Genome-scale analysis of positionally relocated genes
Genome-scale analysis of positionally relocated genes
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DOI：
10.1101/gr.7062307
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发表时间：
2007-12-01
期刊：
影响因子：
7
通讯作者：
Gelbart, William M.
中科院分区：
文献类型：
--
作者：
Bhutkar, Arjun;Russo, Susan M.;Gelbart, William M.
在进化过程中，基因组重组包括大规模的事件，如倒位，易位，片段甚至全基因组复制，以及精细的事件，如单个基因的重新定位。后一类，我们将称为位置重新定位基因（PRG），是本报告的主题。这种PRG的大小和可能的贡献机制的评估是通过相关基因组的比较分析来帮助的，其中保守的染色体组织可以帮助识别在这些基因组的谱系中已经获得新位置的基因。在这里，我们利用两种方法来全面确定重新定位的蛋白质编码基因在最近测序的果蝇属的12种基因组。我们使用例外的染色体臂（穆勒元件）协会大多数果蝇基因的维护的一般规则，以确定一个主要类别的PRG。我们还确定了一个部分重叠的PRG之间的“嵌入式基因”，位于其他周围的基因的范围内。我们提供的证据表明，PRG运动至少有两个不同的起源：一些事件发生通过反转录转座加工RNA和其他通过DNA为基础的转座机制。总体而言，我们确定了几百PRG内出现的一个谱系的属果蝇的生殖系统，并提供了暗示性的证据，几千个这样的事件发生在辐射的昆虫双翅目，从而说明了PRG运动的贡献的大小在进化过程中染色体重组。
During evolution, genome reorganization includes large-scale events such as inversions, translocations, and segmental or even whole-genome duplications, as well as fine-scale events such as the relocation of individual genes. This latter category, which we will refer to as positionally relocated genes (PRGs), is the subject of this report. Assessment of the magnitude of such PRGs and of possible contributing mechanisms is aided by a comparative analysis of related genomes, where conserved chromosomal organization can aid in identifying genes that have acquired a new location in a lineage of these genomes. Here we utilize two methods to comprehensively identify relocated protein-coding genes in the recently sequenced genomes of 12 species of genus Drosophila. We use exceptions to the general rule of maintenance of chromosome arm ( Muller element) association for most Drosophila genes to identify one major class of PRGs. We also identify a partially overlapping set of PRGs among "embedded genes," located within the extents of other surrounding genes. We provide evidence that PRG movements have at least two different origins: Some events occur via retrotransposition of processed RNAs and others via a DNA-based transposition mechanism. Overall, we identify several hundred PRGs that arose within a lineage of the genus Drosophila phylogeny and provide suggestive evidence that a few thousand such events have occurred within the radiation of the insect order Diptera, thereby illustrating the magnitude of the contribution of PRG movement to chromosomal reorganization during evolution.