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

Cyril Degletagne 1 Céline Keime 2 Benjamin Rey 3 Marc de Dinechin 4 Fabien Forcheron 5 Paul Chuchana 6, 7 Pierre Jouventin 4 Christian Gautier 8, 9 Claude Duchamp 1
1 LEHNA - Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés
2 Institute of Genetics [Illkirch]
3 LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
4 CEFE - Centre d’Ecologie Fonctionnelle et Evolutive
5 Agressions vasculaires et réponses tissulaires
6 Cellules souches mésenchymateuses, environnement articulaire et immunothérapies de la polyarthrite rhumatoide
7 UMR INTERTRYP - Interactions hôtes-vecteurs-parasites-environnement dans les maladies tropicales négligées dues aux trypanosomatides
8 Baobab
PEGASE - Département PEGASE [LBBE]
9 BAMBOO - An algorithmic view on genomes, cells, and environments
Inria Grenoble - Rhône-Alpes, LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
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.
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https://hal.inria.fr/hal-00851240
Contributor : Marie-France Sagot <>
Submitted on : Tuesday, August 13, 2013 - 10:05:08 AM
Last modification on : Tuesday, March 17, 2020 - 3:04:35 AM

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Cyril Degletagne, Céline Keime, Benjamin Rey, Marc de Dinechin, Fabien Forcheron, et al.. Transcriptome analysis in non-model species: a new method for the analysis of heterologous hybridization on microarrays.. BMC Genomics, BioMed Central, 2010, 11, pp.344. ⟨10.1186/1471-2164-11-344⟩. ⟨hal-00851240⟩

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