Zhou Qi, Zhang Guojie, Zhang Yue, Xu Shiyu, Zhao Ruoping, Zhan Zubing, Li Xin, Ding Yun, Yang Shuang, Wang Wen
CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
Genome Res. 2008 Sep;18(9):1446-55. doi: 10.1101/gr.076588.108. Epub 2008 Jun 11.
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 approximately 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 approximately 10% of the new genes; (5) approximately 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.
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，控制这一基本过程的一般原则仍不清楚。在这里，我们揭示了导致新基因的突变机制及其在黑腹果蝇物种亚组不同时间节点上随后的谱系特异性进化的全基因组模式。我们发现：（1）串联基因复制产生了约80%的仅限于单个物种（黑腹果蝇或雅库布果蝇）的新生重复基因；（2）多个物种共有的最丰富的新基因（44.1%）是分散重复基因，并且更有可能被保留并具有功能；（3）从非编码序列从头起源的基因在新基因起源过程中发挥了意想不到的重要作用，占新基因的11.9%；（4）逆转座也是一种重要机制，产生了约10%的新基因；（5）黑腹果蝇物种复合体中约30%的新基因招募了各种基因组序列并形成嵌合基因结构，表明结构创新是帮助新基因固定的重要方式；（6）估计黑腹果蝇亚组中新功能基因的起源速率为每百万年5至11个基因。最后，我们调查了19个全球来源的黑腹果蝇菌株中黑腹果蝇特异性新基因的基因频率，发现其中44.4%在种群中表现出拷贝数多态性。总之，我们提供了一幅果蝇物种新基因起源的全景图。
