Detection of Distribution of New Genes in Drosophila Phylogeny

描述(申请人提供)：这项研究的目的是系统地研究果蝇亚群中的新基因，并调查新基因起源的速度和模式。我们将集中于通过RNA参与的逆转创建的新嵌合基因，这些嵌合基因通常进化出与镶嵌基因结构相关的新功能。为了达到这些目标，我们将以黑腹隐翅虫亚群为模式分类群，寻求以下四个方面的综合方法。(1)通过基因组分析检测新基因：利用亚组内已知的分化时间(50万-1200万年)，新基因检测将基于一种结合计算和实验基因组分析的跨学科方法。我们的计算分析将利用现有的基因组序列，并与使用DMA微阵列的荧光多物种基因组原位杂交(MFISH)和比较基因组杂交(CGH)一起工作。这些分析将在全基因组范围内检测并提供新的候选基因。(2)新基因功能的推断：为了推断这些新基因的功能，我们将研究每个新基因的分子进化和转录限制及其时空表达模式。还将进行分子进化和群体遗传学分析，以检测新功能基因的适应性进化。(3)新基因起源的系统发育分布分析：我们将所有检测到的新基因起源事件都定位在黑腹鱼亚群物种的系统发育树上。我们将使用包括最大似然法在内的相关统计分析来估计新基因起源的速度及其沿系统发育分支的变异。(4)新基因起源的性别染色体依赖性：我们将利用已发现的新基因的年轻年龄(0.5-12岁)，通过分析新基因及其亲本基因的染色体位置分布，来研究我们在古代逆转录基因样本中观察到的男性基因交流是否是一个持续的过程。这四类研究的结果将首次产生新基因的系统发育分布，并提供对基因组中新基因起源的比率和模式的新见解。

DESCRIPTION (provided by applicant): The objective of this research is to systematically study new genes in the Drosophila melanogaster subgroup and to investigate the tempo and mode of new gene originations. We will focus on the new chimerical genes created by RNA-involved retroposition that often evolve novel functions associated with the mosaic gene structures. To meet these objectives, the following four-prong integrated approaches will be pursued using the D. melanogaster subgroup as our model taxa. (1) Detection of New Genes by Genomic Analyses: Taking advantage of the known divergence times within the subgroup (0.5-12 million years (mys)), new gene detection will be based upon an interdisciplinary approach that integrates computational and experimental genomic analyses. Our computational analyses will utilize available genome sequences and work in conjunction with Fluorescence In Situ Hybridization with multiple species genomes (MFISH) and Comparative Genomic Hybridization (CGH) using DMA microarrays. These analyses will detect and provide new gene candidates on the genome-wide scale. (2) Inference of the Functionality of the New Genes: To infer functionality for these new genes we will examine the molecular evolutionary and transcriptional constraints of each new gene and their temporal-spatial expression patterns. Molecular evolution and population genetic analyses will be also conducted to detect adaptive evolution of new functional genes. (3) Analysis of phylogenetic Distribution of New Gene Originations: We will map all detected origination events of new genes on the phylogenetic tree of the melanogaster subgroup species. We will estimate the rate of new gene origination and its variation along branches of the phylogeny, using related statistical analyses including maximum likelihood approach. (4) Sex Chromosome-dependence of the Origination of New Genes: Taking advantage of the young ages of the identified new genes (between 0.5 and 12 mys), we will investigate whether or not the male gene traffic that we observed in ancient retrogene samples is an on- going process by analyzing the chromosomal location distribution of new genes and their parental genes. The results from these four categories of studies will generate the first phylogenetic distribution of new genes and provide the fresh-insight into the rates and patterns of new gene originations in genomes.