The promises and challenges of applying public omics datasets to the development of advanced biofuels producers

Today, advanced biofuels receive increased consideration due to their high energy densities and compatibility with current fuel infrastructure. Rapid technology progress in next-generation sequencing (NGS), systems biology, and synthetic biology has increased the reservoir of public omics data explosively, which facilitates the deep understanding of microbial metabolism and regulation at the systematic level which is critical for guiding metabolic engineering research. Using a model fungal cellulase producer, Trichoderma reesei, as an example, we demonstrated the feasibility of harnessing public genomic and transcriptomic data to guide metabolic engineering. Specifically, we will discuss approaches for utilizing public genomic and transcriptomic datasets to help reconstruct metabolic pathways and identify potential genetic targets for advanced hydrocarbon production improvement. The examination of known regulators and the identification of promoters with different strengths in T. reesei using public databases will also be addressed. Additionally, we will discuss the overall technical challenges encountered in utilizing public omics datasets and review potential solutions to these challenges.