A modular all-in-one genetic engineering tool for the diatom Phaeodactylum tricornutum based on CRISPR-Cas12a

The marine diatom Phaeodactylum tricornutum is a model microalgal species that is emerging as a platform for the photosynthetic production of industrial chemicals such as carotenoids and polyunsaturated fatty acids, but it lacks efficient genetic tools to realize this potential. In this study, we expanded the toolbox for P. tricornutum by developing an all-in-one-plasmid Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas12a genome engineering tool. We achieved efficient (88-93%) knockout of the adenine phosphoribosyl transferase gene, and we validated the tool by targeting the uridine monophosphate synthase gene and two putative prenyltransferases (Phatr3_J15180 and Phatr3_J16615). Moreover, we demonstrated multiplexed editing of different genetic loci simultaneously using a single pre-CRISPR RNA molecule that was processed by Cas12a. Finally, we enabled homology-directed repair-mediated gene knock-in by delivering a repair template on the same plasmid as the CRISPR-Cas12a components, which had not been previously achieved in P. tricornutum. This genetic engineering tool can either complement or substitute currently available ones.