homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes
homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes
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DOI：
10.1111/2041-210x.14072
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发表时间：
2023-03-13
影响因子：
6.6
通讯作者：
Rothfels, Carl J.
中科院分区：
文献类型：
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作者：
Freyman, William A.;Johnson, Matthew G.;Rothfels, Carl J.
1.生物体如异源多倍体和F1杂种包含多个不同的亚基因组，每个亚基因组都可能有自己的进化历史。这些生物体对多位点系统发育推断和其他分析提出了挑战，因为不清楚来自不同位点的哪些基因拷贝来自相同的亚基因组，从而共享进化历史.在这里，我们介绍homologizer，一种灵活的贝叶斯方法，使用系统发育框架来推断基因拷贝在基因座之间的相位到各自的亚基因组中。通过使用模拟测试，我们证明了同源是强大的范围广泛的因素，如不完整的谱系排序和基因座的系统发育信息。此外，我们还建立了同源子在真实的数据上的效用，通过分析一个多位点数据集，该数据集由来自蕨类植物Cystopteridaceae的9个二倍体和19个四倍体组成.最后，我们描述了同源物如何可能被用于超出其核心定相功能，以确定非同源序列，如隐藏的旁系同源物或污染物。
1. Organisms such as allopolyploids and F1 hybrids contain multiple distinct subgenomes, each potentially with its own evolutionary history. These organisms pre-sent a challenge for multilocus phylogenetic inference and other analyses since it is not apparent which gene copies from different loci are from the same subgenome and thus share an evolutionary history.2. Here we introduce homologizer, a flexible Bayesian approach that uses a phylogenetic framework to infer the phasing of gene copies across loci into their respective subgenomes.3. Through the use of simulation tests, we demonstrate that homologizer is robust to a wide range of factors, such as incomplete lineage sorting and the phylogenetic informativeness of loci. Furthermore, we establish the utility of homologizer on real data, by analysing a multilocus dataset consisting of nine diploids and 19 tetraploids from the fern family Cystopteridaceae.4. Finally, we describe how homologizer may potentially be used beyond its core phasing functionality to identify non-homologous sequences, such as hidden paralogs or contaminants.