| Summary: | The Amazonian rainforest is a hyper-diverse ecosystem in the number of species and the myriad of intertaxon relationships that are mostly understudied. In order to characterize a dominant and economically important Amazonian species, the Brazil nut tree (<i>Bertholletia excelsa</i> Bonpl.), at the genome level, wegenerated high-coverage long-read sequencing data from the leaves of a single individual. The genome assembly revealed an unexpected discovery: two circular contigs that could be assigned to the chromosome and a plasmid of a <i>Pantoea stewartii</i> strain. Comparative genomics revealed that this strain belongs to the <i>indologenes</i> subspecies and displays high synteny with other strains isolated from diseased leaves of the neotropical palm <i>Bactris gasipaes</i> Kunth. Investigation of pathogenicity-related genes revealed the absence of the entire type III secretion system gene cluster in the plasmid, which was otherwise highly similar to a plasmid from an isolate known to cause disease in <i>Dracaena sanderiana</i> Mast. In contrast, several genes associated with plant-growth promoting traits were detected, including genes involved in indole-3-acetic acid (IAA) production, phosphate solubilization, and biosynthesis of siderophores. In summary, we report the genome of an uncultivated <i>P. stewartii</i> subsp. <i>indologenes</i> strain associated with the Brazil nut tree and potentially a plant growth-promoting bacteria.
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