Unraveling A Genome of Spongospora subterranea from North America

Abstract

Spongospora subterranea f. sp. subterranea, a biotrophic soil-borne plasmodiophorid pathogen causes powdery scab of potato and vectors Potato mop-top virus (PMTV). Here, we present a genome of S. subterranea which will enhance our understanding of the pathogen’s genomic architecture. DNA was isolated from root galls from a single field-grown plant cv. Russet Burbank for Oxford Nanopore long-read sequencing and polished with Illumina sequences from sporosori collected from tuber pustules (SssMN22-1). The resulting high-quality genome assembled to 31.51 Mb, with a GC content of 45.7% and 10,325 predicted protein-coding genes. Functional annotations revealed extensive biological insights, including 1,981 genes associated with Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, 2,644 genes linked to Cluster of Orthologous Genes (COG) classifications, and 2,249 genes containing Protein Family (Pfam) domains. Additionally, the analysis identified 135 carbohydrate-active enzyme (CAZyme) profiles and 321 effector proteins, underscoring its pathogenic potential. The genome exhibited high completeness, with 96.1% Benchmarking Universal Single-Copy Ortholog (BUSCO) genes detected based on the fungal lineage in the eukaryotic database. This improved genome resource advances our understanding of the poorly characterized S. subterranea, providing critical tools for deciphering its biology and pathogenesis. This knowledge will play a crucial role in developing effective strategies to manage powdery scab.