Torreya plants produce dry fruits with assorted functions. Here, we report the 19-Gb chromosome-level genome assembly of T. grandis. The genome is shaped by ancient whole-genome duplications and recurrent LTR retrotransposon bursts. Comparative genomic analyses reveal key genes involved in reproductive organ development, cell wall biosynthesis and seed storage. Two genes encoding a C₁₈ Δ⁹-elongase and a C₂₀ Δ⁵-desaturase are identified to be responsible for sciadonic acid biosynthesis and both are present in diverse plant lineages except angiosperms. We demonstrate that the histidine-rich boxes of the Δ⁵-desaturase are crucial for its catalytic activity. Methylome analysis reveals that methylation valleys of the T. grandis seed genome harbor genes associated with important seed activities, including cell wall and lipid biosynthesis. Moreover, seed development is accompanied by DNA methylation changes that possibly fuel energy production. This study provides important genomic resources and elucidates the evolutionary mechanism of sciadonic acid biosynthesis in land plants.

香榧植物产生具有多种功能的干果。在这里，我们报告了T. grandis的 19-Gb 染色体级基因组组装。基因组是由古老的全基因组复制和反复出现的 LTR 逆转录转座子爆发形成的。比较基因组分析揭示了参与生殖器官发育、细胞壁生物合成和种子储存的关键基因。编码 C ₁₈ Δ ⁹ - 延长酶和 C ₂₀ Δ ⁵ - 去饱和酶的两个基因被鉴定为负责 sciadonic 酸生物合成，并且两者都存在于除被子植物之外的多种植物谱系中。^{我们证明了 Δ 5}的富含组氨酸的盒子-去饱和酶对其催化活性至关重要。甲基化组分析表明，T. grandis种子基因组的甲基化谷含有与重要种子活动相关的基因，包括细胞壁和脂质生物合成。此外，种子发育伴随着可能促进能量产生的 DNA 甲基化变化。该研究提供了重要的基因组资源，并阐明了陆地植物中 sciadonic 酸生物合成的进化机制。