Patchouli (Pogostemon cablin (Blanco) Benth.), a member of the Lamiaceae family, is an important aromatic plant that has been widely used in medicine and perfumery. Here, we report a 1.94 Gb chromosome-scale assembly of the patchouli genome (contig N50 = 7.97 Mb). The gene annotation reveals that tandem duplication of sesquiterpene biosynthetic genes may be a major contributor to the biosynthesis of patchouli bioactivity components. We further phase the genome into two distinct subgenomes (A and B), and identify a chromosome substitution event that have occurred between them. Further investigations show that a burst of universal LTR-RTs in the A subgenome lead to the divergence between two subgenomes. However, no significant subgenome dominance is detected. Finally, we track the evolutionary scenario of patchouli including whole genome tetraploidization, subgenome divergency, hybridization, and chromosome substitution, which are the key forces to determine the complexity of patchouli genome. Our work sheds light on the evolutionary history of patchouli and offers unprecedented genomic resources for fundamental patchouli research and elite germplasm development.

广藿香 ( Pogostemon cablin(Blanco) Benth.) 是唇形科的一员，是一种重要的芳香植物，已广泛用于医药和香料。在这里，我们报告了广藿香基因组的 1.94 Gb 染色体规模组装（重叠群 N50 = 7.97 Mb）。基因注释表明，倍半萜生物合成基因的串联重复可能是广藿香生物活性成分生物合成的主要贡献者。我们进一步将基因组分为两个不同的亚基因组（A 和 B），并确定它们之间发生的染色体替换事件。进一步的研究表明，A 亚基因组中的普遍 LTR-RT 爆发导致两个亚基因组之间的分歧。然而，没有检测到显着的亚基因组优势。最后，我们追踪了广藿香的进化情景，包括全基因组四倍体化、亚基因组趋异、杂交和染色体置换，是决定广藿香基因组复杂性的关键力量。我们的工作揭示了广藿香的进化史，并为广藿香的基础研究和优良种质开发提供了前所未有的基因组资源。