A high quality genome assembly for Xenopus tropicalis

描述(由申请人提供)： 对非洲爪哇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手术和显微注射来操纵，而且它们的大小和丰富，无论是正常的还是被操纵的卵子，都为生化和细胞生物学分析提供了极好的材料。为了使非洲爪哇在现代“系统生物学”中发挥作用，蛋白质组和基因组分析有望全面了解生命的过程，需要高质量的非洲爪哇基因组组装。高质量的基因组结构将提供一个全面的基因内容和蛋白质组目录，提供关于与其他脊椎动物保持染色体结构的权威数据，并将改善误组装的区域，将短支架区域带入染色体规模的组装。这项提议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草稿组装的基础上。虽然在基因丰富的区域质量很好，但基因组的远程组装不如其他四足动物。这一提议将通过避免基于克隆的序列映射和远程组装方法，绕过以前远距离组装的困难。相反，我们将使用高通量DNA测序和基于统计的图谱组合来生成物理和遗传图谱，包括新发现的单核苷酸多态(SNPs)和先前发现的简单序列长度多态(SSLP)。我们将为Metazome和Xenbase的基因组注释提供支持，并确保资源的广泛使用。与公共卫生相关：对模型生物的研究使人们能够发现动物的许多基本特性，从而对人类胚胎的发育和功能有了新的见解。非洲爪哇提供了在母体外发育的大胚胎，这使得对细胞增殖和许多发育事件的发现成为可能。基因组结构和全套基因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。

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.