Transcriptome analysis in non-model species: a new method for the analysis of heterologous hybridization on microarrays.
BACKGROUND
Recent developments in high-throughput methods of analyzing transcriptomic profiles are promising for many areas of biology, including ecophysiology. However, although commercial microarrays are available for most common laboratory models, transcriptome analysis in non-traditional model species still remains a challenge. Indeed, the signal resulting from heterologous hybridization is low and difficult to interpret because of the weak complementarity between probe and target sequences, especially when no microarray dedicated to a genetically close species is available.


RESULTS
We show here that transcriptome analysis in a species genetically distant from laboratory models is made possible by using MAXRS, a new method of analyzing heterologous hybridization on microarrays. This method takes advantage of the design of several commercial microarrays, with different probes targeting the same transcript. To illustrate and test this method, we analyzed the transcriptome of king penguin pectoralis muscle hybridized to Affymetrix chicken microarrays, two organisms separated by an evolutionary distance of approximately 100 million years. The differential gene expression observed between different physiological situations computed by MAXRS was confirmed by real-time PCR on 10 genes out of 11 tested.


CONCLUSIONS
MAXRS appears to be an appropriate method for gene expression analysis under heterologous hybridization conditions.
Degletagne
Cyril
C
Pôle Rhône Alpes de Bioinformatique, Université Lyon 1, Bâtiment Gregor Mendel, 16 rue Raphaël Dubois, 69622 Villeurbanne cedex, France.
Keime
Céline
C
Rey
Benjamin
B
de Dinechin
Marc
M
Forcheron
Fabien
F
Chuchana
Paul
P
Jouventin
Pierre
P
Gautier
Christian
C
Duchamp
Claude
C
D000818:Animals; D020869:Gene Expression Profiling / Q000379:methods*; D018507:Gene Expression Regulation, Developmental; D009693:Nucleic Acid Hybridization / Q000379:methods*; D009792:Oceans and Seas; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010369:Pectoralis Muscles / Q000254:growth & development / Q000378:metabolism; D016133:Polymerase Chain Reaction; D015203:Reproducibility of Results; D013050:Spectrometry, Fluorescence; D046429:Spheniscidae / Q000235:genetics / Q000254:growth & development