Diversity and Taxonomic Classification of Plasmids in Pantoea

Plasmids play a key role in prokaryotic evolution, as their acquisition can lead to the emergence of novel traits that confer adaptive advantages during niche colonization. Members of the genus Pantoea harbor diverse plasmids, many of which encode metabolic functions or mechanisms relevant for interactions with eukaryotic hosts, predominantly plants and insects. Several Pantoea plasmids have been characterized as domesticated, that is, vertically inherited similarly to chromosomes, whereas others are mobile or mobilizable. Although knowledge of Pantoea plasmid function and evolution is expanding, a general framework for their classification is still lacking. Here, we propose a framework for classifying Pantoea plasmids into plasmid taxonomic units (PTUs). This approach integrates phylogenetic analysis of plasmid backbone genes with gene content similarity. Using this framework, we recover previously described plasmid groups across broader species ranges and identify novel PTUs characterized by distinct functional traits. Our study establishes a unified framework for plasmid classification in Pantoea.