Abstract
Common scab of potato causes important economic losses worldwide following the development of necrotic lesions on tubers. In this study, the genomes of 14 prevalent scab-causing Streptomyces spp. isolated from Prince Edward Island, one of the most important Canadian potato production areas, were sequenced and annotated. Their phylogenomic affiliation was determined, their pan-genome was characterized, and pathogenic determinants involved in their virulence, ranging from weak to aggressive, were compared. 13 out of 14 strains clustered with Streptomyces scabiei, while the last strain clustered with Streptomyces acidiscabies. The toxicogenic and colonization genomic regions were compared, and while some atypical gene organizations were observed, no clear correlation with virulence was observed. The production of the phytotoxin thaxtomin A was also quantified and again, contrary to previous reports in the literature, no clear correlation was found between the amount of thaxtomin A secreted, and the virulence observed. Although no significant differences were observed when comparing the presence/absence of the main virulence factors among the strains of S. scabiei, a distinct profile was observed for S. acidiscabies. Several mutations predicted to affect the functionality of some virulence factors were identified, including one in the bldA gene that correlates with the absence of thaxtomin A production despite the presence of the corresponding biosynthetic gene cluster in S. scabiei LBUM 1485. These novel findings obtained using a large number of scab-causing Streptomyces strains are challenging some assumptions made so far on Streptomyces’ virulence and suggest that other factors, yet to be characterized, are also key contributors.
Highlights
Potato plants are subjected to various stresses, including diseases caused by numerous bacterial, oomycete and fungal plant pathogens, affecting yield and market values (Stevenson et al, 2001)
The analyses performed in this study provide up-to-date information on the genomic diversity of pathogenic Streptomyces spp. found under commercial potato production conditions in Eastern Canada as well as its implication in virulence
All Streptomyces strains except strain LBUM 1476 belong to the S. scabiei species with an average genome to genome distance calculator (GGDC) and Average Nucleotide Identity (ANI) values of 95.68 and 99.56%, respectively
Summary
Potato plants are subjected to various stresses, including diseases caused by numerous bacterial, oomycete and fungal plant pathogens, affecting yield and market values (Stevenson et al, 2001). CS causes necrotic lesions on the tuber surface, which affect potato transformation and commercialization, resulting in economic losses estimated between 15.3 and 17.3 million dollars per year in Canada (Hill and Lazarovits, 2005). This worldwide disease is caused by a few closely related Streptomyces species (Braun et al, 2017). Only few plant pathogenic Streptomyces spp. genomes have been sequenced (18 S. scabiei; ten S. acidiscabies, and two S. turgidiscabies, NCBI May 2021) These genomic sequences have provided new opportunities to perform comparative genomic studies, additional genomes will be required to perform large-scale analyses. Functional analyses of some of these genetic determinants have confirmed their implication in the development of CS symptoms (Bignell et al, 2010)
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