Phylotranscriptomic analyses reveal asymmetrical gene duplication dynamics and signatures of ancient polyploidy in mints

Ancient duplication events and retained gene duplicates have contributed to the evolution of many novel plant traits and, consequently, to the diversity and complexity within and across plant lineages. While mounting evidence highlights the importance whole-genome duplication (WGD; polyploidy) and its key role as an evolutionary driver, gene duplication dynamics and mechanisms, both of which are fundamental to our understanding of evolutionary process and patterns of plant diversity, remain poorly characterized in many clades. We use newly available transcriptomic data and a robust phylogeny to investigate the prevalence, occurrence, and timing of gene duplications in Lamiaceae (mints), a species-rich and chemically diverse clade with many ecologically, economically, and culturally important species. We also infer putative WGDs—an extreme mechanism of gene duplication—using large-scale data sets from synonymous divergence (KS), phylotranscriptomic, and divergence time analyses. We find ...

古复制事件与保留的基因重复拷贝，推动了诸多植物新颖性状的演化，进而塑造了植物类群内部及跨类群的多样性与复杂性。尽管越来越多的证据凸显了全基因组复制（whole-genome duplication, WGD；多倍化（polyploidy））的重要性及其作为演化驱动力的核心作用，但基因复制的动态过程与分子机制——二者均是我们理解演化过程与植物多样性格局的基础——在诸多演化支中仍未得到充分解析。我们借助新近公开的转录组数据与稳健的系统发育树，对唇形科（Lamiaceae，薄荷类）中基因复制的普遍性、发生情况与发生时间展开研究。该类群物种丰富、化学多样性突出，包含诸多具有重要生态、经济与文化价值的物种。我们还通过同义替换分歧（synonymous divergence, KS）、系统转录组学与分歧时间分析的大规模数据集，推断推定的全基因组复制事件——这是一种极端的基因复制机制。我们发现……