On the origin of new genes in Drosophila
On the origin of new genes in Drosophila
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关于果蝇新基因的起源。
DOI：
10.1101/gr.076588.108
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发表时间：
2008-09-01
期刊：
影响因子：
7
通讯作者：
Wang, Wen
中科院分区：
文献类型：
--
作者：
Zhou, Qi;Zhang, Guojie;Wang, Wen
已经提出了几种机制来解释新基因的起源。尽管有大量的案例研究，但在全基因组水平上，管理这一基本过程的一般原则仍然不清楚。在这里，我们揭示了全基因组模式的突变机制，导致新的基因和随后的谱系特异性进化在不同的时间节点的果蝇种亚组。我们发现：（1）串联基因重复产生了大约80%的新生重复，这些新生重复仅限于单个物种（D。黑腹果蝇或果蝇yakuba）;（2）多个物种共享的最丰富的新基因（3）来自非编码序列的新基因在新基因的起源中起着意想不到的重要作用，占新基因的11.9%;（4）逆转录也是一种重要的机制，并产生了类似于10%的新基因;（5）类似于30%的新基因在D.黑腹果蝇种复合体的基因组序列多样，并形成嵌合基因结构，表明结构创新是新基因固定的重要途径;（6）新功能基因的起源速率估计为每百万年5 ~ 11个基因。黑腹亚群最后，我们调查了19个全球衍生株D。黑色素瘤特异的新基因，并揭示44.4%的人在群体内表现出拷贝数多态性。总之，我们提供了一个全景图片的新基因在果蝇物种的起源。
Several mechanisms have been proposed to account for the origination of new genes. Despite extensive case studies, the general principles governing this fundamental process are still unclear at the whole-genome level. Here, we unveil genome-wide patterns for the mutational mechanisms leading to new genes and their subsequent lineage-specific evolution at different time nodes in the Drosophila melanogaster species subgroup. We find that ( 1) tandem gene duplication has generated similar to 80% of the nascent duplicates that are limited to single species ( D. melanogaster or Drosophila yakuba); ( 2) the most abundant new genes shared by multiple species (44.1%) are dispersed duplicates, and are more likely to be retained and be functional; ( 3) de novo gene origination from noncoding sequences plays an unexpectedly important role during the origin of new genes, and is responsible for 11.9% of the new genes; ( 4) retroposition is also an important mechanism, and had generated similar to 10% of the new genes; ( 5) similar to 30% of the new genes in the D. melanogaster species complex recruited various genomic sequences and formed chimeric gene structures, suggesting structure innovation as an important way to help fixation of new genes; and ( 6) the rate of the origin of new functional genes is estimated to be five to 11 genes per million years in the D. melanogaster subgroup. Finally, we survey gene frequencies among 19 globally derived strains for D. melanogaster-specific new genes and reveal that 44.4% of them show copy number polymorphisms within a population. In conclusion, we provide a panoramic picture for the origin of new genes in Drosophila species.