Deciphering the soybean root rot pathogen <i>Phytophthora sojae</i> : Signaling pathways, transcriptional regulation, and effector biology

Abstract Phytophthora sojae , the causal agent of soybean root and stem rot, is one of the most destructive oomycete pathogens threatening global soybean production. Unlike fungi, P. sojae possesses a highly unconventional signaling architecture, characterized by the absence of several canonical eukaryotic modules and the emergence of lineage‐specific innovations. Advances in genomics and functional studies have revealed that its pathogenicity is orchestrated by multiple gene families and signaling networks that diverge substantially from classical eukaryotic paradigms. In this review, we summarize recent progress on four major categories of functional genes: G protein signaling pathways, protein kinases, transcription factors, and effectors. The simplified heterotrimeric G protein system of P. sojae is compensated by the expansion of dual‐domain G protein‐coupled receptors, an oomycete‐specific innovation that integrates seven‐transmembrane signal perception with intracellular catalytic domains to coordinate chemotaxis and development. The kinome is unusually large, with expanded tyrosine kinase‐like and MAPK families, highlighting its role in stress responses and host recognition. Transcription factors, including basic leucine zipper, myeloblastosis, C 2 H 2 , and RWP‐RK families, show stage‐specific and stress‐induced expression, with some directly regulating effector gene transcription. Effectors, both apoplastic and cytoplasmic, represent the most rapidly evolving gene class, mediating sophisticated manipulation of host immune and metabolic processes. Collectively, these gene families form a multilayered regulatory network that integrates environmental sensing, intracellular signaling, and host manipulation. We also discuss challenges and perspectives, emphasizing the need for systematic functional validation, network‐level analyses, and the integration of multi‐omics and structural biology. These insights not only expand our understanding of oomycete biology but also provide potential molecular targets for breeding and chemical interventions against soybean root rot.