This thesis, supervised by Rosario Gil and Andrés Moya, proposes a wide analysis of minimized genomes of endosymbiotic bacteria from insects illuminating a diversity of genomic, evolutionary and metabolic properties of these ancient obligate endosymbionts. Part of the results have been published in the journals Environmental Microbiology, Frontiers in Microbiology, Database and Biology. The thesis was defended on September 21, 2023.
Over the last decades, symbioses between insects and bacterial endosymbionts have been the focus of remarkable empirical studies. Models of symbiosis between specific bacterial lineages and their hosts have been described, but no large-scale analyses have been done in order to begin deciphering the overall evolutionary path of the endosymbiosis phenomenon. Insects represent about 85% of animal diversity, and about 60% maintain symbiotic relationships with microbes, which mainly allow their hosts to live in niches otherwise unavailable to them by providing them with nutrients, protection, and even new forms of energy. Bacterial endosymbionts often live within specialized cells in insects called bacteriocytes; they generally have a base compositional bias towards A+T in their genomes, undergo genomic shrinkage, and have an accelerated sequence evolution, all of which are convergent attributes with organelles resembling their extended and combined evolutionary histories. Thus, in this thesis entitled “Towards minimal cells and beyond, the development and application of bioinformatic tools for large-scale genomic data analysis of endosymbiotic bacteria of insects”, the term "symbionelles" for long-term obligate bacterial endosymbionts of insects have been proposed. Most of these organisms have the smallest genomes found in nature. This makes them good models for studying minimal cells through genomic and metabolomic analyses. Recent changes in technology have made it necessary to look for new and creative ways to handle and process large amounts of data. With completely sequenced and annotated genomes from endosymbiotic bacteria of insects, databases are indispensable tools for organizing and easily accessing specific biological information. This work offers a publicly accessible, composite database that includes the genomic data of symbiotic relationships between bacteria and insects, as well as all symbiotic relationships found in primary databases. This database includes the confirmation of the symbiotic relationships, the associated publication, the organization and availability of the sequences of all genes, genomes, and orthologs of each prokaryotic symbiont, and the metabolic network of all organisms included in this repository as a new reaction-based methodology applied on genomic data to create contracted metabolic diagrams. By comparing these reaction-based metabolic networks to metabolite-based ones, it was possible to look at the differences and similarities between organisms that have evolved in different ways.
Mariana Reyes-Prieto carried out her doctoral research in the Evolutionary Genetics group under the supervision of Rosario Gil and Andrés Moya, professors of the Department of genetics (University of Valencia) and researchers at the Institute of Integrative Systems Biology I2SysBio (UV-CSIC) and at the joint unit of genomics and health (Fisabio-UV). During the development of the thesis, Mariana Reyes-Prieto made a stay at Trinity College (Dublin) and enjoyed a contract within SYMBIOMICS, a Marie-Curie Initial Training Network, as well as a fellowship from CONACYT (Mexico). The examining board was formed by Amparo Latorre (UV), Giuseppe D'Auria (Fisabio) and José A. Castro (Universitat de les Illes Balears), who graded the thesis as outstanding.
