When less is more: the untold stories in Cetacea genomes

Tese de mestrado, Biologia Molecular e Genética, 2023, Universidade de Lisboa, Faculdade de CiênciasCetacea are one of the very few mammalian lineages to be composed of uniquely aquatic species, commonly known as whales, dolphins and porpoises. As the first cetacean ancestors explored and colonized aquatic niches, multiple morphological, physiological, behavioural and metabolic modifications ensued. While gene loss and gene duplication events have been considered prime sources for the emergence of phenotypic novelty, their precise role in many of adaptations exhibited by marine mammals is poorly documented. Yet, a few examples have been described showing how modifications at the DNA level shaped the radical phenotype transformation of cetacean species. In the past decade, the emergence of numerous genome sequence assemblies from mammalian species has been transformative, allowing the comprehension of variations in morphology, senses, dietary specializations, energy metabolism or longevity. In Cetacea, despite multiple analysis and studies, the molecular origin of many of their unique trait and adaptations remains to be investigated. Thus, the central aim of this thesis is to investigate the role of gene loss and duplication in the “making” of the unique phenotype of these animals. Specifically, focusing in reproductive, dietary and longevity trait-associated genes, that have been highly modified in this lineage. In this thesis, seventeen genes were examined in twelve cetacean genomes with the assistance of two automated software tools PseudoChecker and Geneious. These were used to detect and validate disruptive mutations and assess eroded or duplicated genes. Genes related to reproduction processes such as CRISP1, DEFB108B, NLRP14, SPEM1, SPEM2, SPEM3, PRSS58, PTX4 and USP51 appear to be lost in most species of cetaceans. In addition, a diet-related gene, BCO1, appears to be missing in some species of Odontoceti. LAMTOR1 appears to be duplicated in Mysticeti and PCNA and PSMD4 appears to be duplicated in Cetacea. The gene loss events and duplications here analysed demonstrated a complex evolutionary scenario in Cetacea, adding up unique reproductive, dietary and longevity traits and culminating in significant adaptations to life on water