A pan‐genome perspective uncovers the core genetic basis and evolutionary adaptation of lipid synthesis and vesicular transport in Nannochloropsis

Nannochloropsis microalgae are widely recognized as sustainable cell factories for producing nutritional oils and biofuels due to their high-lipid content. However, a comprehensive understanding of the genetic basis of their oleaginous traits across diverse species has been limited. Here, we constructed a pan-genome of 17 Nannochloropsis species comprising 14,851 gene families. Our analysis defined a distinct genetic architecture for lipid metabolism: Gene families associated with vesicular transport formed a conserved core functional module, whereas the genetic collection for lipid metabolism showed greater plasticity and was primarily classified as part of the soft-core genome. This finding establishes a genetic blueprint for the coevolution between a stable cellular "logistics network" and an adaptable "biosynthetic factory." Evolutionary analysis further indicated that the DGAT and fatty acid desaturase families have species-specific expansions in Nannochloropsis, suggesting a potential role in enhancing lipid accumulation. By integrating 231 transcriptome datasets, we identified key genes (ACP2 and DGAT2) that were highly upregulated under nitrogen deprivation and pinpointed a set of core genes with high expression levels involved in vesicular transport. This "Infrastructure-Toolkit" model provides both genetic targets for strain improvement and a broader framework for understanding lipid accumulation in oleaginous microorganisms.