Phytophthora cactorumis a homothallic oomycete pathogen, which has a wide host range and high capability to adapt to host defense compounds and fungicides. Here we report the 121.5 Mb genome assembly of theP. cactorumusing the third-generation single-molecule real-time (SMRT) sequencing technology. It is the second largest genome sequenced so far in thePhytophthoragenera, which contains 27,981 protein-coding genes. Comparison with otherPhytophthoragenomes showed thatP. cactorumhad a closer relationship withP. parasitica,P. infestansandP. capsici.P. cactorumhas similar gene families in the secondary metabolism and pathogenicity-related effector proteins compared with other oomycete species, but specific gene families associated with detoxification enzymes and carbohydrate-active enzymes (CAZymes) underwent expansion inP. cactorum.P. cactorumhad a higher utilization and detoxification ability against ginsenosides–a group of defense compounds fromPanax notoginseng–compared with the narrow host pathogenP. sojae. The elevated expression levels of detoxification enzymes and hydrolase activity-associated genes after exposure to ginsenosides further supported that the high detoxification and utilization ability ofP. cactorumplay a crucial role in the rapid adaptability of the pathogen to host plant defense compounds and fungicides.

Interspecies interactions play a key role in soil-borne disease suppression in intercropping systems. However, there are limited data on the underlying mechanisms of soil-borne Phytophthora disease suppression. Here, a field experiment confirmed the effects of maize and soybean intercropping on Phytophthora blight of soybean caused by Phytophthora sojae. Experimentally, the roots and root exudates of maize were found to attract P. sojae zoospores and inhibit their motility and the germination of cystospores. Furthermore, five phenolic acids (p-coumaric acid, cinnamic acid, p-hydroxybenzoic acid, vanillic acid, and ferulic acid) that were consistently identified in the root exudates and rhizosphere soil of maize were found to interfere with the infection behavior of P. sojae. Among them, cinnamic acid was associated with significant chemotaxis in zoospores, and p-coumaric acid and cinnamic acid showed strong antimicrobial activity against P. sojae. However, in the rhizosphere soil of soybean, only p-hydroxybenzoic acid, low concentrations of vanillic acid, and ferulic acid were identified. Importantly, the coexistence of five phenolic acids in the maize rhizosphere compared with three phenolic acids in the soybean rhizosphere showed strong synergistic antimicrobial activity against the infection behavior of P. sojae. In summary, the types and concentrations of phenolic acids in maize and soybean rhizosphere soils were found to be crucial factors for Phytophthora disease suppression in this intercropping system.