Comparative Genetics and Genomics of Xenopus

描述(申请人提供)：对两栖动物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。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或显微注射进行操作，并可能受到基因功能获得或丧失的影响。为了使非洲爪哇对现代“系统生物学”更有用，蛋白质组和基因组分析承诺全面了解生命的过程，我们建议在这里继续改进热带非洲爪哇和非洲爪哇的短期和远程(染色体水平)组装。为了对非洲爪哇分支中编码和非编码DNA的功能有新的认识，并增加来自外群的新信息，我们将组装非洲爪哇、表观非洲爪哇和北方非洲爪哇的伪四倍体基因组。这些异源四倍体非洲爪哇物种将为四倍体基因组的进化提供新的见解，并有助于对非洲爪哇非编码序列的注释。此外，我们还将组装其他外类群的基因组，包括直接发育的青蛙Eleutherodactylus coqui、金枪鱼Engystomops和铁蹄蟾蜍Spea，所有这些都是发育、神经生物学或行为研究的模型。这些还将提供用于比较和注释的外群序列，并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，并将基因和蛋白质集合存储在公共数据库中，以确保资源广泛可用。

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.