Regulation of pre-mRNA splicing is a key process for most if not all eukaryotes. The process can, in the abstract, be considered as a series of trans-acting factors that interact with cis-motifs in the RNA to enable the removal of introns and joining of exons. As the cis factors need not only be the splice sites themselves, but also motifs in the exons, the splicing process has the potential to impose selective constraint on exonic sequence in addition to the normal selection on the amino acid content of the protein. To understand this more clearly, in this thesis, I mainly focus on a type of important and widely investigated cis-motifs, exonic splicing enhancers (ESEs), which bind with SR proteins to re-enforce the splice sites and so ensure splicing correctly. First, I explore splice-related cis-motif usage of the Ectocarpus genome, which is a species phylogenetically very distant from vertebrates but, like vertebrates in having abundant large introns. A deep phylogenetic conservation of exonic splice-related constraints is observed (Chapter II). Then I extend the analysis across taxa in a phylogenetically explicit framework. In this section stronger selection on exon end synonymous sites can be detected within humans when the exons are flanked by larger introns. Additionally I report evidence that reduced Ne might lead to larger introns and weakened splice sites. Thus I suggest an unusual circumstance in which selection (for cis-motifs to control error-prone splicing) might be stronger when population sizes are smaller; this is unexpected and would be a necessary complement to nearly-neutral theory (Chapter III). Third, I ask whether what we know about biases in the usage of ESEs and splicing control elements allows us to understand where in human genes pathogenic mutations tend to occur (Chapter IV). By examining the relationship between determinants of the usage of splice-associated cis-motifs and the distribution of human pathogenic SNPs, I found certain exons are vulnerable to splice disruption owing to low ESE density and a “fragile” exon model we proposed could describe and explain this phenomenon (Chapter IV). Finally I perform preliminary analysis, with a view to biotechnological optimization of transgenes, to address whether there might be such a thing as a tissue specific ESE. To this end I examine ESE usage in tissue specific genes. I find some preliminary evidence for tissue specific biased usage of certain ESEs.

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Viruses constitute the vast majority of all biological entities in the biosphere and represent one of the biggest reservoirs of undetected genetic diversity on Earth. Of all the viral particles inhabiting the ocean, phages are the most abundant and can affect the overall microbial composition of marine ecosystems and the dynamics of global biogeochemical cycles. The interaction between prokaryotic cells and their phages is among the oldest and most intertwined host-parasite relationships on the planet. It has been extensively studied by culture, molecular biology, and experimental evolution. However, due to the difficulties of culture with environmental samples, only a few studies have analyzed the mechanisms of phage-host interaction in the marine environment. Here, we have studied the genes involved in viral host recognition and their evolutionary dynamics by focusing on two species of the marine copiotrophic bacterium Alteromonas and several phages infecting them. We described the genomic and morphological characterization of the first Alteromonas phage belonging to the Myoviridae family (Alteromonas myovirus V22) that was isolated in coastal waters of the Mediterranean Sea, and we identified its receptor-binding protein (RBP) used for host recognition by combining fluorescence microscopy and spectrometry. In addition, using size-exclusion chromatography, we showed how this protein required co-expression with a downstream protein to be functional, which later was identified as a new type of intermolecular chaperone crucial for RBP maturation. We also identified a conserved host recognition module in V22 and other unrelated alterophages belonging to different viral families and with completely different morphologies, suggesting horizontal gene transfer between the ancestors of these phages. Furthermore, we described the first coevolution study of a host-parasite system performed with Alteromonas using a metagenomics-like approach. Finally, we analyzed the micro- and macrodiversity of an alterophage population that was able to survive over a long period of time and showed remarkable genomic stability, indicating stable interactions over time between phage-host recognition structures. Overall, this study has contributed to extend the knowledge of known phage-host recognition mechanisms present in the marine ecosystem and has provided a first glimpse of the evolutionary dynamics in phages infecting Alteromonas.