Comparative Genomics of Potato Common Scab-Causing Streptomyces spp. Displaying Varying Virulence

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.

Seventeen Ustilaginaceae High-Quality Genome Sequences Allow Phylogenomic Analysis and Provide Insights into Secondary Metabolite Synthesis

“…The phylogenetic tree is based on the core genes (2370 genes) of the selected strains. The SH-like local support values were computed using FASTtree within the comparative genomics tool EDGAR 3.0 [49]. 1,2 Two isolates were sequenced.…”

“… Gene-based comparison of Ustilaginaceae. Venn diagrams of ( A ): U. maydis and ( B ): Sporisorium isolates obtained from the comparative genomics tool EDGAR 3.0 [ 49 ]. Two isolates were sequenced in the case of U. maydis No.…”

Chemical Composition, Antibacterial, Antioxidant and Enzyme Inhibitory Activities of the Essential Oil from Leaves of Psidium guajava L.

“…Diseases have continuously and significantly impacted crop yield. For instance, plant scab, bacterial wilt, and soft rot of plants have brought about the greatest economic losses in recent years [1–3] . More specifically, the typical bacteria that cause these diseases are Streptomyces acidiscabies ( S. acidiscabies ), Ralstonia solanacearum ( R. solanacearum ), and Erwinia carotovora subsp carotovora borgey ( E. carotovora subsp carotovora borgey) which affect plants, including potatoes, beets, carrots, and tomatoes [4–6] .…”

Intraspecific Comparative Analysis Reveals Genomic Variation of Didymella arachidicola and Pathogenicity Factors Potentially Related to Lesion Phenotype

“…Next-generation sequencing technologies have been widely used to study plant pathogens and greatly facilitated understanding of fungal evolution and virulence factors [ 22 , 23 , 24 , 25 , 26 , 27 ]. The lifestyle of fungal species in Dothideomycetes evolves in four major transitions from non-phytopathogenic to phytopathogenic, along with the pathogenicity-related genes carried in different genera varying considerably [ 28 ].…”