Domazet-Loso Tomislav, Tautz Diethard
Institut für Genetik der Universität zu Köln, 50931 Köln, Germany.
Genome Res. 2003 Oct;13(10):2213-9. doi: 10.1101/gr.1311003.
Orphan genes are protein-coding regions that have no recognizable homolog in distantly related species. A substantial fraction of coding regions in any genome sequenced consists of orphan genes, but the evolutionary and functional significance of orphan genes is not understood. We present a reanalysis of the Drosophila melanogaster proteome that shows that there are still between 26% and 29% of all proteins without a significant match with noninsect sequences, and that these orphans are underrepresented in genetic screens. To analyze the characteristics of orphan genes in Drosophila, we used sequence comparisons between cDNAs retrieved from two Drosophila yakuba libraries and their corresponding D. melanogaster orthologs. We find that a cDNA library from adults yields twice as many orphan genes as such a library from embryos. The orphan genes evolve on average more than three times faster than nonorphan genes, although the width of the evolutionary rate distribution is similar for the two classes. In particular, some orphan genes show very low substitution rates that are comparable to otherwise highly conserved genes. We propose a model suggesting that orphans may be involved in the evolution of adaptive traits, and that slow-evolving orphan genes may be particularly interesting candidate genes for identifying lineage-specific adaptations.
孤儿基因是指在远缘物种中没有可识别同源物的蛋白质编码区域。任何已测序基因组中的相当一部分编码区域都由孤儿基因组成，但孤儿基因的进化和功能意义尚不清楚。我们对黑腹果蝇蛋白质组进行了重新分析，结果表明，所有蛋白质中仍有26%至29%与非昆虫序列没有显著匹配，并且这些孤儿基因在遗传筛选中的代表性不足。为了分析果蝇中孤儿基因的特征，我们对从两个雅库布果蝇文库中检索到的cDNA与其相应的黑腹果蝇直系同源物进行了序列比较。我们发现，来自成虫的cDNA文库产生的孤儿基因数量是来自胚胎的文库的两倍。孤儿基因的平均进化速度比非孤儿基因快三倍多，尽管这两类基因的进化速率分布宽度相似。特别是，一些孤儿基因显示出非常低的替代率，与其他高度保守的基因相当。我们提出了一个模型，表明孤儿基因可能参与适应性性状的进化，而进化缓慢的孤儿基因可能是识别谱系特异性适应性的特别有趣的候选基因。
