Comparative Genetics and Genomics of Xenopus

描述（由申请人提供）：对两栖动物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度，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。在胚胎学实验中，胚胎很容易通过显微手术或显微注射进行操作，并且可能受到基因功能的获得或丧失的影响。为了使非洲爪蟾在现代“系统生物学”中更有用，蛋白质组学和基因组学分析承诺对生命过程的全面理解，我们建议在这里继续改进热带爪蟾和非洲爪蟾的近程和长距离（染色体水平）组装。为了获得编码和非编码DNA在非洲爪蟾进化支系中的功能的新见解，并增加来自外群的新信息，我们将组装X. mulleri， X. epitoppicalis和X. borealis的伪四倍体基因组。这些异源四倍体非洲爪蟾物种将为四倍体基因组的进化提供新的见解，并有助于非洲爪蟾非编码序列的注释。此外，我们将收集其他外群的基因组，包括直接发育的蛙Eleutherodactylus coqui， Tungara蛙Engystomops，和spadefoot toad， Spea，所有这些都是发育，神经生物学或行为研究的模型。这也将为比较和注释提供外群序列，以及为研究这些青蛙的发育或神经生物学优势的社区提供分子方法。我们将向Xenbase提供基因组组装和比较信息的自动注释，并将基因和蛋白质收集存放在公共数据库中，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.