To date, little is known about the evolution of fern genomes, with only two small genomes published from the heterosporous Salviniales. Here we assembled the genome of Alsophila spinulosa, known as the flying spider-monkey tree fern, onto 69 pseudochromosomes. The remarkable preservation of synteny, despite resulting from an ancient whole-genome duplication over 100 million years ago, is unprecedented in plants and probably speaks to the uniqueness of tree ferns. Our detailed investigations into stem anatomy and lignin biosynthesis shed new light on the evolution of stem formation in tree ferns. We identified a phenolic compound, alsophilin, that is abundant in xylem, and we provided the molecular basis for its biosynthesis. Finally, analysis of demographic history revealed two genetic bottlenecks, resulting in rapid demographic declines of A. spinulosa. The A. spinulosa genome fills a crucial gap in the plant genomic landscape and helps elucidate many unique aspects of tree fern biology.

迄今为止，人们对蕨类植物基因组的进化知之甚少，仅发表了异孢子萨尔维尼亚目中的两个小型基因组。在这里，我们将桫椤（也被称为飞蜘蛛猴树蕨）的基因组组装到 69 条假染色体上。尽管同线性的显着保存是由一亿多年前的古代全基因组复制造成的，但这在植物中是前所未有的，这可能说明了树蕨的独特性。我们对茎解剖学和木质素生物合成的详细研究为树蕨茎形成的进化提供了新的线索。我们鉴定了木质部中丰富的酚类化合物，即还亲素，并为其生物合成提供了分子基础。最后，对人口统计历史的分析揭示了两个遗传瓶颈，导致刺无花果的人口统计迅速下降。刺蕨基因组填补了植物基因组景观中的一个关键空白，并有助于阐明树蕨生物学的许多独特方面。