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

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.