Polyunsaturated fatty acids (PUFAs) are important nutrients that play critical roles in sea urchin reproduction and early development. Strongylocentrotus intermedius, the only commercially cultured sea urchin species in China with substantial economic value, has edible gonads that are particularly rich in PUFAs. In this study, we investigated the molecular mechanisms underlying fatty acid biosynthesis and metabolism through chromosome-level genome assembly, evolutionary analysis, and transcriptomic profiling across developmental and gonadal stages. We assembled a chromosome-level genome (704.9 Mb; Scaffold N50 30 Mb) and identified an expansion of the Elovl gene family, indicating a strong endogenous capacity for fatty acid synthesis. To systematically characterize metabolic changes during gonadal development, raw RNA-seq data from previously published gonadal samples were re-analyzed together with newly generated stage 4 gonadal samples. Pathway analysis revealed that unsaturated fatty acid biosynthesis was more active during early gonadal development in males, whereas in females it remained elevated during later developmental stages, suggesting that females maintain sustained fatty acid biosynthesis throughout gonadal development, while males prioritize rapid sperm production at immature stages. During larval development, the expression of key fatty acid synthesis genes (Fads, Elovl5, Elovl4, and ACSL6) gradually decreased as planktonic larvae transitioned to benthic juveniles and endogenous lipid reserves were progressively consumed, reflecting metabolic adaptation to environmental and developmental changes. Collectively, these findings advance our understanding of fatty acid metabolism in echinoderms and provide a valuable genomic and transcriptomic resource for future studies on lipid biosynthesis and metabolism in marine invertebrates.
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