Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.

中文翻译：

---

四倍体鼠尾草（唇形科）基因组的染色体规模组装和进化

多倍体化在植物进化中起着关键作用，但驱动多倍体基因组中同源物（即由全基因组复制（WGD）事件产生的旁系同源物）命运的力量仍有待阐明。在这里，我们展示了四倍体猩红鼠尾草的染色体规模基因组组装（鼠尾草)，最多样化的观赏植物之一。我们在大多数真双子叶植物共享的较老的 WGD 事件（γ 事件）之后发现了三个 WGD 事件的证据。对来自最近 WGD 的同源物进行的全面、时空、全基因组分析揭示了表达不对称性，这可能与基因组重排、转座因子邻近差异、编码序列变异、选择压力和转录因子结合位点差异有关。观察到的同源物之间的差异可能反映了亚功能化和/或新功能化的第一步。该组件为了解 WGD 以及基因和基因组进化提供了强大的工具，可用于开发猩红鼠尾草和其他唇形科物种的功能基因组学和基因工程策略。