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BMC Genomics
2026 Mar 24;271:. doi: 10.1186/s12864-026-12764-1.
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Chromosome-level genome provides new insights into the fatty acid biosynthesis and metabolism of the sea urchin Strongylocentrotus intermedius.
Han L, Ding J, Wang H, Zhang Y, Sun J, Zhao C, Zhang W, Zuo R, Wang W, Tian Y, Chang Y.
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UNLABELLED: 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.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-026-12764-1.
No.: 32373109 The National Natural Science Foundation of China, No.: 2023JH1/10200007 The Major Agricultural Project of the Liaoning Provincial Science and Technology Department, No.: XLYC2202001 Liaoning Province "Xingliao Talents Plan" project, No.: 2018YFD0901600 The National Key Research and Development Program of China
Fig. 1. Chromosome-level genome assembly of S. intermedius. A
S. intermedius. B Interactive thermography of Hi-C assembly chromosomes. C A schematic representation of the genomic characteristics of S. intermedius. From outside to inside: 1. miRNA distribution location, 2. chromosome, 3. repeat sequence distribution, 4. gene distribution. they are sliding window 500k. D Statistics for the final corrected S. intermedius genome. E BUSCO assessment results of the S. intermedius genome assembly completeness. F Summary of predicted genes
Fig. 2. Comparative genomic analysis between S. intermedius and others. A Phylogenetic placement of S. intermedius within the metazoan tree. The numbers on the branches indicate the number of gene gains (+) and the number of gene losses (−), which are also displayed as bar plots: gene gain (in green), gene loss (in red), and the remaining gene families (in blue). The divergence times were estimated and displayed below the phylogenetic tree. B Comparison of the gene repertoire of 11 metazoan genomes. C The shared and unique gene families in 4 species of Echinoidea are shown in the Venn diagram
Fig. 3. Functional enrichment analysis (GO and KEGG) of expanded and contracted gene families. A GO enrichment analysis of significantly expanded gene families. B KEGG pathway enrichment analysis of significantly expanded gene families. C GO enrichment analysis of significantly contracted gene families. D KEGG enrichment analyses of the significantly contracted gene families
Fig. 4. Phylogenetic relationship of Elovl (A) and GST (B) genes between S. intermedius and related species. The green branch indicates the S. intermedius lineage that underwent a significant expansion of the Elovl gene family or contraction of the GST gene family
Fig. 5. Fatty acid synthesis-related pathways and gene expression during gonadal development in sea urchins S. intermedius. A Histological features of the sea urchin S. intermedius gonads at different gonad development stages. Paraffin-embedded sections were stained with hematoxylin and eosin. Scale bar: 100 μm. Stage 4 gonads (Ost4, female; Tst4, male) were newly prepared for this study. Samples Ost1–Ost3 and Tst1–Tst3 were derived from our previously published data (PRJNA532998). B Venn diagram of DEGs in each comparison group
Fig. 6. Screening and functional analysis of key genes in S. intermedius at different developmental periods. A Different development stage of S. intermedius. a: fertilized egg (FE), b: 2 cell stage (CS-2), c: 4 cell stage (CS-4), d: 8 cell stage (CS-8), e: 16 cell stage (CS-16), f: 32 cell stage (CS-32), g: multicellular stage (MS), h: blastula stage (BS), i: gastrula stage (GS), j: prism larvae (PL), k: 2-armed larvae (AL-2), l: 4-armed larvae (AL-4), m: 6-armed larvae (AL-6), n: 8-armed larvae (AL-8), o: juvenile sea urchin (JSU). B The number of DEGs in each comparison group, red represents up-regulated genes, and blue represents down-regulated genes. C KEGG enrichment analysis of DEGs at key developmental stages (BS vs GS, AL4 vs AL6, and AL8 vs JSU) in S. intermedius
D Heatmap of key gene expression for growth and development and fatty acid synthesis
