Defining a large set of full-length clones from a Xenopus tropicalis EST project.
Amphibian embryos from the genus Xenopus are among 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 behavior 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 X. 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 7000 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.gurdon.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 toward a large-scale systematic analysis of gene sequence, gene expression, and gene function in this vertebrate species.
Gilchrist
Michael J
MJ
Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge CB21QR, UK. m.gilchrist@gurdon.cam.ac.uk
Zorn
Aaron M
AM
Voigt
Jana
J
Smith
James C
JC
Papalopulu
Nancy
N
Amaya
Enrique
E
D000818:Animals; D001483:Base Sequence; D003001:Cloning, Molecular / Q000379:methods*; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D015723:Gene Library; D020407:Internet; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D014981:Xenopus / Q000196:embryology / Q000235:genetics*