Methods Mol Biol 2012 Jan 01;917:43-65. doi: 10.1007/978-1-61779-992-1_4.

Navigating the Xenopus tropicalis genome.

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The frog Xenopus laevis has for more than 60 years served as a model system for the study of vertebrate embryogenesis, molecular and cell biology, and physiology. Recently, there has been great interest in the related species Xenopus tropicalis, in part because it is diploid, unlike the allotetraploid X. laevis, and therefore amenable to forward genetics, adding to the strengths of the frog system. The genome sequence of X. tropicalis was published in 2010 and this resource is facilitating rapid progress in applying transcriptomic, genomic, proteomic, and systems biological approaches for which the Xenopus system is well suited. However, the availability of the primary nucleotide sequence is only the first step in using the genome. Accessing information embedded in the genome sequence requires well-annotated genes and knowledge of how to navigate the data. The current chapter provides a step-by-step guide for the novice to finding genes of interest in the current genome assembly, supplemented with detailed notes to improve understanding. Several publically available internet-based tools for examining the X. tropicalis genome are discussed, with special emphasis placed on the examination of synteny. Accurate determination of gene identity is enhanced by examination of orthology relationships with other organisms and thus synteny is a powerful tool. This chapter provides an access path into the Xenopus genome to enhance the researchers' ability to manipulate the organism.

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