A pan-genome perspective uncovers the core genetic basis and evolutionary adaptation of lipid synthesis and vesicular transport in Nannochloropsis.
TL;DR
A pan-genome of 17 Nannochloropsis species comprising 14,851 gene families is constructed and a distinct genetic architecture for lipid metabolism is defined: 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.
Abstract
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.