Scientific reportsNov 27, 2025

Precise genome editing in the microalga Nannochloropsis oceanica without DNA breaks or added genes using removable CRISPR base editing tools

CRISPR Gene Editing Weekly Brief ↗PubMed ↗DOI ↗OA ↗

Updated Jun 27, 2026

Abstract

Essence

A removable cytidine vector enabled double-strand-break-free and transgene-free genome editing in Nannochloropsis oceanica.

Evidence

This microalgal genome-editing platform experiment induced cytidine-to-thymidine substitutions at six target sites across five endogenous genes, with 29.2% to 47.6% activity at cytidines in positions 16 to 19 from the PAM and detectable plasmid removal.

Caveat

The study demonstrates editing feasibility in selected targets but does not show improved lipid productivity or industrial performance.

Simplified

The accumulation of lipids by algae makes them attractive for carbon-neutral fuel production; however, the industrial-scale production of algal lipids has yet to be achieved. Currently, researchers are trying to improve the lipid productivity of algal strains using genome editing for molecular breeding with CRISPR-Cas9, which allows the efficient alteration of genomic information. However, CRISPR-based gene modification via double-strand breaks sometimes induces unintended large deletions that are toxic to host cells. Here, we applied the cytidine base editor combined with an backbone containing a centromere and autonomous replication sequence to the microalga Nannochloropsis oceanica. The cytosine base editor introduces cytidine-to-thymidine base substitutions using deaminase without double-strand breaks, and an episomal vector enables plasmid removal after base substitution. We succeeded in inducing cytidine-to-thymidine substitution at the six target sites of five endogenous genes. The base substitution activity ranged from 29.2% to 47.6% on cytidine bases at the 16th to 19th positions from the protospacer adjacent motifs. The removal of base editor plasmids was also detected, which is essential for constructing transgene-free strains. Our results provide insights into the applicability of further technologies in the genetic modification of microalgae.

Key numbers

29.2% to 47.6%

C-to-T Substitution Efficiency Range

Substitution rates at various target sites in Nannochloropsis oceanica.

6 of 5

Target Genes Edited

Total number of target sites across five endogenous genes.

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Precise genome editing in the microalga Nannochloropsis oceanica without DNA breaks or added genes using removable CRISPR base editing tools

Abstract

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