A Xenopus tropicalis oligonucleotide microarray works across species using RNA from Xenopus laevis

A. D. Chalmers, K. Goldstone, J. C. Smith, M. Gilchrist, E. Amaya and N. Papalopulu

Mechanisms of Development 122:355-363 (2005) (Full Article, 632 Kb).

ABSTRACT

Microarrays have great potential for the study of developmental biology. As a model system Xenopus is well suited for making the most of
this potential. However, Xenopus laevis has undergone a genome wide duplication meaning that most genes are represented by two
paralogues. This causes a number of problems. Most importantly the presence of duplicated genes mean that a X. laevis microarray will have
less or even half the coverage of a similar sized microarray from the closely related but diploid frog Xenopus tropicalis. However, to date,
X. laevis is the most commonly used amphibian system for experimental embryology. Therefore, we have tested if a microarray based on
sequences from X. tropicalis will work across species using RNA from X. laevis. We produced a pilot oligonucleotide microarray based on
sequences from X. tropicalis. The microarray was used to identify genes whose expression levels changed during early X. tropicalis
development. The same assay was then carried out using RNA from X. laevis. The cross species experiments gave similar results to those
using X. tropicalis RNA. This was true at the whole microarray level and for individual genes, with most genes giving similar results using
RNA from X. laevis and X. tropicalis. Furthermore, the overlap in genes identified between a X. laevis and a X. tropicalis set of experiments
was only 12% less than the overlap between two sets of X. tropicalis experiments. Therefore researchers can work with X. laevis and still
make use of the advantages offered by X. tropicalis microarrays.

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