Aristolochia, a genus in the magnoliid order Piperales, has been famous for centuries for its highly specialized flowers and wide medicinal applications. Here, we present a new, high-quality genome sequence of Aristolochia fimbriata, a species that, similar to Amborella trichopoda, lacks further whole-genome duplications since the origin of extant angiosperms. As such, the A. fimbriata genome is an excellent reference for inferences of angiosperm genome evolution, enabling detection of two novel whole-genome duplications in Piperales and dating of previously reported whole-genome duplications in other magnoliids. Genomic comparisons between A. fimbriata and other angiosperms facilitated the identification of ancient genomic rearrangements suggesting the placement of magnoliids as sister to monocots, whereas phylogenetic inferences based on sequence data we compiled yielded ambiguous relationships. By identifying associated homologues and investigating their evolutionary histories and expression patterns, we revealed highly conserved floral developmental genes and their distinct downstream regulatory network that may contribute to the complex flower morphology in A. fimbriata. Finally, we elucidated the genetic basis underlying the biosynthesis of terpenoids and aristolochic acids in A. fimbriata.

马兜铃属木兰属 Piperales，几个世纪以来一直以其高度专业化的花卉和广泛的药用应用而闻名。在这里，我们提出了一种新的、高质量的Aristolochia fimbriata基因组序列，该物种与Amborella trichopoda相似，自现存被子植物起源以来缺乏进一步的全基因组重复。因此，A. fimbriata基因组是推断被子植物基因组进化的极好参考，能够检测 Piperales 中两种新的全基因组重复，并确定之前报道的其他木兰中全基因组重复的年代。A. fimbriata之间的基因组比较和其他被子植物促进了古代基因组重排的鉴定，表明木兰科植物作为单子叶植物的姐妹，而基于我们汇编的序列数据的系统发育推断产生了模棱两可的关系。通过鉴定相关的同源物并研究它们的进化历史和表达模式，我们揭示了高度保守的花发育基因及其独特的下游调控网络，这可能有助于A. fimbriata中复杂的花形态。最后，我们阐明了A. fimbriata中萜类化合物和马兜铃酸生物合成的遗传基础。