Abstract
The Xenopus community has made concerted efforts over the last 10–12 years systematically to improve the available sequence information for this amphibian model organism ideally suited to the study of early development in vertebrates. Here I review progress in the collection of both sequence data and physical clone reagents for protein coding genes. I conclude that we have cDNA sequences for around 50% and full-length clones for about 35% of the genes in Xenopus tropicalis, and similar numbers but a smaller proportion for Xenopus laevis. In addition, I demonstrate that the gaps in the current genome assembly create problems for the computational elucidation of gene sequences, and suggest some ways to ameliorate the effects of this. genesis 50:143–154, 2012. © 2012 Wiley Periodicals, Inc.
Highlights
Xenopus is an excellent model system for the study of early development in vertebrates, with its accessible and manipulated embryos
The purpose of this review is to find out how close we have come to defining the full complement of Xenopus gene sequences, and for what proportion of these we have a physical reagent available
There are three rather different sources of useful gene sequence data: (i) full-insert sequencing of single mRNA molecules from a cloned cDNA, (ii) EST contig assembly from large scale end-sequencing of cDNA libraries, and (iii) gene modeling on assembled genome sequence
Summary
Xenopus is an excellent model system for the study of early development in vertebrates, with its accessible and manipulated embryos. One of the key advantages of the Xenopus system is the ability to generate protein directly in the early stage embryo by simple injection of mRNA, and observe the result of the consequent over-expression of the gene (Smith and Harland, 1991; Voigt et al, 2005). Loss-of-function effects can be studied efficiently in Xenopus, using antisense morpholino oligonucleotides to knock down gene function (Chang et al, 2006; Sander et al, 2007) For this technique precise knowledge of the gene sequence is required: the true initiator methionine for translation blocking, and the position and sequence of exon boundaries for splice interference. The purpose of this review is to find out how close we have come to defining the full complement of Xenopus gene sequences, and for what proportion of these we have a physical reagent available
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