A genome assembly for Xenopus laevis

描述(由申请人提供)： 对非洲爪哇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。由于其巨大的体积和丰富的数量，它们为细胞周期和染色体力学等复杂过程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手术和显微注射进行操纵，可能会受到基因功能的获得或丧失的影响。为了使非洲爪哇在现代“系统生物学”时代更有用，蛋白质组和基因组分析有望全面了解生命的过程，我们建议在这里用非洲爪哇的基因和蛋白质水平的基因组组装来补充热带非洲爪哇的基因组组装。异源四倍体非洲爪哇比较小的二倍体热带非洲爪哇应用更广泛，因为它的历史、健壮性以及可以为胚胎学和细胞生物学实验获得的卵子的大小和数量。我们建议对莱氏X.laevis进行高通量测序，并产生基因规模的组装。通过选择与热带X线虫序列互补的区域，我们将能够从相对便宜的短读取数据中组装莱维氏X.laevis基因。该项目提供了一些需要克服的计算挑战，所开发的方法将在描述其他生物的基因组特征方面广泛有用。我们将为Xenbase的基因组注释提供支持，并将基因和蛋白质集合存储在公共数据库中，以确保资源的广泛可用。 公共卫生相关性： 非洲爪哇的卵和胚胎一直是脊椎动物实验胚胎学和细胞周期生化解剖工作的首选材料，为人类生物学提供了洞察力。我们建议填补这项工作的基本资源的一个很大空白，即基因和蛋白质含量的目录。

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. PUBLIC HEALTH RELEVANCE: Xenopus laevis eggs and embryos have been the material of choice for work on vertebrate experimental embryology and biochemical dissection of the cell cycle, providing insights into human biology. We propose to fill a large gap in the essential resources for this work, namely a catalogue of the gene and protein content.