Genome architecture and rearrangement: Interplay of genomic, transcriptomic, and epigenetic features in mammals.

Understanding the evolutionary mechanisms driving speciation requires examining changes at the sequence, transcriptomic, and epigenetic levels. Mammalian genomes can be partitioned into multi-species homologous synteny blocks (msHSBs), which preserve collinearity across species, and evolutionary breakpoint regions (EBRs), which mark genomic rearrangements. While msHSBs are enriched for functionally essential genes, EBRs have been associated with lineage-specific features. However, few studies have integrated multiple genomic layers to assess the forces shaping these regions. This thesis combined methodological development with biological investigation to address this gap. At the methodological level, two tools were created: an automated pipeline for codeML, transforming single-gene selection analyses into a scalable framework for thousands of orthologues, and SyntenyPlotteR, an R package for flexible visualisation of synteny across species, now widely adopted. The codeML pipeline reduces analysis time by over 100-fold and syntenyPlotteR provides a user friendly tool for visualisation in comparative genomics. At the biological level, ~9,000 human genes were classified into categories of selection pressures, housekeeping status, dynamic expression, and regulatory control. Most followed stable evolutionary paths, consistent with essential roles, while a subset diverged in primates and humans, reflecting lineage-specific adaptation. Integration of these categories with EBRs and msHSBs revealed distinct patterns. EBRs localised to repeat-rich, gene-dense, and euchromatic regions near the nuclear centre, but were depleted of housekeeping genes and genes under purifying selection. In contrast, msHSBs were enriched for essential and ultraconserved functions, including genes constrained across sequence, expression, and regulatory levels. These results support the "Integrative Breakage Model", in which fragility promotes rearrangement in accessible chromatin, while constraint preserves essential loci. Overall, this thesis provides new insights into the mechanisms of genome stability and change. By combining tool development with integrative analysis, it highlights how fragility and constraint shape genome evolution, driving both conserved organisation and lineage-specific adaptation.