Improved genome assemblies of plant-associated Streptomyces spp. as a resource for understanding plant pathogenicity in the genus

Common scab disease, affecting potato and other tuber and root crops, is caused by various pathogenic Streptomyces species. Researchers have increasingly turned to genome-enabled methods to analyze these Streptomyces strains responsible for the disease. However, studying phytopathogenic Streptomyces is hindered by the scarcity of high-quality genome sequences.

In this study, the quality and completeness of genome assemblies for 12 pathogenic Streptomyces type strains and six closely related non-pathogenic strains have been enhanced. The improved assemblies boast an average N50 of 7.4 megabases and have BUSCO scores exceeding 98.5% in all cases. The findings reveal that phytopathogenic Streptomyces genomes are among the largest among sequenced Streptomyces species.

Moreover, these phytopathogenic genomes exhibit a higher enrichment of genes associated with carbohydrate and amino acid metabolism, compared to non-pathogenic strains.

Interestingly, plasmids were not consistently detected across the genome assemblies, indicating that plasmids may not be conserved across species and are not essential for pathogenicity. Additionally, the analysis of genome assemblies across both closely and distantly related strains exposed multiple rearrangements within linear chromosomes and reduced synteny near telomeric regions.

These upgraded genome assemblies, many of which correspond to type strains, serve as a valuable resource for the scientific community to deepen their understanding of pathogenicity within the Streptomyces genus.