Genome Assembly, Pan-Genome Analysis, Taxonomic Re-Assignment, and Biosynthetic Gene Clusters of a Plant Growth-Promoting Bacterium, Streptomyces cavourensis SAI-25

Aims: A Streptomyces strain SAI-25, isolated from the rice rhizosphere, was previously reported to have several plant growth-promoting (PGP) and biocontrol potential. Since the previous studies were targeted for particular traits, this study focused on mining the genome to explore its full biosynthetic potential, which were unknown so far. Methods and Results: To address that, its genome was sequenced to obtain a chromosome-level assembly, which was analyzed to identify its secondary metabolite potential, taxonomic positioning, genes/pathways responsible for PGP and biocontrol traits, strain-specific genes, and potential enzymes for biosynthesis of a diketopiperazine class compound, Cyclo(Trp-Phe), previously reported in this strain. Sixteen Biosynthetic Gene Clusters (BGCs) out of thirty-two predictions were annotated to diverse functions; majority with biocontrol properties. The strain was reclassified to another species, S. cavourensis. The pan-genome analysis showed the presence of a relatively higher number of unique genes in the SAI-25 strain. Genes/pathways identified for the PGP and biocontrol traits were largely similar to those of other Streptomyces species. The potential BGCs that might be involved in the biosynthesis of Cyclo(Trp-Phe) were also predicted. Conclusions: The presence of BGCs with diverse functions, beneficial for agricultural and industrial purposes, highlights the potential of SAI-25 strain. Impact Statement: Decoding the complete genome of a Streptomyces strain having insecticidal, antifungal, and several PGP traits, along with their underlying BGCs. While the annotated BGCs included biocontrol agents (such as, Valinomycin, Bafilomycin-B1), growth-promoting agents (siderophores), and chemotherapeutic agents (Montanastatin), observing many unannotated BGCs highlight its potential for characterization in the future.