Chapter 17 - CRISPR-Cas9 system for functional genomics of filamentous fungi: applications and challenges

Abstract

Functional genomics enhances the understanding of fundamental fungal biology and aids in improving the production of valuable bioactive fungal compounds. Available gene manipulation approaches to study filamentous fungi are generally inefficient, time-consuming, and laborious. A robust genomic technology CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) is a simple, effective, and precise genome editing tool that has revolutionized gene editing and systematic research on filamentous fungi. This chapter provides an insight into the concepts and recent developments of CRISPR-Cas9 tools for the precise change of endogenous genes and for the complete knockout of their expression, transcriptional regulation and multiplex genome editing. In addition, the current and potential applications of the CRISPR-Cas9 system for decoding and confirmation of the fungal pathogenesis, metabolite engineering, biocontrol, chromatin dynamics, multiple signaling cascades, and cell imaging are highlighted. The chapter also describes various challenges faced in the development and applications of the CRISPR-Cas9 system. Further, the dilemmas associated with the potential applications of these tools in filamentous fungi are explored.