23andMe Inc., Sunnyvale, CA, USA.
University Herbarium and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA.
Methods Mol Biol. 2023;2545:123-138. doi: 10.1007/978-1-0716-2561-3_6.
This chapter describes the usage of homologizer to phase gene copies into polyploid subgenomes. Allopolyploids contain multiple copies of each genetic locus, where each copy potentially belongs to a different subgenome with its own distinct evolutionary history. If gene copies across different loci are incorrectly phased (i.e., assigned to the wrong subgenome), then the bifurcating tree assumption underlying multilocus phylogenetic inference and related analyses will be violated, leading to unsound results. homologizer is a highly flexible Bayesian method that uses a phylogenetic framework to infer the posterior probabilities of the phasing of gene copies into subgenomes. We describe how to prepare input data and other considerations needed to perform homologizer analyses and demonstrate how to visualize and interpret the results. We first walk through a basic example using homologizer to phase gene copies into polyploid subgenomes and then demonstrate how homologizer can be used as a hypothesis-testing tool to detect non-homeologous sequences such as hidden paralogs or allelic variation through the tools of Bayesian model comparison.
这一章描述了 homologizer 如何将基因拷贝相位到多倍体亚基因组中。异源多倍体包含每个遗传基因座的多个拷贝，每个拷贝可能属于不同的亚基因组，具有自己独特的进化历史。如果不同基因座的拷贝相位不正确（即，被分配到错误的亚基因组），那么基于多基因座系统发育推断和相关分析的分支树假设将被违反，导致结果不可靠。homologizer 是一种高度灵活的贝叶斯方法，它使用系统发育框架来推断基因拷贝相位到亚基因组的后验概率。我们描述了如何准备输入数据和进行 homologizer 分析所需的其他考虑因素，并演示了如何可视化和解释结果。我们首先使用 homologizer 来将相基因拷贝相位到多倍体亚基因组中，然后演示了如何将 homologizer 用作假设检验工具，通过贝叶斯模型比较的工具来检测非同源序列，例如隐藏的旁系同源物或等位基因变异。
