Chromosome-level genome assembly and annotation of a novel potato common scab pathogen

Potato common scab, caused by pathogenic Streptomyces species, severely impairs tuber quality and restricts potato industry development. Streptomyces lincolnensis is traditionally known for lincomycin biosynthesis, with no prior association with plant pathogenicity.

In this study, 31 actinomycete strains were isolated from scab-infected potato tubers, and strain D6 was identified as a highly virulent pathogen. Chromosome-level complete genome sequencing of strain D6 was performed, followed by phylogenetic and phylogenomic analyses. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were used to determine its taxonomic status. Comparative genomic analysis was conducted between strain D6, pathogenic Streptomyces scabiei, and non-pathogenic S. lincolnensis to identify virulence-related genes.

Phylogenomic analyses confirmed that strain D6 belongs to the S. lincolnensis clade. ANI and dDDH values between strain D6 and strain S. lincolnensis NRRL 2936 were 87.2% and 28.9%, respectively, indicating that strain D6 represents a novel sister species of S. lincolnensis. Comparative genomics further revealed a core set of 74 virulence-associated genes shared by strain D6 and the typical pathogen S. scabiei LBUM848, but absent in the non-pathogenic S. lincolnensis NRRL 2936. Four key candidate virulence genes were screened from this core set: PROKKA_06934 (encoding a class III pyridoxal-phosphate-dependent aminotransferase), PROKKA_02771 (a TxtC homolog, encoding a cytochrome P450 enzyme), PROKKA_05140 (a phage-derived gene), and PROKKA_08104 (encoding a glycoside hydrolase family 32 protein).

These findings provides both experimental and genomic evidence supporting that strain D6, a novel sister species of S. lincolnensis, is a causal agent of potato common scab. This study expands the diversity of plant-pathogenic Streptomyces and offers genomic insights into the evolution of virulence in pathogenic Streptomyces species.