Drosophila is involved in a wide range of interactions with parasites and pathogens (parasitoid wasps, bacteria, fungi, viruses). Drosophila hosts vary greatly at the species, population and individual level, in their response against such organisms, and much of this variation has a genetic basis. In this thesis I explored three aspects of this variation. First, using recombination mapping based on SNPs and a variation of bulk segregant analysis, I identified a QTL region on the right arm of the third chromosome of D. melanogaster associated with resistance to at least some of the parasitoid species / strains used in the experiments. The location of the QTL was further explored with deficiency complementation mapping and was narrowed down to the 96D1-97B1 region. The success of the deficiency mapping suggests that the resistant allele is not completely dominant. Second, I investigated patterns of molecular evolution in a set of immunity-related genes, using sequences from a D. melanogaster and a D. simulans population and a set of genes without known involvement in immunity for comparison. I found evidence that several of these genes have evolved under different selection pressure in each species, possibly indicating interactions with different parasites. The immunity genes tested appear to be evolving faster compared to non-immunity genes, supporting the idea that the immune system is evolving under strong selective pressure from parasites. Finally, in a D. melanogaster – sigma virus system, I measured genetic variation in the transmission of different virus genotypes, in different environments. There was poor correlation between temperatures, suggesting that environmental heterogeneity could constraint evolution of resistance (to virus transmission). The correlation between viral genotypes was also low, although relatively stronger for more closely phylogenetically related viral strains. Such interactions between host genotypes, virus genotypes and environmental conditions can maintain genetic variation in virus transmission.

In this study the molecular evolution of duplicated HoxA genes in zebrafish and fugu has been investigated. All 18 duplicated HoxA genes studied have a higher non-synonymous substitution rate than the corresponding genes in either bichir or paddlefish, where these genes are not duplicated. The higher rate of evolution is not due solely to a higher non-synonymous-to-synonymous rate ratio but to an increase in both the non-synonymous as well as the synonymous substitution rate. The synonymous rate increase can be explained by a change in base composition, codon usage, or mutation rate. We found no changes in nucleotide composition or codon bias. Thus, we suggest that the HoxA genes may experience an increased mutation rate following cluster duplication. In the non-Hox nuclear gene RAG1 only an increase in non-synonymous substitutions could be detected, suggesting that the increased mutation rate is specific to duplicated Hox clusters and might be related to the structural instability of Hox clusters following duplication. The divergence among paralog genes tends to be asymmetric, with one paralog diverging faster than the other. In fugu, all b-paralogs diverge faster than the a-paralogs, while in zebrafish Hoxa-13a diverges faster. This asymmetry corresponds to the asymmetry in the divergence rate of conserved non-coding sequences, i.e., putative cis-regulatory elements. These results suggest that the 5′ HoxA genes in the same cluster belong to a co-evolutionary unit in which genes have a tendency to diverge together.

The ParaHox cluster contains three Hox‐related homeobox genes. The evolution of this sister of the Hox‐gene clusters has been studied extensively in metazoans with a focus on its early evolution. Its fate within the vertebrate lineage, and in particular following the teleost‐specific genome duplication, however, has not received much attention. Three of the four human ParaHox loci are linked with PDGFR family tyrosine kinases. We demonstrate that these loci arose as duplications in an ancestral vertebrate and trace the subsequent history of gene losses. Surprisingly, teleost fishes have not expanded their ParaHox repertoire following the teleost‐specific genome duplication, while duplicates of the associated tyrosine kinases have survived, supporting the hypothesis of a large‐scale duplication followed by extensive gene loss.

Evolutionarily conserved non-coding genomic sequences represent a potentially rich source for the discovery of gene regulatory regions. Since these elements are subject to stabilizing selection they evolve much slower than adjacent non-functional DNA. These so-called phylogenetic footprints can be detected by comparison of the sequences surrounding orthologous genes in different species. In this paper we present a new method and an effcient software tool for the identifcation of corresponding footprints in long sequences from multiple species. This allows the evolutionary study of the origin and loss of phylogenetic footprints if suffcient number and appropriately placed species are included. We apply this method to the published sequences of HoxA clusters of shark, human, and the duplicated zebrafish and Takifugu clusters as well as the published HoxB cluster sequences. We find that there is a massive loss of sequence conservation in the intergenic region of the HoxA clusters, consistent with the finding in [Chiu et al., PNAS 99, 5492-5497 (2002)]. We further propose a simple model to estimate the loss of sequence conservation that can be attributed to gene loss and other structural reasons. We find that the loss of conservation after cluster duplication is more extensive than expected by this model. This suggests that binding site turnover and/or adaptive modification may also contribute to the loss of sequence conservation. We conclude that this method is suitable for the large scale study of the evolution of (putative) cis-regulatory elements.

The statistical analysis of phylogenetic footprints in the two known horn shark Hox clusters and the four mammalian clusters shows that the shark HoxN cluster is HoxD-like. This finding implies that the most recent common ancestor of jawed vertebrates had at least four Hox clusters, including those which are orthologous to the four mammalian Hox clusters.

Higher teleost fishes, including zebrafish and fugu, have duplicated their Hox genes relative to the gene inventory of other gnathostome lineages. The most widely accepted theory contends that the duplicate Hox clusters orginated synchronously during a single genome duplication event in the early history of ray-finned fishes. In this contribution we collect and re-evaluate all publicly available sequence information. In particular, we show that the short Hox gene fragments from published PCR surveys of the killifish Fundulus heteroclitus, the medaka Oryzias latipes and the goldfish Carassius auratus can be used to determine with little ambiguity not only their paralog group but also their membership in a particular cluster. Together with a survey of the genomic sequence data from the pufferfish Tetraodon nigroviridis we show that at least percomorpha, and possibly all eutelosts, share a system of 7 or 8 orthologous Hox gene clusters. There is little doubt about the orthology of the two teleost duplicates of the HoxA and HoxB clusters. A careful analysis of both the coding sequence of Hox genes and of conserved non-coding sequences provides additional support for the “duplication early” hypothesis that the Hox clusters in teleosts are derived from eight ancestral clusters by means of subsequent gene loss; the data remain ambiguous, however, in particular for the HoxC clusters. Assuming the “duplication early” hypothesis we use the new evidence on the Hox gene complements to determine the phylogenetic positions of gene-loss events in the wake of the cluster duplication. Surprisingly, we find that the resolution of redundancy seems to be a slow process that is still ongoing. A few suggestions on which additional sequence data would be most informative for resolving the history of the teleostean Hox genes are discussed.

Du fait de sa taille (17 Gb), de sa nature allohexaploïde et de son fort taux de séquences répétées (>80%), le génome du blé tendre a toujours été considéré comme trop complexe pour des analyses moléculaires efficaces. En conséquence, la connaissance de la structure de son génome reste limitée. Utilisant une approche chromosome-spécifique, la carte physique du chromosome 3B du blé a récemment été établie et a permis le développement de ressources génomiques uniques. Pendant ma thèse, la mise en oeuvre d‟approches transcriptomiques utilisant ces ressources m‟a permis d‟analyser les relations entre la structure du génome, l‟évolution, la fonction et la régulation des gènes le long du chromosome 3B de blé. Tout d‟abord, des filtres portant les BAC du « Minimal Tiling Path » (MTP) du chromosome 3B ont été hybridés avec 15 échantillons d‟ARNm pour identifier les BAC portant des gènes. Ensuite, des puces Agilent 15K d‟expression d‟orge ont été hybridées avec les pools tridimensionnels (3D) du MTP du chromosome 3B pour localiser les gènes plus précisément sur la carte physique. Afin de construire la première carte transcriptionnelle d‟un chromosome de blé, ces mêmes pools 3D ainsi que les 15 échantillons d‟ARNm ont été hybridés sur des puces NimbleGen 40K d‟expression de blé. Les résultats obtenus à partir de ces expériences ont permis de tirer des conclusions quant à l‟organisation de l‟espace génique sur le chromosome 3B. Ainsi les gènes sont répartis tout le long du chromosome 3B selon un gradient de densité de gènes du centromère vers les télomères avec une plus forte proportion de gènes regroupés en îlots au niveau des télomères. Une analyse évolutive a montré que les îlots seraient essentiellement constitués de gènes ayant subi des réarrangements dans le génome du blé. De plus, la carte transcriptionnelle a également mis en évidence qu'une part significative des gènes organisés en îlot présentent des profils d‟expression similaires et / ou ont la même fonction et / ou interviennent dans le même processus biologique. De plus, à l‟échelle du chromosome 3B entier, des mécanismes de régulation à longue distance entre îlots de gènes ont été suspectés. En conclusion, cette étude a permis pour la première fois de mettre en évidence des relations entre la structure du génome, l‟évolution, la fonction et la régulation des gènes à l‟échelle d‟un chromosome de blé. Le séquençage et l‟annotation du chromosome 3B ainsi que l'utilisation de technologies telles que le RNAseq permettront d‟analyser ces relations de façon encore plus précise et exhaustive. / Because of its size (17 Gb), allohexaploid nature and high repeat content (>80%), the bread wheat genome has always been perceived as too complex for efficient molecular studies. As a consequence, our knowledge of the wheat genome structure is still limited. Following a chromosome-specific approach, the physical map of wheat chromosome 3B has recently been constructed and allowed the development of unique genomic resources. During my PhD the use of transcriptomic approaches based on these resources allowed me analysing the relationships between the structure of the genome, the evolution, the function and the regulation of the genes along wheat chromosome 3B. First macroarrays carrying the BACs of the chromosome 3B “Minimal Tiling Path” (MTP) were hybridised with 15 mRNA samples to identify the BACs carrying genes. Then barley Agilent 15K expression microarrays were hybridised with the MTP of chromosome 3B pooled in three-dimension (3D) to precisely locate the genes on the physical map. To build the first transcription map of a wheat chromosome, the 3D pools as well as the 15 mRNA samples were hybridised onto wheat NimbleGen 40K expression microarrays. The results from these experiments allowed drawing some conclusions about gene space organisation on chromosome 3B. Thus the genes are spread all along chromosome 3B with a gradient of the gene density from the centromere to the telomeres with a higher proportion of genes organised in islands at the telomeres. An evolutionary analysis demonstrated that the islands would essentially be composed of genes that have undergone rearrangements in the wheat genome. Furthermore the transcription map also showed that a significant fraction of the genes organised in islands display similar expression profiles and / or share the same function and / or play a role in the same biological process. Moreover, at the scale of the whole chromosome 3B, mechanisms of long distance regulation between gene islands were suspected. In conclusion this study allowed for the first time to find relationships between the genome structure, the evolution, the function and the regulation of the genes at a wheat chromosome scale. The sequencing and the annotation of chromosome 3B as well as the use of technologies like RNAseq will enable to analyse these relationships in an even more precise and exhaustive way.