Liu Xiling, Han Bin
National Center for Gene Research/Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China.
Gene. 2009 May 15;437(1-2):71-9. doi: 10.1016/j.gene.2009.02.012. Epub 2009 Mar 2.
Evolutionary conservation of neighbouring gene pairs has been widely explored in many species, but remains poorly understood in plants. The availability of several plant genome sequences allows for an in-depth investigation of this problem in plants. Here, we analyzed the phylogenetic conservation of physically linked gene pairs in nine plant genomes and compared the conservation in different orientations. We also examined several potential determinants to detect whether they affect the conservation of neighbouring gene pairs. Our results suggested that among the three types of neighbouring gene pairs, closely linked parallel pairs might be the least conserved. Intergenic distance was shown to be a major determinant of linkage conservation, suggesting that the conservation of gene order in plants was determined primarily by chance. The enrichment of housekeeping genes was identified to contribute to the conservation of all three types and the enrichment of genes involved in protein metabolism might contribute to the conservation of parallel pairs. Moreover, a co-expressed signal was detected in conserved divergent pairs, which might be determined by intergenic distance.
相邻基因对的进化保守性已在许多物种中得到广泛研究，但在植物中仍了解甚少。多个植物基因组序列的可得性使得对植物中这一问题进行深入研究成为可能。在此，我们分析了九个植物基因组中物理连锁基因对的系统发育保守性，并比较了不同方向上的保守性。我们还研究了几个潜在的决定因素，以检测它们是否影响相邻基因对的保守性。我们的结果表明，在三种类型的相邻基因对中，紧密连锁的平行对可能是最不保守的。基因间距离被证明是连锁保守性的一个主要决定因素，这表明植物中基因顺序的保守性主要由偶然因素决定。已确定管家基因的富集有助于所有三种类型的保守性，而参与蛋白质代谢的基因的富集可能有助于平行对的保守性。此外，在保守的分歧对中检测到共表达信号，这可能由基因间距离决定。
