With the assembly of increasing numbers of plant genomes, it is becoming accepted that a single reference assembly does not reflect the gene diversity of a species. The production of pangenomes, which reflect the structural variation and polymorphisms in genomes, enables in depth comparisons of variation within species or higher taxonomic groups. In this review, we discuss the current and emerging approaches for pangenome assembly, analysis and visualisation. In addition, we consider the potential of pangenomes for applied crop improvement, evolutionary and biodiversity studies. To fully exploit the value of pangenomes it is important to integrate broad information such as phenotypic, environmental, and expression data to gain insights into the role of variable regions within genomes.

中文翻译：

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植物基因组学：方法，应用和进步。

随着越来越多的植物基因组的组装，人们越来越接受单一参考组装不能反映物种的基因多样性。泛基因组的产生反映了基因组中的结构变异和多态性，可以深入比较物种或更高分类群内的变异。在这篇综述中，我们讨论了全基因组组装，分析和可视化的当前和新兴方法。此外，我们考虑了全基因组在应用作物改良，进化和生物多样性研究中的潜力。为了充分利用泛基因组的价值，重要的是整合广泛的信息，例如表型，环境和表达数据，以深入了解基因组中可变区的作用。