A Xenopus tropicalis oligonucleotide microarray works across species using RNA from Xenopus laevis.
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.
Chalmers
Andrew D
AD
Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, CB2 1QR, Cambridge, UK. adc33@cam.ac.uk
Goldstone
Kim
K
Smith
James C
JC
Gilchrist
Mike
M
Amaya
Enrique
E
Papalopulu
Nancy
N
D000818:Animals; D004625:Embryo, Nonmammalian / Q000502:physiology; D018507:Gene Expression Regulation, Developmental; D016678:Genome; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009841:Oligonucleotides / Q000235:genetics; D012313:RNA / Q000378:metabolism; D013045:Species Specificity; D014981:Xenopus / Q000235:genetics*; D029867:Xenopus Proteins / Q000378:metabolism; D014982:Xenopus laevis / Q000235:genetics*
D009841:Oligonucleotides; D029867:Xenopus Proteins; D012313:RNA