Inferring Ancestral Gene Orders for a Family of Tandemly Arrayed Genes
Inferring Ancestral Gene Orders for a Family of Tandemly Arrayed Genes
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DOI：
10.1089/cmb.2008.0025
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发表时间：
2008-10-01
影响因子：
1.7
通讯作者：
El-Mabrouk, Nadia
中科院分区：
文献类型：
--
作者：
Bertrand, Denis;Lajoie, Mathieu;El-Mabrouk, Nadia
串联排列基因（TAG）构成了大多数基因组的很大一部分，并发挥着重要的生物学作用。它们通过不等重组进化，将重复的基因放在原始基因旁边（串联重复）。已经提出了许多算法来推断 TAG 簇的串联复制历史。然而，许多簇中不同转录方向的存在凸显了一个事实，即倒位等过程也有助于它们的进化。此外，现有算法仅限于研究单个物种中的TAG进化（仅考虑旁系同源基因）。为了规避这些限制，我们考虑了一种涉及重复、基因丢失、倒位和物种形成事件的 TAG 进化模型。提出了一个推断祖先基因顺序的通用框架，该框架可以最大限度地减少整个进化历史中的倒转次数。在方法论层面，本文整合了基因组进化的三种方法：重复树重建、基因树/物种树协调理论以及基于顺序的系统发育重建中使用的倒置中值概念。提出了四种哺乳动物嗅觉受体基因簇的应用。
Tandemly arrayed genes (TAG) constitute a large fraction of most genomes and play important biological roles. They evolve through unequal recombination, which places duplicated genes next to the original ones (tandem duplications). Many algorithms have been proposed to infer a tandem duplication history for a TAG cluster. However, the presence of different transcriptional orientations in many clusters highlights the fact that processes such as inversions also contribute to their evolution. Moreover, existing algorithms are restricted to the study of TAGs evolution in a single species (only paralogous genes are considered). To circumvent these limitations, we consider an evolutionary model for TAGs involving duplication, gene loss, inversion, and speciation events. A general framework to infer ancestral gene orders that minimize the number of inversions in the whole evolutionary history is presented. At the methodological level, this paper integrates three approaches to genome evolution: the duplication tree reconstruction, the gene tree/species tree reconciliation theory, and the concept of inversion median used in order-based phylogeny reconstruction. An application on a cluster of olfactory receptor genes in four mammals is presented.