Omics-Based Approaches in Studying Fungal Endophytes and Their Associated Secondary Metabolites

The microbial communities that reside in the plant endosphere without exhibiting any apparent disease symptoms are known as endophytes, and they have the most distinct relationships in close proximity with their host plants in comparison to other plant-associated microbiota. The sturdy foundation for natural metabolic scaffolds with a wide range of applications is provided by bioactive secondary metabolites from endophytic fungus. The highly significant metabolites of these filamentous fungi are encoded by gene clusters, but many of these gene clusters are hidden in lab-like environments. Due to this reason, various approaches involving genetic modification(s) and/or metabolomic interventions are essential for stimulating such dormant gene clusters and enhancing metabolite production. In this chapter, chemical profiling of fungal endophyte-derived bioactive compounds has been discussed using omics-based approaches. The study about the association between plants and fungal endophytes using a variety of techniques, including genome sequencing, comparative genomics, microarray, next-generation sequencing, metagenomics, and metatranscriptomics, has also been covered in this topic.