Detection of Distribution of New Genes in Drosophila Phylogeny

果蝇系统发育中新基因分布的检测

• 批准号: 7251327
• 负责人: Manyuan LONG
• 金额: $ 30.07万
• 依托单位: UNIVERSITY OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-05-01 至 2011-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7251327
• 关键词: Age; Candidate Disease Gene; Categories; Chromosomes; Complement; Computer Analysis; Daughter; Dependence; Detection; Development; Drosophila genome; Drosophila genus; Drosophila melanogaster; Ensure; Event; Evolution; Fluorescent in Situ Hybridization; Gene Structure; Genes; Genetic Transcription; Genome; Genomics; Goals; Investigation; Knowledge; Location; Maps; Medical; Methods; Modeling; Molecular; Molecular Evolution; Movement; Nucleotides; Numbers; Pattern; Phylogenetic Analysis; Phylogeny; Population; Process; Rate; Reporting; Research; Research Personnel; Sampling; Sex Chromosomes; Shotguns; Staging; Subgroup; Taxon; Techniques; Testing; Time; Tissues; Trees; Variant; Work; X Chromosome; aged; autosome; base; comparative genomic hybridization; gene function; genetic analysis; genome sequencing; insight; interdisciplinary approach; male; novel; trafficking

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.

描述（由申请人提供）：这项研究的目的是系统地研究果蝇Melanogaster子组中的新基因，并研究新基因起源的节奏和模式。我们将重点关注由RNA涉及的重新布置产生的新嵌合基因，这些基因经常进化与镶嵌基因结构相关的新功能。为了实现这些目标，将使用D. Melanogaster子组作为我们的模型分类单元进行以下四个统一的综合方法。 （1）通过基因组分析检测新基因：利用亚组中已知的差异时间（0.5-1200万年（MYS）），新基因检测将基于跨学科方法，该方法整合了计算和实验基因组分析。我们的计算分析将利用可用的基因组序列，并与多种物种基因组（MFISH）和比较基因组杂交（CGH）一起使用荧光原位杂交使用DMA微阵列。这些分析将在全基因组量表上检测并提供新的基因候选物。 （2）推断新基因的功能：为这些新基因推断功能，我们将检查每个新基因的分子进化和转录约束及其时间空间表达模式。还将进行分子进化和种群遗传分析，以检测新功能基因的适应性进化。 （3）分析新基因起源的系统发育分布：我们将在Melanogaster亚组物种的系统发育树上绘制所有发现的新基因的起源事件。我们将使用相关的统计分析（包括最大似然方法）来估计新基因起源的速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：利用已鉴定的新基因的年轻年龄（0.5至12 mys之间），我们将通过分析新基因及其母子基因的染色体位置分布，研究我们在古代倒逆转录样品中观察到的男性基因流量是否是一种正在进行的过程。这四类研究的结果将产生新基因的第一个系统发育分布，并对基因组中新基因起源的速率和模式进行新的概念。