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系统发生转录组分析揭示薄荷属植物中不对称基因复制的动态和古老多倍体的特征。

Phylotranscriptomic Analyses Reveal Asymmetrical Gene Duplication Dynamics and Signatures of Ancient Polyploidy in Mints.

机构信息

Florida Museum of Natural History, University of Florida.

Department of Biology, University of Florida.

出版信息

Genome Biol Evol. 2019 Dec 1;11(12):3393-3408. doi: 10.1093/gbe/evz239.

Abstract

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. Although mounting evidence highlights the importance of 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 evidence for widespread but asymmetrical levels of gene duplication and ancient polyploidy in Lamiaceae that correlate with species richness, including pronounced levels of gene duplication and putative ancient WGDs (7-18 events) within the large subclade Nepetoideae and up to 10 additional WGD events in other subclades. Our results help disentangle WGD-derived gene duplicates from those produced by other mechanisms and illustrate the nonuniformity of duplication dynamics in mints, setting the stage for future investigations that explore their impacts on trait diversity and species diversification. Our results also provide a practical context for evaluating the benefits and limitations of transcriptome-based approaches to inferring WGD, and we offer recommendations for researchers interested in investigating ancient WGDs in other plant groups.

摘要

远古的复制事件和保留下来的基因重复为许多新的植物特征的进化做出了贡献,从而导致了植物谱系内部和之间的多样性和复杂性。尽管越来越多的证据强调了全基因组复制(WGD;多倍体)的重要性及其作为进化驱动因素的关键作用,但对于基因复制的动态和机制,这两者都是理解进化过程和植物多样性模式的基础,在许多进化枝中仍然没有得到很好的描述。我们利用新获得的转录组数据和稳健的系统发育关系,研究了唇形科(薄荷科)基因重复的普遍性、发生和时间,该科是一个物种丰富、化学成分多样的进化枝,拥有许多具有生态、经济和文化重要性的物种。我们还使用来自同义分歧(KS)、系统发生转录组学和分化时间分析的大规模数据集,推断了可能的 WGD-一种极端的基因复制机制。我们发现唇形科存在广泛但不对称的基因复制和远古多倍体水平的证据,这与物种丰富度相关,包括 Nepetoideae 这个大的亚科中明显的基因重复水平和可能的远古 WGD(7-18 个事件)以及其他亚科中多达 10 个额外的 WGD 事件。我们的研究结果有助于将 WGD 衍生的基因重复与其他机制产生的基因重复区分开来,并说明了薄荷科基因复制动态的非均匀性,为未来的研究提供了基础,这些研究将探索它们对性状多样性和物种多样化的影响。我们的研究结果还为评估基于转录组的推断 WGD 的方法的优势和局限性提供了实际背景,并为有兴趣在其他植物类群中研究远古 WGD 的研究人员提供了建议。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/52ec/7145710/605ea4ca443e/evz239f1.jpg

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