Comparative Genetics and Genomics of Xenopus

非洲爪蟾的比较遗传学和基因组学

• 批准号: 8856259
• 负责人: Richard M Harland
• 金额: $ 29.08万
• 依托单位: UNIVERSITY OF CALIFORNIA BERKELEY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-01-01 至 2016-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8856259
• 关键词: Accounting; African; Age; Amphibia; Area; Automated Annotation; Behavioral; Biochemical; Bioinformatics; Biological; Biological Models; Breeding; Cataloging; Catalogs; Cell Cycle; Cells; Chromosome Mapping; Chromosomes; Code; Collection; Communities; Complex; DNA; Data; Databases; Deposition; Development; Developmental Biology; Developmental Cell Biology; Diploidy; Embryo; Embryology; Ensure; Evolution; Gene Expression Regulation; Gene Frequency; Gene Proteins; Genes; Genetic; Genetic Polymorphism; Genetic Variation; Genome; Genomics; Genotype; Goals; Grant; Hand; Health; Inbreeding; Japanese Population; Life; Link; Mammals; Maps; Mechanics; Microinjections; Microsurgery; Modeling; Molecular; Nematoda; Neurobiology; Phylogenetic Analysis; Polyploidy; Population; Process; Proteomics; Rana; Reagent; Relative (related person); Research; Resources; Source; Synteny; System; Systems Biology; Untranslated RNA; Update; Variant; Work; Xenopus; Xenopus laevis; Xenopus sp.; behavioral study; comparative; comparative genomics; density; egg; fly; gene function; genome annotation; genome sequencing; improved; insertion/deletion mutation; insight; interest; novel; research study; scaffold; toad; tool; trait; transcriptome sequencing; xenopus genome

DESCRIPTION (provided by applicant): Research on the amphibian Xenopus has provided numerous new insights into cell and developmental biology. With their large size and abundance, they provide unparalleled material for biochemical and cell biological analysis of complex processes such as the cell cycle and chromosome mechanics. For embryological experiments, the embryos are readily manipulated by microsurgery or microinjection, and can be subjected to both gain or loss of gene function. In order to make Xenopus more useful for the modern age of "systems biology" where proteomic and genomic analyses promise a comprehensive understanding of life's processes, we propose here to continue improvement of both the short range, and long range (chromosome level) assemblies of Xenopus tropicalis and Xenopus laevis. To achieve new insights into the function of both coding and non-coding DNA in the Xenopus clade, and add new information from outgroups, we will assemble the pseudotetraploid genomes of X. mulleri, X. epitropicalis, and X. borealis. These allotetraploid Xenopus species will provide new insights into the evolution of tetraploid genomes and aid in annotating non-coding sequences of Xenopus. In addition, we will assemble genomes for other outgroups, including the direct developing frog Eleutherodactylus coqui, the Tungara frog Engystomops, and the spadefoot toad, Spea, all of which are models for developmental, neurobiological or behavioral studies. These will also provide outgroup sequences for comparison and annotation, as well as enabling molecular approaches for the communities who study these frogs for their developmental or neurobiological advantages. We will provide genome assemblies and automated annotation of the comparative information to Xenbase and deposit gene and protein collections in public databases to ensure that the resources are widely available.

描述（由申请人提供）：关于两栖动物的研究为细胞和发育生物学提供了许多新的见解。凭借其较大的尺寸和丰度，它们为复杂过程（例如细胞周期和染色体力学）的生化和细胞生物学分析提供了无与伦比的材料。对于胚胎学实验，胚胎很容易通过显微外科手术或显微注射来操纵，并且可以遭受基因功能的增益或丧失。为了使爪诺乱对于“系统生物学”的现代时代更有用，蛋白质组学和基因组分析有望对生活过程有全面的理解，我们在这里建议继续改善短范围和远距离（染色体）的组合。 Xenopus tropicalis和Xenopus laevis。为了对Xenopus进化枝中编码和非编码DNA的功能进行新的见解，并添加来自外部的新信息，我们将组装X. Mulleri，X。Epitropicalis和X. Borealis的伪二核基因组。这些同种四倍体异植物种类将为四倍体基因组的进化提供新的见解，并有助于注释爪蟾的非编码序列。此外，我们还将为其他群体组装基因组，包括直接开发的青蛙Eleutherodactylus coqui，Tungara Frog Engystomops和Spadefoot Toad，Spea，所有这些都是发展，神经生物学或行为研究的模型。这些还将为比较和注释提供外部序列，并为研究这些青蛙的发育或神经生物学优势的社区提供分子方法。我们将在公共数据库中提供对XENBase的比较信息，并存入基因和蛋白质收集的基因组组件和自动注释，以确保资源可广泛可用。