Analysis of Gene Order Evolution Beyond Single-Copy Genes
Analysis of Gene Order Evolution Beyond Single-Copy Genes
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DOI：
10.1007/978-1-61779-582-4_15
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发表时间：
2012-01-01
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影响因子：
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通讯作者：
Sankoff, David
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文献类型：
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作者：
El-Mabrouk, Nadia;Sankoff, David
本章的目的是提供基因组重排领域的全面回顾，即比较基因组学，基于基因组作为符号基因的有序序列的表示。我们特别关注基因组重排的“困难部分”，即如何处理重复基因。主要的问题是：今天的基因组是如何从一个共同的祖先进化而来的？解释观察到的基因顺序的最现实的进化情景是什么？祖先基因组的内容和结构是什么？我们的目标是提供一个简洁但完整的领域概述，从寻找基因组作为有序基因或块序列的适当表示的实际问题开始，即正畸学，谬误学和合成块识别的问题。然后，我们考虑了基因组织的三个层次：基因家族水平（通过复制、丢失和物种形成的进化）、集群水平（通过串联复制的进化）和基因组水平（所有类型的重排事件，包括全基因组复制）。
The purpose of this chapter is to provide a comprehensive review of the field of genome rearrangement, i.e., comparative genomics, based on the representation of genomes as ordered sequences of signed genes. We specifically focus on the "hard part" of genome rearrangement, how to handle duplicated genes. The main questions are: how have present-day genomes evolved from a common ancestor? What are the most realistic evolutionary scenarios explaining the observed gene orders? What was the content and structure of ancestral genomes? We aim to provide a concise but complete overview of the field, starting with the practical problem of finding an appropriate representation of a genome as a sequence of ordered genes or blocks, namely the problems of orthology, paralogy, and synteny block identification. We then consider three levels of gene organization: the gene family level (evolution by duplication, loss, and speciation), the cluster level (evolution by tandem duplications), and the genome level (all types of rearrangement events, including whole genome duplication).