Lin Yu, Moret Bernard M E
Laboratory for Computational Biology and Bioinformatics, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
J Comput Biol. 2011 Sep;18(9):1055-64. doi: 10.1089/cmb.2011.0098.
Genomic rearrangements have been studied since the beginnings of modern genetics and models for such rearrangements have been the subject of many papers over the last 10 years. However, none of the extant models can predict the evolution of genomic organization into circular unichromosomal genomes (as in most prokaryotes) and linear multichromosomal genomes (as in most eukaryotes). Very few of these models support gene duplications and losses--yet these events may be more common in evolutionary history than rearrangements and themselves cause apparent rearrangements. We propose a new evolutionary model that integrates gene duplications and losses with genome rearrangements and that leads to genomes with either one (or a very few) circular chromosome or a collection of linear chromosomes. Our model is based on existing rearrangement models and inherits their linear-time algorithms for pairwise distance computation (for rearrangement only). Moreover, our model predictions fit observations about the evolution of gene family sizes and agree with the existing predictions about the growth in the number of chromosomes in eukaryotic genomes.
自现代遗传学诞生之初起，基因组重排就一直被研究，在过去十年里，关于此类重排的模型已成为众多论文的主题。然而，现存的模型中没有一个能够预测基因组组织向环状单染色体基因组（如大多数原核生物那样）和线性多染色体基因组（如大多数真核生物那样）的进化。这些模型中很少有支持基因复制和丢失的——然而这些事件在进化史上可能比重排更为常见，并且它们自身也会导致明显的重排。我们提出了一种新的进化模型，该模型将基因复制和丢失与基因组重排整合在一起，并且会产生具有一条（或极少数）环状染色体或一组线性染色体的基因组。我们的模型基于现有的重排模型，并继承了它们用于成对距离计算（仅针对重排）的线性时间算法。此外，我们的模型预测符合关于基因家族大小进化的观察结果，并且与关于真核生物基因组中染色体数量增长的现有预测一致。
