Fungi such as yeast and filamentous fungi are the best-known eukaryotic model organism capable of post-transitional modification and secreting industrially important products (Nevalainen et al., 2005; Sharma et al., 2009). Fungi are exploited for the vast production of secondary metabolites, enzymes and antibiotics (Dufossé, 2014). Some of the properties that make yeast particularly suitable for biological studies include rapid growth, dispersed cells, the ease of replica plating and mutant isolation, well-defined genetic system, and most importantly, a highly versatile DNA transformation system (Schneiter, 2004). Strain improvement of fungi relies on random mutagenesis or on classical breeding and genetic
crossing of two strains, followed by screening for mutants and progeny exhibiting enhanced properties of interest. Classical approaches such as the use of mutagenesis and selection (random screening) and recombination, is still considered to be very important in strain improvement. Considering the fact that classical approach is based on trial and error, strain development searches for new strains that give better results and more products that are capable of further development and are convenient in use. Biotechnological approaches have paved the way for bioprocess technology through newer approaches of strain improvement with retaining the impact of classical approaches. Genomics and proteomics have revolutionized the bioprocess industry with newer strain improvement techniques and bringing genetic variation and desirable characters to the microbes have resulted in huge profits of the bioprocess industries. Thus, a set of immensely powerful experimental and modeling techniques have become available in the last few decades that have enabled us to change the genome of the fungi and their products (secondary metabolites).