Abstract:[Background] A fungal strain B-48 was isolated from diseased Echinochloa crus-galli in a paddy field in Hubei Province and identified as Colletotrichum echinochloae. This strain demonstrated a strong biocontrol effect on E. crus-galli and was safe for major crops including rice, wheat, and maize.[Objective] To optimize the cultural conditions for the growth and sporulation, analyze the genomic sequence information, and mine the gene resources of secondary metabolite synthesis of C. echinochloae B-48 for further research on the herbicidal natural products and their biosynthetic mechanisms.[Methods] C. echinochloae B-48 was characterized regarding the culture media, temperature, pH, light, carbon/nitrogen source, and lethal condition. Then, Nanopore and Illumina platforms were used for the whole-genome sequencing of the strain. Bioinformatic tools were used for the assembly of the genome sequence, prediction of the genome structure, functional annotation of the genome, and prediction of the biosynthetic gene clusters (BGCs) for secondary metabolites. [Results] C. echinochloae B-48 grew well on the PSA plate at 30 ℃ and pH 7.0 with constant light. Starch and yeast extract as an effective carbon and nitrogen source stimulating the growth and sporulation of strain B-48, respectively. The lethal conditions for the strain were incubation at 55 ℃ for 10 min. The genome of C. echinochloae B-48 had a total length of 62.25 Mb and G+C content of 46.59%, containing 11 324 protein-coding genes and 76 BGCs for secondary metabolites. [Conclusion] C. echinochloae B-48 has the potential to be developed as a mycoherbicide for the control of E. crus-galli. The BGCs for secondary metabolites in its genome indicate that the strain can produce natural products with herbicidal effects. The findings provide important genetic information for the further research and application of the strain for the production of secondary metabolites by fermentation.
