Pathogenicity and genome assembly of a Pythium aphanidermatum isolate causing damping-off in amaranth in controlled environment agriculture

Several species of Pythium are destructive soilborne pathogens, causing root rot and damping-off of seedlings and posing significant challenges in controlled environment agriculture (CEA). In this study, four isolates (PT2-1-1, PT2-1-2, PT5, and PT6) were obtained from infected amaranth seedlings and confirmed as P. aphanidermatum through morphology and ITS rDNA sequencing. 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 susceptible amaranth genotypes. Genome sequencing of isolate PT2-1-1 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. Analysis of the predicted P. aphanidermatum secretome revealed potential intracellular and apoplastic effectors, including Crinkler and 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.