Clustering criteria affect pangenome functional characterization, core genome inference, and reconstruction of ancestral gene content to different extents. Species-wise estimates of pangenome and core genome sizes change by the same factor when using different clustering criteria, allowing robust cross-species comparisons regardless of the clustering criterion. However, cross-species comparisons of genome plasticity and functional profiles are substantially affected by inconsistencies among clustering criteria. Such inconsistencies are driven not only by mobile genetic elements, but also by genes involved in defense, secondary metabolism, and other accessory functions. In some pangenome features, the variability attributed to methodological inconsistencies can even exceed the effect sizes of ecological and phylogenetic variables.
Choosing an appropriate criterion for gene clustering is critical to conduct unbiased pangenome analyses. We provide practical guidelines to choose the right method depending on the research goals and the quality of genome assemblies, and a benchmarking dataset to assess the robustness and reproducibility of future comparative studies.
结果:聚类标准影响pangenome功能表征,核心基因组推断,并在不同程度上重建祖先基因的含量。使用不同的聚类标准时,pangenome和核心基因组大小的物种估计变化相同的因素,无论聚类标准如何,都允许进行稳健的跨物种比较。然而,基因组可塑性和功能谱的跨物种比较受到聚类标准之间不一致的影响。这种不一致不仅是由可移动的遗传因素驱动的,还有参与防御的基因,次生代谢,和其他附件功能。在一些令人惊奇的特征中,归因于方法不一致的可变性甚至可以超过生态和系统发育变量的影响大小。
结论:选择合适的基因聚类标准对于进行无偏全基因组分析至关重要。我们提供实用指南,根据研究目标和基因组组装的质量选择正确的方法,和基准数据集,以评估未来比较研究的稳健性和可重复性。