Long-Read Sequencing Genome Assembly of Enables Development of Molecular Diagnostics for Sweetpotato Black Rot.

is a destructive fungal pathogen of sweetpotato () that leads to losses at all stages of sweetpotato production. Accurate detection of would allow for more efficient deployment of management tactics in sweetpotato production. To develop a diagnostic assay, a hybrid genome assembly of isolate AS236 was generated. The resulting 31.7-MB assembly was near-chromosome level, with 18 contigs, 6,481 predicted genes, and a BUSCO completion score of 98.4% when compared with the fungus-specific lineage database. Additional Illumina DNA reads from , and a second isolate (C1421) were then mapped to the assembled genome using BOWTIE2 and counted using HTSeq, which identified 148 genes present only within as molecular diagnostic candidates; 6 single-copy and 35 highly multi-copy (>40 BLAST hits), as determined through a self-BLAST-P alignment. Primers for PCR were designed in the 200-bp flanking region of the first exon for each candidate, and the candidates were validated against a diverse DNA panel containing species, sweetpotato pathogens, and plants. After validation, two diagnostic candidates amplified only DNA and were considered to be highly specific to the species. These genetic markers will serve as valuable diagnostic tools with multiple applications including the detection of in seed, soil, and wash water in sweetpotato production.