新基因的不断出现是生物进化的重要基础。中国科学院昆明动物研究所马普青年科学家小组在王文研究员的领导下与国际一些研究小组合作，已陆续报道了包括“sphinx”、“猴王”、“Hun”、BSC4等等一系列新近产生的新基因。这些研究成果表明新基因的起源是一个重要的生物学现象。但在全基因组水平，具体有哪些重要的新基因起源机制，它们各自的角色是什么，却一直不清楚。

    最近，马普小组的博士研究生周琦和张国捷等利用最新发表的12个果蝇种的全基因组序列，将新基因起源的研究提升到了阐明全基因组水平模式的高度。通过大规模的基因组比较，鉴定了300多个果蝇物种特异的年轻基因。对这些基因起源机制的分析发现，基因重复(gene duplication)是产生新基因最主要的机制，80%的新生基因拷贝由串联重复产生，它们之后又可能转化成散在形式的基因重复。有趣的是，研究发现有12%左右的新基因是由非编码序列“变废为宝”而来。这一发现颠覆了该领域长期存在的“进化不可能从头产生”的观点，证明从头起源（de novo origination）是新基因起源不可忽略的重要机制。同时，对所有新基因及其祖先基因的结构比较发现，有30%的新基因通过外显子重排等方式招募祖先基因不具有的序列，形成了新的嵌合基因(chimeric gene)。这样的结构为新基因提供了立即获得新的结构域和功能的机会，促使它们可以快速在群体内被自然选择固定。

    上述工作于9月2日被国际基因组学知名杂志《基因组研究》（Genome Research）正式发表。本论文对理解新遗传特征的进化有重要意义，引起了国际同行的广泛关注，Nature Review Genetics特别推荐报道，发表于当天的英国The Scientist杂志也采访了王文研究员。

推荐原始出处：

Genome Res. Published online before print July 30, 2008, 10.1101/gr.076588.108

On the origin of new genes in Drosophila

Qi Zhou^1,2,4, Guojie Zhang^1,2,3,4, Yue Zhang^1,4, Shiyu Xu¹, Ruoping Zhao¹, Zubing Zhan^1,2, Xin Li^1,2, Yun Ding^1,2, Shuang Yang^1,3, and Wen Wang^1,5

1 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; 2 Graduate School of Chinese Academy Sciences, Beijing 100086, China; 3 Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China

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 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 10% of the new genes; (5) 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.