Comparative Genetics and Genomics of Xenopus

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，胚胎易于通过显微外科手术或显微注射进行操作，并且可以经受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，我们建议在这里继续改善的短期和长期（染色体水平）组件的热带爪蟾和非洲爪蟾。为了获得对非洲爪蟾进化枝中编码和非编码DNA功能的新见解，并从外群中添加新信息，我们将组装X的假四倍体基因组。mulleri，刺角木X. epitropicalis和X.北极光这些异源四倍体非洲爪蟾物种将提供新的见解，四倍体基因组的进化和非编码序列的非洲爪蟾注释援助。此外，我们将组装其他外群的基因组，包括直接发育的青蛙Eleutherodactylus coqui，Tungara青蛙Engystomops和Spea，所有这些都是发育，神经生物学或行为研究的模型。这些还将提供外群序列进行比较和注释，以及使分子方法的社区谁研究这些青蛙的发育或神经生物学优势。我们将向Xenbase提供基因组组装和比较信息的自动注释，并在公共数据库中存款基因和蛋白质集合，以确保资源的广泛可用。

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.