Deciphering genomes: comparative genomic analysis of legume associated Micromonospora”

Abstract

[EN] Micromonospora is now considered as a plant growth promoting bacterium (PGPB), but until 2015, the genomes of only two endophytic strains had been sequenced. In this thesis, a comparative genomic approach was used to elucidate some of the biological processes that drive the relationship between Micromonospora and the plant at a genomic level. To achieve this, the following specific objectives were proposed: 1. Creation of new bioinformatic tools that complement or enhance widely used programs in microbial genomic characterization and creation of a pipeline to characterize plant-related bacterial features in the genus Micromonospora. 2. Characterization of the main genomic features that drives the relationship between Micromonospora and the plant, using a comparative genomic approach. 3. Genome based characterization of strains isolated from different parts of the plant, closely related to the main species found in the nodules, Micromonospora saelicesensis and Micromonospora noduli. This thesis is therefore divided in three parts, one for each objective. In the first part some of the most popular programs and applications in microbial genomic characterization were briefly analyzed and their strong and weak features were singled out. Several bioinformatic solutions were proposed, to help improve the end-user management of some of these frequently used programs. Finally, an R based pipeline was proposed to analyze and manage genomic data, to decipher significant differential features that drive the relationship between Micromonospora and its host plants. All these bioinformatic solutions were implemented as R based scripts, with the additional benefit that they can be easily introduced in future pipelines with only a minimal amount of commands and variables needed. The second chapter was focused on the second objective, the characterization of the main genomic features that drive the plant-bacteria relationship in Micromonospora. The genomes of seventeen Micromonospora strains isolated from different legumes (Cicer sp., Medicago sp., Lupinus sp., Ononis sp., Pisum sp. and Trifolium sp.), and plant tissues (nodule and leaves) were sequenced. With the addition of these newly sequenced genomes, we constructed a database of 74 genomes, with an almost equal number of soil-related and endophytic-related Micromonospora representatives. Using a novel comparative genomic approach, based on the database generated in 2018 (Levy et al., 2018) and the proteome of known host plants, we determined several genomic features that could potentially be related to the Micromonospora-plant interaction. The third chapter focused on the final objective. As the most frequently isolated Micromonospora in plant nodules (Carro, 2009; Carro et al., 2012; Cerda, 2008; de la Vega, 2010; Trujillo et al., 2010, 2015), the species M. saelicesensis and its close phylogenetic neighbor M. noduli probably play an important role in the relationship with their legume host. However, these two species share many features, and the question arose whether they should be merged into a single species. Using different genomic approaches, in chapter III we have studied the taxonomic relationship between the species Micromonospora saelicesensis and Micromonospora noduli using genome-based data.