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Microalgae and cyanobacteria can produce a large portfolio of biocompounds, commonly pursued by several industries. Despite the general interest and knowledge of microalgae cultivation and processing, optimizing product quality and generating higher yields are always desired. Meanwhile, a majority of valuable metabolites are often synthesized at higher quantities upon exposure to stress, creating an inverse correlation between biomass productivity and product titres. As metabolism combines both anabolic and catabolic reactions, it is utmost important to comprehend key gene regulation and pathway mechanisms to understand final accumulation of target metabolites. In this chapter, we have provided a general overview of ‘omics’ tools covering genomics, transcriptomics, metabolomics, and proteomics to understand metabolic pathways related to commercial scale production of key microalgae and cyanobacteria metabolites, such as carotenoids (beta-carotene, astaxanthin, lutein, fucoxanthin), omega fatty acids, and phycocyanin. Information provided in this chapter is meant to demonstrate the power of these tools to help improve production metrics of metabolites relevant to commercial scale production.

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