species, reflecting a strong signature of natural selection for rRNA function. A better understanding of the factors that control or affect copy number in these arrays, as well as their rates and patterns of evolution, will be critical for informing estimates of global biodiversity
A phylogenomic study quantifies competing mechanisms for pseudogenization in prokaryotes—The <i>Mycobacterium leprae</i> case
Full text linkBackgroundPseudogenes are non-functional sequences in the genome with homologous sequences that are functional (i.e. genes). They are abundant in eukaryotes where they have been extensively investigated, while in prokaryotes they are significantly scarcer and less well studied. Here we conduct a comprehensive analysis of the evolution of orthologs of Mycobacterium leprae pseudogenes in prokaryotes. The leprosy pathogen M. leprae is of particular interest since it contains an unusually large number of pseudogenes, comprising approximately 40% of its entire genome. The analysis is conducted in both broad and narrow phylogenetic ranges.ResultsWe have developed an informatics-based approach to characterize the evolution of pseudogenes. This approach combines tools from phylogenomics, genomics, and transcriptomics. The results we obtain are used to assess the contributions of two mechanisms for pseudogene formation: failed horizontal gene transfer events and disruption of native genes.ConclusionsWe conclude that, although it was reported that in most bacteria the former is most likely responsible for the majority of pseudogenization events, in mycobacteria, and in particular in M. leprae with its exceptionally high pseudogene numbers, the latter predominates. We believe that our study sheds new light on the evolution of pseudogenes in bacteria, by utilizing new methodologies that are applied to the unusually abundant M. leprae pseudogenes and their orthologs.</div
Genomic consequences of asexuality in animais
No full textAsexuality is predicted to have profound genome-wide consequences due to the absence of recombination and need of chromosomal pairing. The predicted consequences of this include: accumulation of deleterious mutations, divergence between haplotypes, changes in the dynamics of transposable elements and genomic rearrangements. Numerous case studies of individual asexual animals have tested these predictions on a genome scale, but usually only in a single asexual lineage. Several of the studied asexual genomes carried peculiar genomic features such as high rates of acquired genes via horizontal gene transfer.
However, it is unclear whether the results of these studies are lineage-specific or general consequences of asexuality. In this thesis I address these gaps in three studies. i) We reanalyzed published genomes of 24 asexual animals and found that not a single genome feature is systematically replicated across a majority of these species, suggesting that there is no genomic feature characteristic of asexuality. We found that high heterozygosity levels characterized only asexuals of hybrid origin. Asexuals that were not of hybrid origin appeared to be largely homozygous, independently of the cellular mechanism underlying asexuality. ii) We sequenced genomes of five asexual Timema stick insects and their sexual sister species to assess the consequences of asexuality on heterozygosity, structural variations and transposable element abundance. We found convergent heterozygosity loss in all five asexual Timema species. We found that the homogenization mechanism applies also to structural rearrangements but to a lesser extent. iii) In a study of transposable element dynamics in experimental sexual and asexual Saccharomyces cerevisiae populations, we provide direct evidence that asexual reproduction drives a reduction of transposable element loads. We show, using simulations, that this reduction occurs via evolution of transposable element activity, most likely via increased excision rates.
Overall, despite the importance of recombination rate variation for understanding the evolution of sexual animal genomes, the genome-wide absence of recombination does not appear to have the dramatic effects which are expected from classical theoretical models. The lack of dramatic effect of asexuality on genome evolution is surprising in the light of the dramatic consequences observed in experimental conditions. The reasons for this are probably a combination of lineage-specific patterns, impact of the origin of asexuality, and a survivor bias of asexual lineages.
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La reproduction asexuée est souvent prédite comme une impasse évolutive. En effet, ce mode de reproduction aurait de profondes conséquences sur l’ensemble du génome, notamment en raison de l’absence de recombinaison, ou encore de l’isolement des chromosomes homologues. Ces conséquences néfastes peuvent se traduire par une accumulation de mutations délétères, une divergence entre haplotypes, un changement dans la dynamique des éléments transposables et/ou des réagencements génomiques. De nombreuses études, en général au sein d’individus d’une même lignée asexuée, ont testé ces prédictions à l’échelle du génome. Les résultats qui en découlent mettent en exergue la présence de caractéristiques génomiques propres aux asexués (par exemple : l'acquisition d’un taux élevé de gènes par transfert horizontal). Cependant, ces observations sont difficiles à interpréter car elles pourraient être spécifiques à la lignée étudiée et ne pas être liées aux conséquences générales de l’asexualité. C’est pourquoi, dans ce travail de thèse, nous avons considéré cette question par le biais de trois études distinctes : (1) Pour commencer, nous avons ré-analysé les génomes de 24 lignées asexuées différentes. Nous avons constaté qu’aucune caractéristique commune n’est répliquée au sein de leurs génomes, ce qui suggère qu’il n’existe donc pas de conséquence générale due à l’asexualité. Seuls les asexués d’origine hybride sont hautement hétérozygotes, les autres étant majoritairement homozygotes, et ce, indépendamment du mécanisme cellulaire sous-jacent. (2) Ensuite, nous avons séquencé les génomes de dix espèces de phasmes du genre Timema, cinq asexuées et leurs espèces sexuées les plus proches, afin d’évaluer les conséquences de l’asexualité sur l’hétérozygotie, les variations structurelles et l’abondance des éléments transposables. Nous avons constaté une perte d’hétérozygotie convergente chez les cinq espèces asexuées, et ce mécanisme d’homogénéisation s’applique également aux réarrangement structurels, mais dans une moindre mesure. (3) Enfin, grâce à une étude expérimentale sur la dynamique des éléments transposables chez Saccharomyces cerevisiae, nous avons apporté la preuve que la quantité d’éléments transposables est drastiquement diminuée par la reproduction asexuée. De plus, à l’aide de simulations, nous avons montré que cette réduction provient de l’évolution de l’activité de ces éléments transposables, très probablement à cause de l’augmentation des taux d’excisions.
En résumé, malgré l’importance de la recombinaison génétique dans le règne animal, phénomène maintenu par la reproduction sexuée, l'absence de cette recombinaison chez les organismes asexués ne semble pas avoir les effets dramatiques prédits par les modèles théoriques. Au vu des résultats obtenus en conditions expérimentales, l’absence d’effets néfastes de l’asexualité sur l’évolution du génome est surprenante, mais pourrait provenir d’une combinaison de raisons. En effet, chaque lignée asexuée possède des caractéristiques qui lui sont propres, une origine différente, et un biais de survie, qui pourraient expliquer ce résultat inattendu
The Genetic Basis of Aging and Longevity in Drosophila melanogaster
No full textWhile much has been learned about the genetics of aging from studies of mutants and transgenes, not much is known about the rôle of natural genetic variants in the évolution of longevity. For my ph.D. thesis, I aimed to identify genes and mechanisms underpinning the évolution of lifespan in the fruit fly, D. melanogaster. We analysed the genomes of a set of populations that have been under selection for longevity for more than 35 years and identified numerous loci presumably subject to selection. Interestingly, we found no enrichment for canonical longevity genes but for immunity genes instead, especiaily in the Toll pathway. To examine whether this immunity signature is causative, I performed infection assays with a rage of pathogens and found that the long-lived lines survive markedly better and differ their age-dependent immune gene expression. Using RNAi, I could show that Toll pathway activity affects lifespan independent of the genomic context of the evolved populations. Since many candidate loci résidé in regulatory régions potentially affecting gene expression, I also examined the transcriptomes of the selection and control lines across three adult âges, using RNA-seq. Age had the largest effect on the transcriptome, including upregulation of genes involved in DNA repair, epigenetic régulation and immunity and downregulation neuronal genes. More than 20% of the transcriptome showed differential expression between the selection regimes; for example, long-lived lines exhibited higher overall expression in genes for chromatin organisation and increased RNA processing characterized expression patterns of postponed aging. In the overlap to our genomic candidates, were genes in the Toll pathway, circadian rhythm and the TOR pathway. Finally, I examined the rôle of the DNA repair factor Prp19 in Drosophila lifespan. Prp19 had been implicated in replicative senescence of cultured human cells and I assessed the effect of its overexpression on a whole organism level. Increasing levels of Prp19 led to an extension of lifespan, improved résistance to oxidative stress, and decreased DNA damage. Together, my dissertation demonstrates a major role of immunity genes in the évolution of aging and identifies Prp19 as an important evolutionarily conserved déterminant of both cellular and organismal lifespan and DNA damage repair.
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Bien qu'une grande quantité d'information à propos des gènes affectant le viellissement a été obtenue à partir d'études de mutants et de transgènes, les variations génétiques naturelles sont actuellement peu connues. Le but de ma thèse de doctorat est d'identifier les variations naturelles soutenant l'évolution de l'espérance de vie chez D. melanogaster. Nous avons étudié les génomes d'un ensemble de populations de mouches maintenues sous sélection pour une longévité accrue pendant plus de 35 ans et nous avons identifié plusieurs loci probablement sujet à la sélection pour longévité. Malgré le fait que nous n'avons pas observé de surreprésentation de gènes canonique de la longévité, nous avons découvert un enrichissement des gènes impliqués dans la réponse immunitaire, en particulier des gènes appartenant à la voie Toll. De plus, nos expériences sur les populations sélectionnées montrent que la longévité est corrélée à une meilleure survie après infection par différents pathogènes et associée à une différence dans le niveau d'expression de ces gènes au cours de vieillissement. J'ai ensuite utilisé des lignes transgéniques d'interférence d'ARN afin de tester l'effet fonctionnel de ces gènes sur la longévité. La baisse d'expression de spâtzle et de Toll augmente légèrement l'espérance de vie, tandis que le silençage génétique de cactus réduit drastiquement l'espérance de vie. En suite, comme de nombreux loci se trouvent dans des régions pouvant potentiellement réguler l'expression des gènes, j'ai examiné le transcriptome des populations sélectionnées et contrôles par RNA-seq à trois stades différents de la vie adulte. De manière générale, le viellissement entraîne une augmentation de l'expression des gènes impliqués dans la réparation de l'ADN, la régulation épigénétique et l'immunité, ainsi qu'une baisse de la transmission synaptique. Plus de 20% du transcriptome montrait une différence d'expression entre les régimes de sélections. Chez les populations sélectionnées qui on une longévité élevée, on a observé une augmentation de la transcription des gènes traitant la chromatine et l'ARN et une baisse des oxydorédutases. En comparant les résultats de cette analyse et l'analyse génomique, nous avons identifié un recoupement pour 179 gènes, qui sont impliqués dans la voie Toll, régulation du rythme circadien et la voie TOR. Pour terminer, j'ai examiné le rôle du facteur de réparation de l'ADN Prp19 sur la longévité, montrant que sa surexpression augmente la longévité et la résistance au stress oxidatif et génotoxique et diminue les dommages à l'ADN. Ma dissertation démontre le r°le majeur des gènes immunitaires dans l'évolution de la longévité et identifie Prp19 comme un déterminant conservé important de la longévité et de la réparation de l'ADN
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