Exploring nervous system transcriptomes during embryogenesis and metamorphosis in Xenopus tropicalis using EST analysis

Ana C Fierro,Gabor Gyapay,Muriel Perron,Nicolas Pollet,Maurice Wegnez,Patrick Wincker,Jean Weissenbach,Raphaël Thuret,André Mazabraud,Laurent Coen,Barbara A Demeneix

doi:10.1186/1471-2164-8-118

Abstract

BackgroundThe western African clawed frog Xenopus tropicalis is an anuran amphibian species now used as model in vertebrate comparative genomics. It provides the same advantages as Xenopus laevis but is diploid and has a smaller genome of 1.7 Gbp. Therefore X. tropicalis is more amenable to systematic transcriptome surveys. We initiated a large-scale partial cDNA sequencing project to provide a functional genomics resource on genes expressed in the nervous system during early embryogenesis and metamorphosis in X. tropicalis.ResultsA gene index was defined and analysed after the collection of over 48,785 high quality sequences. These partial cDNA sequences were obtained from an embryonic head and retina library (30,272 sequences) and from a metamorphic brain and spinal cord library (27,602 sequences). These ESTs are estimated to represent 9,693 transcripts derived from an estimated 6,000 genes. Comparison of these cDNA sequences with protein databases indicates that 46% contain their start codon. Further annotation included Gene Ontology functional classification, InterPro domain analysis, alternative splicing and non-coding RNA identification. Gene expression profiles were derived from EST counts and used to define transcripts specific to metamorphic stages of development. Moreover, these ESTs allowed identification of a set of 225 polymorphic microsatellites that can be used as genetic markers.ConclusionThese cDNA sequences permit in silico cloning of numerous genes and will facilitate studies aimed at deciphering the roles of cognate genes expressed in the nervous system during neural development and metamorphosis. The genomic resources developed to study X. tropicalis biology will accelerate exploration of amphibian physiology and genetics. In particular, the model will facilitate analysis of key questions related to anuran embryogenesis and metamorphosis and its associated regulatory processes.

Highlights

The western African clawed frog Xenopus tropicalis is an anuran amphibian species used as model in vertebrate comparative genomics
Even though phylogenetic studies indicate that 30 to 50 MY evolution separate the two species [3,4], it has been shown that most methods and resources developed for X. laevis can be readily applied to X. tropicalis [5]
About 500 retinas were dissected from stage 32 X. tropicalis embryos, a stage where differentiating retinal neurons are getting organized into layers

Summary

Introduction

The western African clawed frog Xenopus tropicalis is an anuran amphibian species used as model in vertebrate comparative genomics It provides the same advantages as Xenopus laevis but is diploid and has a smaller genome of 1.7 Gbp. X. tropicalis is more amenable to systematic transcriptome surveys. Working on X. laevis constitutes a challenge when dealing with large-scale transcriptomics, such as microarrays experiments or systematic cDNA sequencing This is because some X. laevis genes are present as diploids, while others form pairs of paralogs ( called "pseudoalleles") that have been conserved with various degrees of divergence, generally less than 10% [7]. An estimated 14% of paralogs show distinct expression profiles based on EST counts [8] Given these complications, it follows that the X. tropicalis genome is more amenable to systematic transcriptome surveys than that of X. laevis

Methods

Results

Conclusion