Systematic Identification of Pathogenic <i>Streptomyces</i> sp. AMCC400023 That Causes Common Scab and Genomic Analysis of Its Pathogenicity Island

Abstract

Potato scab, a serious soilborne disease caused by <i>Streptomyces</i> spp., occurs in potato-growing areas worldwide and results in severe economic losses. In this paper, the pathogenicity of <i>Streptomyces</i> strain AMCC400023, isolated from potato scabs in Hebei Province, China, was verified systematically by the radish seedling test, the potato tuber slice assay, the potted back experiment, and the detection of phytotoxin thaxtomin A. Morphological, physiological, and biochemical characteristics were determined, and the 16S ribosomal RNA analyses of <i>Streptomyces</i> sp. AMCC400023 were carried out. To obtain the accurate taxonomic status of the pathogen strain, the whole genome was sequenced, and the phylogenetic tree among 31 <i>Streptomyces</i> genomes was formed. The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) were analyzed, and at the same time, the toxicity-related genes between <i>Streptomyces</i> sp. AMCC400023 and <i>Streptomyces scabiei</i> were compared, all based on the whole-genome level. All of the data supported that, instead of a member of <i>S. scabiei</i>, test strain <i>Streptomyces</i> sp. AMCC400023 was a distinct phytopathogen of potato common scab, which had a relatively close relationship with <i>S. scabiei</i> while separating clearly from <i>S. scabiei</i> at least in the species level of taxonomic status. The complete pathogenicity island (PAI) composition of <i>Streptomyces</i> sp. AMCC400023 was identified, which contained a toxin region and a colonization region. It was conjectured that the PAI of <i>Streptomyces</i> sp. AMCC400023 might be directly or indirectly acquired from <i>S. scabiei</i> 87-22 by horizontal gene transfer, or at the very least, there was a very close homologous relationship between the two pathogens as indicated by a series of analyses, such as phylogenetic relationships among 31 <i>Streptomyces</i> species, ANI and isDDH analyses, PAI structure mapping, thaxtomin A synthetic gene cluster tree construction, and most important, the collinearity analysis at the genome level.