A high quality genome assembly for Xenopus tropicalis

热带爪蟾的高质量基因组组装

基本信息

批准号：
7753229
负责人：
Richard M Harland
金额：
$ 38.38万
依托单位：
UNIVERSITY OF CALIFORNIA BERKELEY
依托单位国家：
美国
项目类别：
财政年份：
2009
资助国家：
美国
起止时间：
2009-01-01 至 2012-12-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7753229
关键词：
Adopted Age Animal Model Animals Automated Annotation Biochemical Biological Bypass Cataloging Catalogs Cell Proliferation Cells Chromosome Mapping Chromosome Structures Chromosomes Communities Complement DNA DNA Sequence Data Databases Department of Energy Development Developmental Cell Biology Disease Embryo Ensure Europe Event Evolution Expressed Sequence Tags Family Female Frequencies Genes Genome Genomics Haploidy Human Human Development Human Genome Hybrids Institutes Ivory Coast Joints Libraries Life Maintenance Mammals Maps Methods Microinjections Microsurgery Mothers Physical Chromosome Mapping Polymerase Chain Reaction Process Property Proteome Proteomics Radiation Hybrid Research Resources Sequence Analysis Shotgun Sequencing Single Nucleotide Polymorphism Source Structure Systems Biology Time Universities Vertebrates Washington Work Xenopus base computerized data processing density egg gene function improved insight public health relevance scaffold sex simple sequence length polymorphism xenopus genome

项目摘要

DESCRIPTION (provided by applicant): Research on Xenopus has provided numerous new insights into cell and developmental biology. The eggs are readily manipulated by microsurgery and microinjection, and with their large size and abundance, either normal or manipulated eggs provide excellent material for biochemical and cell biological analysis. In order to make Xenopus useful for the modern age of "systems biology" where proteomic and genomic analyses promise a comprehensive understanding of life's processes, a high quality assembly of the Xenopus genome is needed. A high quality genome structure will provide a comprehensive catalog of gene content and proteome, authoritative data on conservation of chromosome structure with other vertebrates, and will improve regions of mis-assembly, bringing short scaffold regions into a chromosome-scale assembly. This proposal builds on the previous high quality draft genome assembly produced at the Department of Energy's Joint Genome Institute. While the quality is good in gene-rich regions, the long-range assembly of the genome is not as good as that for other tetrapods. This proposal will bypass the previous difficulties in assembling over the long range, by avoiding cloning-based methods of sequence mapping and long-range assembly. Instead we will use high throughput DNA sequencing and statistically based map assembly to generate a physical and genetic map, incorporating newly identified Single Nucleotide Polymorphisms (SNPs) and previously identified Simple sequence length polymorphisms (SSLPs). We will provide support for genome annotation by Metazome and Xenbase and ensure that the resources are made widely available. PUBLIC HEALTH RELEVANCE: Work on model organisms has allowed the discovery of many fundamental properties of animals, and thereby allowed new insights into how human embryos develop and function. Xenopus offers large embryos that develop outside the mother, which has enabled discoveries on cell proliferation and many developmental events. The genome structure and full gene set will permit new genes and functions to be identified, functions that are highly relevant to human development and disease.

描述（由申请人提供）：对非洲爪蟾的研究为细胞和发育生物学提供了许多新的见解。这些卵子很容易通过显微外科和显微注射进行操作，并且由于其尺寸大且丰富，无论是正常的还是经过操作的卵子都为生化和细胞生物学分析提供了极好的材料。为了使非洲爪蟾在现代“系统生物学”中发挥作用，蛋白质组学和基因组分析有望全面了解生命过程，需要对非洲爪蟾基因组进行高质量的组装。高质量的基因组结构将提供基因内容和蛋白质组的全面目录、其他脊椎动物染色体结构保守性的权威数据，并将改善错误组装的区域，将短支架区域引入染色体规模的组装中。该提案建立在能源部联合基因组研究所之前制作的高质量基因组组装草案的基础上。虽然基因丰富区域的质量很好，但基因组的远程组装不如其他四足动物。该提议将通过避免基于克隆的序列作图和长程组装方法，绕过以前长程组装的困难。相反，我们将使用高通量 DNA 测序和基于统计的图谱组装来生成物理和遗传图谱，结合新鉴定的单核苷酸多态性 (SNP) 和先前鉴定的简单序列长度多态性 (SSLP)。我们将为 Metazome 和 Xenbase 提供基因组注释支持，并确保资源广泛可用。公共健康相关性：对模型生物体的研究使动物的许多基本特性得以发现，从而使人们对人类胚胎的发育和功能有了新的认识。非洲爪蟾提供在母体外发育的大型胚胎，这使得细胞增殖和许多发育事件的发现成为可能。基因组结构和完整的基因集将允许识别新的基因和功能，这些功能与人类发育和疾病高度相关。