Abstract
BackgroundRecent 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.ResultsWe 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.ConclusionsMAXRS appears to be an appropriate method for gene expression analysis under heterologous hybridization conditions.
Highlights
Recent developments in high-throughput methods of analyzing transcriptomic profiles are promising for many areas of biology, including ecophysiology
We developed a new method (MAXRS, for maximum rank sum) to analyze heterologous hybridization transcriptomic profiles
This method enabled us to analyze the transcriptome of king penguin by using microarrays dedicated to the chicken
Summary
Recent developments in high-throughput methods of analyzing transcriptomic profiles are promising for many areas of biology, including ecophysiology. Heterologous hybridization is usually considered a non-standard utilization of microarrays [1] It raises a number of difficulties, essentially due to the sequence divergence between the reference and the studied species [2]. A major consequence of heterologous hybridization is a global reduction of hybridization fluorescence signal ([1] and references therein) This reduction artificially decreases the number of differentially expressed genes detected by standard statistical tests, leading to a misrepresentation of the variation in transcriptomic profiles ([1] and references therein). Another issue of heterologous hybridization is cross-hybridization [3]. The use of heterologous hybridization does not amplify the problem of differentiating paralog expression levels compared to the use of the dedicated platform species
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