Genome sequence of Talaromyces trachyspermus, a biocontrol fungus isolated from broomrape

Abstract

Applying antimicrobial compounds derived from microorganisms for plant disease management is one of the objectives of sustainable agriculture. The genus Talaromyces is known for its species ability to produce a diverse group of antimicrobial compounds. For example, T. trachyspermus has been reported to produce secondary metabolites, cell wall-degrading enzymes, and plant growth-promoting factors. Identification of novel promising metabolites and enzymes from T. trachyspermus is still in its infancy. Also, there is a lack of information about the genomic resources for its secondary metabolites and hydrolytic enzymes. Therefore, this study aimed to analyse the genome of a biocontrol isolate of this species to investigate its biocontrol mechanisms at the genomic level, focusing on secondary metabolites and cell wall degrading enzymes. The whole genome of T. trachyspermus isolate IRAN 3054C, obtained from necrotic Orobanch ramosa stems in Iran with biocontrol ability, was sequenced using the Illumina platform. We performed both de novo and resequencing analyses of the genome, obtaining a 31.3 Mb assembly. The abundance of protein groups associated with biocontrol activities was assessed in the studied genome. Fungismash was used to detect and annotate secondary metabolites. The analysis revealed the presence of several secondary metabolite biosynthesis gene clusters (BGCs), with a high frequency of polyketide synthases (T1PKS) and nonribosomal peptide synthetases (NRPS), which are known to produce bioactive compounds with antimicrobial properties. Among the identified secondary metabolites, Fusarin, YWA1, Dimethylcoprogen, and Squalestatin S1 exhibited the highest similarity to known compounds. Furthermore, sequences similar to Phyllostictine A/B and Cornexistin indicate potential herbicidal properties. The genome also had domains for enzymes involved in phosphate solubilisation, siderophore production, and fungal cell wall degradation, which are essential for biocontrol and plant growth promotion. Our findings highlight the genomic richness of T. trachyspermus IRAN 3054C for biocontrol. Further metabolomics studies are needed to validate the actual production of these secondary metabolites and explore their functional roles in biocontrol.