Microalgae are in focus because of its tremendous potential to produce different value added compounds such as pigments, polysaccharides, cosmetics, fatty acids, proteins, vitamins and so on. Genetic engineering of microalgae promises broader applications in the field of molecular farming for the production of above mentioned industrially valuable compounds. For transformation of any of these gene widely used molecular tools such as particle bombardment, Agrobacterium mediated transformation, electroporation, and less commonly used Conjugation, Agitation with glass beads, Agitation with silicon carbon whiskers, Protoplast transformation with polyethylene glycol and dimethyl sulfoxide are used. The basic mechanism of these methods is to somehow disturb the cell wall and cell membrane of the algal cell and allow the gene to reach the nucleus via nuclear pore to integrate into the nucleus. Using above mentioned methods genes responsible for lipids, terpenoids, carotenoids and other different therapeutic recombinant proteins have been overexpressed. There are different challenges and existing problems for transformation and integration of genes in microalgae which needs to be overcome to fully utilize the potential of this microbe for molecular cloning and overproduction of different value added compounds.

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