Defining a large set of full length clones from a Xenopus tropicalis EST project

M. Gilchrist, A. M. Zorn, J.Voigt, J. C. Smith, N. Papalopulu and E. Amaya

Dev. Biol . in press (2004)

Abstract

Amphibian embryos from the genus Xenopus are amongst the best species for understanding early vertebrate development

and for studying basic cell biological processes. Xenopus, and in particular the diploid Xenopus tropicalis, is also ideal for

functional genomics. Understanding the behaviour of genes in this accessible model system will have a significant and

beneficial impact on the understanding of similar genes in other vertebrate systems. Here we describe the analysis of

219,270 Xenopus tropicalis Expressed Sequence Tags (ESTs) from four early developmental stages. From these, we have

deduced a set of unique expressed sequences comprising approximately 20,000 clusters and 16,000 singletons. Furthermore

we developed a computational method to identify clones that contain the complete coding sequence and describe the creation

for the first time of a set of approximately 7,000 such clones, the full-length (FL) clone set. The entire EST set is cloned in a

eukaryotic expression vector and is flanked by bacteriophage promoters for in vitro transcription, allowing functional experiments

to be carried out without further subcloning. We have created a publicly available database containing the FL clone set and related

clustering data (http://www.welc.cam.ac.uk/informatics/Xenopus.html) and we make the FL clone set publicly available as a resource

to accelerate the process of gene discovery and function in this model organism. The creation of the unique set of expressed sequences

and the FL clone set pave the way towards a large-scale systematic analysis of gene sequence, gene expression and gene function in

this vertebrate species.

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