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Open Access Highly Accessed Methodology article

Transcriptome analysis in non-model species: a new method for the analysis of heterologous hybridization on microarrays

Cyril Degletagne1, Céline Keime2*, Benjamin Rey3, Marc de Dinechin45, Fabien Forcheron1, Paul Chuchana67, Pierre Jouventin4, Christian Gautier2 and Claude Duchamp1

  • * Corresponding author: Céline Keime keime@prabi.fr

  • † Equal contributors

Author Affiliations

1 Université de Lyon, F-69000, Lyon; Laboratoire de Physiologie Intégrative, Cellulaire et Moléculaire, UMR 5123 CNRS - Université Lyon 1, 43 Bvd 11 Novembre 1918, F-69622 Villeurbanne Cedex, France

2 Pôle Rhône Alpes de Bioinformatique, Université Lyon 1, Bâtiment Gregor Mendel, 16 rue Raphaël Dubois, 69622 Villeurbanne cedex, France

3 Université de Lyon, F-69000, Lyon; Laboratoire de Biométrie et Biologie Evolutive, UMR 5558 CNRS - Université Lyon 1, 43 Bvd 11 Novembre 1918, F-69622 Villeurbanne Cedex, France

4 UMR 5175 Centre d'Ecologie Fonctionnelle et Evolutive - CNRS, 1919 route de Mende 34293 Montpellier CEDEX 5, France

5 UMR 2724 Génétique et Évolution des Maladies Infectieuses - CNRS-IRD, 911 avenue Agropolis, 34394 Montpellier Cedex 5, France

6 CIRAD UMR 17 [UMR 177 IRD-CIRAD], TA A-17/G, Campus International de Baillarguet, 34398 Montpellier CEDEX 5, France

7 U844, 80 avenue Augustin Fliche F-34295 Montpellier, France

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BMC Genomics 2010, 11:344  doi:10.1186/1471-2164-11-344

Published: 31 May 2010

Abstract

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.