The infinitely many genes model with horizontal gene transfer
The infinitely many genes model with horizontal gene transfer
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DOI：
10.1214/ejp.v19-2642
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发表时间：
2014-12-14
影响因子：
1.4
通讯作者：
Pfaffelhuber, Peter
中科院分区：
文献类型：
--
作者：
Baumdicker, Franz;Pfaffelhuber, Peter
细菌物种的基因组比真核生物的基因组灵活得多。特别是，细菌的分布式基因组假说指出，细菌种群中存在的基因总数大于每个个体的基因组。泛基因组，即细菌物种（或样品）的所有基因的集合，包括存在于所有活个体中的核心基因和仅由一些个体携带的辅助基因。细菌已经发展出水平交换基因的机制，即没有直接关系。在这里，我们扩展了Baumdicker，Hess和Pfaffelhuber（2010）的无限多基因模型，用于这种水平基因转移。我们采取谱系的观点，并给出了泛基因组中所有基因的联合谱系的构造-称为祖先基因转移图。作为应用，我们计算了水平基因转移的无限多基因模型下的几个统计量（如两个个体之间的差异数和基因频率谱）的矩。
The genome of bacterial species is much more flexible than that of eukaryotes. In particular, the distributed genome hypothesis for bacteria states that the total number of genes present in a bacterial population is greater than the genome of every single individual. The pangenome, i.e. the set of all genes of a bacterial species (or a sample), comprises the core genes which are present in all living individuals, and accessory genes, which are carried only by some individuals. Bacteria have developed mechanisms in order to exchange genes horizontally, i.e. without a direct relationship. Here, we extend the infinitely many genes model from Baumdicker, Hess and Pfaffelhuber (2010) for such horizontal gene transfer. We take a genealogical view and give a construction - called the Ancestral Gene Transfer Graph - of the joint genealogy of all genes in the pangenome. As application, we compute moments of several statistics (e.g. the number of differences between two individuals and the gene frequency spectrum) under the infinitely many genes model with horizontal gene transfer.