Integrative analysis of the oil biosynthesis of Hippophae rhamnoides through chromosome-level genome and whole-transcriptome analyses

Sea buckthorn ( Hippophae rhamnoides L.) is a perennial woody oil and horticultural crop from the Elaeagnaceae family with high nutritional and economic value. The novel cultivar 'Gaoyou No.1' (PVR No. 20190345) exhibits superior seed oil yield and quality. However, the lack of a high-quality reference genome for this cultivar has greatly hindered molecular studies on the accumulation of unsaturated fatty acids (FAs) and triacylglycerols (TAGs) in its seed oil. Here, we report a chromosome-level genome assembly of 'Gaoyou No.1', with a final size of 1.27 Gb and a scaffold N50 of 99.72 Mb, alongside 26 429 annotated protein-coding genes. Repetitive sequences accounted for 72.35% of the genome. Comparative genomic analysis dated the divergence of H. rhamnoides from Juglans regia to approximately 107.5 million years ago. We identified 14 298 structural variations (SVs) in 'Gaoyou No.1' compared with a common cultivated sea buckthorn accession. Through whole-transcriptome profiling, 49 and 55 enzymatic genes involved in the FA and TAG biosynthesis pathways were identified, respectively; 21 of these genes harbored SVs, in which the copy number variations of SAD_0.613 and LPCAT_ 16.398 enhanced their expression via a gene dosage effect, and further promoted the oil biosynthesis in 'Gaoyou No.1'. Furthermore, 90 lncRNA–mRNA pairs, 88 miRNA–mRNA pairs, and 42 lncRNA–miRNA–mRNA regulatory modules were predicted. The interactions within 12 key modules, such as lncRNA051245–miRn43– FAD2 and lncRNA111000–miRn275– LPAT were experimentally verified. We propose that these SVs and regulatory modules collectively contribute to the improved seed oil yield and quality of 'Gaoyou No.1', providing promising targets for genetic improvement. Our research yields novel insights into the molecular mechanisms underlying high FA and TAG accumulation in sea buckthorn, while also furnishing valuable genomic resources for evolutionary research in Elaeagnaceae and molecular breeding development.