• ciliate
• hydrogenosome
• mitochondrion

Although Ciliates (Protist kingdom, superphylum Alveolata, phylum Ciliophora) are among the most studied Protists and a plethora of scientific publications are dedicated to them, a valid database based on the genomes of their organelles is missing. This database would be useful in order to identify events of recent speciation or cryptic biodiversity, for which the nuclear genome is not very informative. The purpose of my thesis was to increase the mitochondria dataset and, where present, available hydrogenosomes, through the assembly of new genomic samples and the annotation of the genomes already present in the current bibliography. The mitogenomic or hydrogenosomic sequences available online have been downloaded and, where missing, annotation has been added. Subsequently, starting from genetic material already sequenced, bioinformatics tools were used in order to assemble the genomes and annotate the gene content in the most complete way possible. Using the the wider and more complete dataset, a number of genes, shared by a threshold of sequences, were chosen. The amino acid sequences of the selected genes have been used for a phylogenomic analysis of the mitochondrial or hydrogenosomal genome, to be compared with the most up-to-date phylogenetic reconstructions based on morphological analysis and or different molecular markers. Concurrently matrix distances between proteins were created and gene maps were produced where possible. The analysis has led to the addition of several representatives to the classes already present in and to add a representative to a fourth class (Heterotrichea) of which the only representative already present in the database, missing annotation (Stentor coeruleus) was also noted. Through the assembled genomes it was possible to observe the evolution of the content between and all within the classes examined. In addition, it was possible to carry out analysis of any sinteny and to underline different evolutionary distances between the proteins. At the end of this work, a phylogenomic tree containing the analyzed species was reconstructed, the first example of this type of analysis among the Ciliophora, which could be taken as a reference and expanded in the future.