Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
Methods Mol Biol. 2023;2545:3-18. doi: 10.1007/978-1-0716-2561-3_1.
Whole-genome sequence data have revealed that numerous eukaryotic organisms derive from distant polyploid ancestors, even when these same organisms are genetically and karyotypically diploid. Such ancient whole-genome duplications (WGDs) have been important for long-term genome evolution and are often speculatively associated with important evolutionary events such as key innovations, adaptive radiations, or survival after mass extinctions. Clearly, reliable methods for unveiling ancient WGDs are key toward furthering understanding of the long-term evolutionary significance of polyploidy. In this chapter, we describe a set of basic established comparative genomics approaches for the inference of ancient WGDs from genomic data based on empirical age distributions and collinearity analyses, explain the principles on which they are based, and illustrate a basic workflow using the software "wgd," geared toward a typical exploratory analysis of a newly obtained genome sequence.
全基因组序列数据表明，许多真核生物源自遥远的多倍体祖先，即使这些生物在遗传和染色体组型上是二倍体。这种古老的全基因组加倍（WGD）对长期的基因组进化很重要，并且经常与重要的进化事件相关联，如关键创新、适应性辐射或大灭绝后的生存。显然，揭示古老 WGD 的可靠方法是进一步了解多倍体长期进化意义的关键。在本章中，我们描述了一组基本的比较基因组学方法，用于根据经验年龄分布和共线性分析从基因组数据推断古老的 WGD，解释它们所基于的原理，并使用“wgd”软件说明一个基本工作流程，旨在对新获得的基因组序列进行典型的探索性分析。
