A Novel Biosynthetic Gene Cluster Across the Species Complex Is Important for Pathogenicity in Onion.

Onion center rot is caused by at least four species of genus (, , , and subsp). Critical onion pathogenicity determinants for were recently described, but whether those determinants are common among other onion-pathogenic species remains unknown. In this work, we report onion pathogenicity determinants in subsp and We identified two distinct secondary metabolite biosynthetic gene clusters present separately in different strains of onion-pathogenic subsp. One cluster is similar to the previously described HiVir phosphonate biosynthetic cluster identified in and another is a novel putative phosphonate biosynthetic gene cluster, which we named Halophos. The Halophos gene cluster was also identified in strains. Both clusters are predicted to be phosphonate biosynthetic clusters based on the presence of a characteristic phosphoenolpyruvate phosphomutase () gene. The deletion of the gene from either HiVir or Halophos clusters in subsp. caused loss of necrosis on onion leaves and red onion scales and resulted in significantly lower bacterial populations compared with the corresponding wild-type and complemented strains. Seven ( to ) of 11 genes ( to ) in the Halophos gene cluster are required for onion necrosis phenotypes. The onion nonpathogenic strain PNA15-2 ( subsp. ) gained the capacity to cause foliar necrosis on onion via exogenous expression of a minimal seven-gene Halophos cluster (genes to . Furthermore, cell-free culture filtrates of PNA14-12 expressing the intact Halophos gene cluster caused necrosis on onion leaves consistent with the presence of a secreted toxin. Based on the similarity of proteins to those with experimentally determined functions, we are able to predict most of the steps in Halophos biosynthesis. Together, these observations indicate that production of the toxin phosphonate seems sufficient to account for virulence of a variety of different strains, although strains differ in possessing a single but distinct phosphonate biosynthetic cluster. Overall, this is the first report of onion pathogenicity determinants in subsp and [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.