Pathogenicity and Genome Assembly of a Pythium aphanidermatum Isolate Causing Damping‐Off in Amaranth in Controlled Environment Agriculture

Several species of Pythium are destructive soil‐borne pathogens, causing root rot and damping‐off of seedlings and posing significant challenges in controlled environment agriculture (CEA). In this study, four isolates were obtained from infected amaranth seedlings and confirmed as P. aphanidermatum . These isolates dramatically reduced the root length of amaranth seedlings in plate‐based pathogenicity assays. In soil‐based post‐emergence assays, damping‐off symptoms were prevalent, with disease incidence reaching up to 100% in some amaranth genotypes. Genome sequencing of one isolate yielded a 51.55 Mb assembly consisting of 120 contigs, with 14,453 predicted protein‐coding genes, including a diverse set of plant cell wall‐degrading enzymes with a likely role in host invasion. The predicted secretome contained potential intracellular and apoplastic effectors, including eight Crinkler and three YxSL[RK] effectors; no RxLR effectors were detected. This work provides a second genome assembly for P. aphanidermatum as well as demonstrating variation in pathogenicity of this isolate on different amaranth accessions. Together these pave the way for investigation of pathogen–host interaction and identification of key virulence and defence strategies.