A genome assembly for Xenopus laevis

描述（由申请人提供）： 对两栖动物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。由于它们的大尺寸和丰富性，它们为复杂过程的生物化学和细胞生物学分析提供了无与伦比的材料，如细胞周期和染色体力学。对于胚胎学实验，胚胎容易通过显微外科手术操作，并且通过显微注射可以使基因功能的获得或丧失。为了使非洲爪蟾更有用的现代“系统生物学”的蛋白质组学和基因组学分析承诺全面了解生命的过程中，我们建议在这里补充非洲爪蟾热带爪蟾的基因组组装与非洲爪蟾的基因和蛋白质水平的基因组组装。异源四倍体非洲爪蟾比较小的二倍体热带爪蟾更广泛地使用，因为它的历史，健壮性以及可以获得胚胎学和细胞生物学实验的卵的大小和数量。我们建议进行X的高通量测序。laevis，并生成基因规模的组装。通过选择与X. tropicalis序列，我们将能够组装X。从相对便宜的短读段数据中获得的基因。该项目提供了一些需要克服的计算挑战，开发的方法将在表征其他生物体的基因组方面具有广泛的实用性。我们将支持Xenbase的基因组注释，并将基因和蛋白质集合存款公共数据库，以确保资源的广泛可用性。

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 and by microinjection can be subjected to 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 complement the genome assembly of Xenopus tropicalis with a gene and protein level genome assembly for Xenopus laevis. The allotetraploid Xenopus laevis is in wider use than the smaller, diploid Xenopus tropicalis, because of its history, robustness, and the size and quantity of eggs that can be obtained for embryological and cell biological experiments. We propose to carry out high throughput sequencing of X. laevis, and generate a gene-scale assembly. By selecting regions complementary to the X. tropicalis sequence we will be able to assemble X. laevis genes from relatively inexpensive, short read data. The project provides some computational challenges that will need to be overcome and the approaches developed will be of wide utility in characterizing genomes of other organisms. We will provide support for genome annotation by Xenbase and deposit gene and protein collections in public databases to ensure that the resources are widely available.