A versatile tool for gene editing in the diatom <i>Thalassiosira pseudonana</i>

Diatoms are major contributors to marine primary production and global CO2 fixation, with the centric diatom Thalassiosira pseudonana a powerful model for understanding biogeochemical processes including carbon fixation and silicification. Whilst there are molecular tools available for fluorescent protein (FP) tagging and CRISPR/Cas9 genome editing in T. pseudonana, these require the delivery of multiple vectors or have limited versatility. Additionally, scarless endogenous tagging, that results in a fluorescent protein fusion expressed from its native genomic location, has yet to be developed. Here we describe a versatile modular Golden Gate-based toolkit for T. pseudonana that through the delivery of a single-episome via bacterial conjugation enables: [1] FP tagging, [2] dual FP tagging, [3] CRISPR/Cas9 genome editing, [4] simultaneous FP tagging with gene editing, and [5] scarless endogenous FP tagging. We further expand the available parts for T. pseudonana by validating three additional FPs and two untested promoter/terminator pairs. We demonstrate the versatility of our system by knocking out Diatom Pyrenoid Component 1 (DPC1), whilst simultaneously GFP tagging the Rubisco small subunit (rbcS); and by endogenously GFP tagging the bestrophin-like protein BST2. Whilst DPC1 knock-out does not result in a major pyrenoid structural defect due to unperturbed rbcS-GFP localization to the pyrenoid, we confirm that BST2 localizes to the pyrenoid and exhibits increased fluorescence under low CO2 - supporting a role in diatom carbon fixation. Our developed genetic tools provide a robust framework for exploring cellular processes in diatoms, accelerating routine studies and enabling systematic, quantitative and large-scale studies.