Genomic and transcriptomic analyses of bacterial symbionts of ciliates

Holosporales (Alphaproteobacteria) are a lineage of mostly intracellular obligate host- associated bacteria. They inhabit a wide range of eukaryotic hosts, both multicellular, such as arthropods, and unicellular, such as ciliates, amoebas, cercozoans, and diplonemids. Most studies were focused on those Holosporales belonging to the Holospora and Caedimonas genera, aiming to understand the interactions with their ciliate hosts. However, for most representatives, the mechanisms of interaction and the importance for the hosts of those relationships are completely unknown. Additionally, despite their environmental abundance, we know little about the physiologies of Holosporales, because none of them was isolated in pure culture. Up to now, only few genomes have been produced of Holosporales members and comprehensive analyses are still lacking. This PhD project was aimed at the investigation of endosymbiotic relationships between Holosporales and ciliates from a genomic and evolutionary perspective. The project was oriented to the comparative and functional genomic analysis of specific endosymbiotic bacteria belonging to the order Holosporales, hosted by ciliates of the genus Paramecium. The production of new genomes of the Holosporales symbionts and their analyses together with the other available members of the order Holosporales allowed to reveal the characteristics of these multiple endosymbiont-host relationships, and to gain insights into the evolutionary history of the entire order, in particular different adaptations to the association with eukaryotic hosts. Moreover, I optimized a Nanopore sequencing protocol and a Dual-RNAseq protocol for bacterial symbionts of ciliates and their hosts. These two approaches allowed me respectively to produce high-quality or even fully closed genome assemblies, and to obtain information on the expression profile of the symbiont and host organisms, thus providing a basis to identify key putative genes involved in these intriguing relationships.