PLoS Genetics：果蝇体内单独进化的新基因

佚名

    生物谷：美国康奈尔大学研究人员在7月6日的网络杂志《PLoS遗传学》上发表文章称，他们在一些果蝇体内发现了一种不与其它任何已知基因有关系的新基因。

    领导该项研究的是康奈尔大学分子生物学与遗传学系的Hsiao-Pei  Yang博士。她及同事发现的这种新基因命名为hydra，它只存在于果蝇很少量的种属中。这说明这种基因诞生的年代在1300万年前，它存在的果蝇种属便是在那个时候脱离了共同祖先开始单独进化。

    Hydra具有自己的功能，它能够表达一种蛋白参与精子的后期生成。Yang表示，人们习惯于认为新基因是由已有基因改造而来，但是hydra不是这样，这就是它的特别之处。

    科学家目前还不能确定hydra是如何产生的。他们推测它可能是由一段“垃圾DNA”发展而成。这段“垃圾DNA”称为转位因子，又称跳跃基因，它可以经由病毒插入到果蝇基因组内。此外，hydra含有9个复制的外显子（exon，含蛋白质编码信息区域），任何一个外显子都可以激活hydra。研究人员发现大多数外显子的旁边都有一个转位因子，从而推测，由转位因子产生复制序列可能是产生新基因的部分机制，因为复制提供了基因更多的进化机会。（科学网  梅进/编译）

原始出处:

PLoS Genetics

Received: January 10, 2007; Accepted: May 15, 2007; Published: July 6, 2007

Evolution of hydra, a Recently Evolved Testis-Expressed Gene with Nine Alternative First Exons in Drosophila melanogaster

Shou-Tao Chen1, Hsin-Chien Cheng1, Daniel A. Barbash2, Hsiao-Pei Yang1,2*

1 Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan, Republic of China, 2 Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America

We describe here the Drosophila gene hydra that appears to have originated de novo in the melanogaster subgroup and subsequently evolved in both structure and expression level in Drosophila melanogaster and its sibling species. D. melanogaster hydra encodes a predicted protein of ~300 amino acids with no apparent similarity to any previously known proteins. The syntenic region flanking hydra on both sides is found in both D. ananassae and D. pseudoobscura, but hydra is found only in melanogaster subgroup species, suggesting that it originated less than ~13 million y ago. Exon 1 of hydra has undergone recurrent duplications, leading to the formation of nine tandem alternative exon 1s in D. melanogaster. Seven of these alternative exons are flanked on their 3′ side by the transposon DINE-1 (Drosophila interspersed element-1). We demonstrate that at least four of the nine duplicated exon 1s can function as alternative transcription start sites. The entire hydra locus has also duplicated in D. simulans and D. sechellia. D. melanogaster hydra is expressed most intensely in the proximal testis, suggesting a role in late-stage spermatogenesis. The coding region of hydra has a relatively high Ka/Ks ratio between species, but the ratio is less than 1 in all comparisons, suggesting that hydra is subject to functional constraint. Analysis of sequence polymorphism and divergence of hydra shows that it has evolved under positive selection in the lineage leading to D. melanogaster. The dramatic structural changes surrounding the first exons do not affect the tissue specificity of gene expression: hydra is expressed predominantly in the testes in D. melanogaster, D. simulans, and D. yakuba. However, we have found that expression level changed dramatically (~ >20-fold) between D. melanogaster and D. simulans. While hydra initially evolved in the absence of nearby transposable element insertions, we suggest that the subsequent accumulation of repetitive sequences in the hydra region may have contributed to structural and expression-level evolution by inducing rearrangements and causing local heterochromatinization. Our analysis further shows that recurrent evolution of both gene structure and expression level may be characteristics of newly evolved genes. We also suggest that late-stage spermatogenesis is the functional target for newly evolved and rapidly evolving male-specific genes.

Figure 1.Evolution of hydra in Drosophila Species

(A) The hydra region of the X-chromosome of D. melanogaster, based on FlyBase genome browser release 4.3. The hydra gene was previously annotated as producing two alternative transcripts, RA and RB, derived from alternative exon 1s. The proposed annotation of seven additional exon 1s is based on evidence presented here.

(B) Evolution of hydra region and hydra gene structure in seven Drosophila species. hydra and the flanking gene CG1835 are located in a recently expanded region between run and cyp6v1. hydra originated in the common ancestor of the melanogaster subgroup (arrow A). In D. melanogaster, this region between run and cyp6v1 is ~32 kb (10 kb from the 3′ end of hydra to cyp6v1 and 17 kb from the 5′ end of hydra to run), but is only ~26 kb apart in D. ananassae and D. pseudoobscura, where both hydra and CG1835 are missing. hydra has gone through multiple cycles of duplication and rearrangement in D. melanogaster and its sibling species, and accumulated insertions of the transposon DINE-1 and other repetitive sequences (arrow B). CG1835 is on the opposite strand from all other genes, as indicated by its leftward-pointing arrow. Three copies of hydra are found on two unlinked scaffolds in D. sechellia. Note that the distances are not to scale.