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

Andrew D. Chalmers, Kim Goldstone, James C. Smith, Mike Gilchrist, Enrique Amaya, Nancy Papalopulu

    Research output: Contribution to journalArticlepeer-review


    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. © 2004 Elsevier Ireland Ltd. All rights reserved.
    Original languageEnglish
    Pages (from-to)355-363
    Number of pages8
    JournalMechanisms of Development
    Issue number3
    Publication statusPublished - Mar 2005


    • Cross species hybridisations
    • Microarray
    • Xenopus laevis
    • Xenopus tropicalis


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