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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.
