Complete genome resources for Xylella fastidiosa strains AlmaEM3 and BB08-1 reveal prophage-associated structural variation among blueberry-infecting strains.

Xylella fastidiosa is a gram-negative plant pathogenic bacterium with wide geographical distribution and host range. X. fastidiosa strains are separated into genetically distinct subspecies, and further categorized into sequence types (ST). Genetic characterization of X. fastidiosa strains infecting blueberry has revealed that strains of subspecies multiplex and fastidiosa are capable of causing bacterial leaf scorch disease of blueberry under field conditions. To better elucidate the relationships among blueberry-infecting X. fastidiosa subsp. multiplex strains, we completed the genomes of an ST 42 strain, AlmaEM3, and a ST 43 strain, BB08-1, using a hybrid assembly approach. Comparison of these assemblies reveals a large (0.95 Mb) chromosomal inversion in BB08-1 relative to AlmaEM3 and the reference strain M12, likely resulting from recombination between prophage regions.