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Abstract

Members of the Pseudomonas genus of gram-negative bacteria are often highly abundant in metagenomic samples collected from plants. To better understand the process of Pseudomonas colonization, we study the evolution of a local collection of plant-associated Pseudomonas strains via comparative genomics. Specifically, we analyzed 1,524 genomes of Arabidopsis thaliana-associated Pseudomonas isolates, collected across several years and sites near Tübingen, Germany. We inferred the pan-genome for all isolates based on their orthologous groups. Out of the 72,397 orthologous groups specified, only 1.3% belonged to the bacterial ‘core genome’, while 36.3% were unique to individual isolates. Analyzing the dynamics of gain-and-loss events within and between orthologous groups with an evolutionary framework allowed us to infer a co-evolutionary network composed of orthology groups gained-and-loss together. Overall, 9.81% of the orthologous groups co-evolve with at least one partner. Further dividing this co-evolutionary network into 1,014 highly connected modules, we identified modules that are associated with specific cellular functions. By comparing closely-related isolates we also discovered genomic islands and further characterized their evolutionary dynamics. Finally, by focusing on a subgroup of phylogenetically close isolates differing in their pathogenicity levels, we could associate specific orthologous groups and co-evolving modules with strain pathogenicity.