Detection of Distribution of New Genes in Drosophila Phylogeny

描述（由申请人提供）：本研究的目的是系统地研究黑腹果蝇亚群中的新基因，并调查新基因起源的速度和模式。我们将重点关注由rna参与逆转录产生的新的嵌合基因，这些基因通常会进化出与马赛克基因结构相关的新功能。为了实现这些目标，我们将以黑腹龙亚群为模型分类群，采用以下四方面的综合方法。(1)通过基因组分析检测新基因：利用已知的亚群内分化时间（50 - 1200万年（mys）），新基因检测将基于集成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，并与多物种基因组荧光原位杂交（MFISH）和使用DMA微阵列的比较基因组杂交（CGH）相结合。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)新基因的功能推断：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分析，以检测新的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：将所有检测到的新基因起源事件绘制到黑腹蛇亚群种的系统发育树上。我们将使用相关的统计分析，包括最大似然方法，估计新基因的起源率及其沿系统发育分支的变异。(4)新基因起源的性染色体依赖性：利用新基因的年轻年龄（0.5 ~ 12岁），我们将通过分析新基因及其亲本基因的染色体定位分布来研究我们在古代逆转录基因样本中观察到的雄性基因运输是否是一个持续的过程。这四类研究的结果将产生新基因的首次系统发育分布，并为基因组中新基因起源的速率和模式提供新的见解。

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.