Fungarium phylogenomics reveals high species diversity in graminicolous downy mildews and upholds the distinction between Peronosclerospora philippinensis and P. sacchari

Authors: GORBEN, GLEN - Oak Ridge Institute For Science And Education (ORISE); DETTMAN, JEREMY - Agriculture And Agri-Food Canada; CASTROAGUDIN, VANINA - Oak Ridge Institute For Science And Education (ORISE); HAMBLETON,, SARAH - Agriculture And Agri-Food Canada; Martin, Frank; MICHELMORE, RICHARD - University Of California, Davis; STANLEY, OLIVE - Oak Ridge Institute For Science And Education (ORISE); NGUYEN, HAI - Agriculture And Agri-Food Canada; Crouch, Joanne

Submitted to: Fungal Systematics and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/29/2026
Publication Date: N/A
Citation: N/A

Interpretive Summary: Downy mildew diseases cause severe losses to cereal crops such as maize, millets, sorghum, and sugarcane in many parts of the world, especially in tropical climates. Some foreign downy mildews pose a high-risk to U.S. agriculture due to their ability to cause significant losses in staple food crops such as corn. Better tools and resources to accurately identify cereal downy mildews are needed to reduce the risk of these pathogens entering the U.S. In this research, we used a unique method to enrich 100-150 year old DNA of original archival reference specimens (called types) of cereal downy mildews, so that DNA sequence data could be generated. This is the first time DNA sequence data has been available for bona fide type materials of several destructive pathogens. The DNA profiles from these types show that our the inclusion of type specimens needs to be a part of the development of diagnostic tools that rely on DNA. These findings will allow professional disease diagnosticians, regulatory officials, and plant pathologists to make accurate pathogen identification and to minimize the spread and impact of foreign cereal downy mildew diseases.

Technical Abstract: Graminicolous downy mildew (GDM) diseases threaten staple food crops such as corn, millets, sorghum, and sugarcane, making accurate pathogen identification critical for global food security and quarantine enforcement. However, identification is hindered by inconclusive morphological characters and unreliable host associations. Progress using molecular data is also challenging; as obligate pathogens, reference materials are often limited to historical fungarium specimens, which contain highly degraded pathogen DNA inextricably embedded within host tissue. To overcome these challenges, we used an oomycete-specific target enrichment protocol to generate high-throughput DNA sequence data for 429 orthologs for 57 fungarium specimens, including 17 types, to construct a phylogeny from 62 ortholog loci. The inclusion of type materials upheld the critical distinction between the high-risk plant pathogens Peronosclerospora philippinensis and P. sacchari and validated most historical species concepts. However, the data also revealed widespread taxonomic confusion, showing that nearly half of the examined specimens were misidentified. Critically, in three instances, presumed isotypes were not conspecific with their nomenclatural types. Based on these results, we reduce Sclerospora northii to a synonym of P. philippinensis, propose the new combination Sclerophthora iseilematis, and identify 12 distinct lineages that may represent undescribed species. This study demonstrates that GDM diversity is substantially greater than previously recognized and empirically confirms that anchoring molecular data to nomenclatural types is a critical prerequisite for building a stable taxonomy and developing accurate diagnostic tools for this group.