9BAMBOO - An algorithmic view on genomes, cells, and environments (Laboratoire de Biométrie et Biologie Évolutive. UMR CNRS 5558 Campus de La Doua - Université Claude Bernard - Lyon 1 Bâtiment Grégoire Mendel - 16 rue Raphael Dubois 69 100 Villeurbanne -- INRIA Grenoble - Rhône-Alpes Inovallée 655 avenue de l'Europe -Montbonnot 38 334 Saint Ismier Cedex France - France)
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.
https://hal.inria.fr/hal-00851240 Contributor : Marie-France SagotConnect in order to contact the contributor Submitted on : Wednesday, May 26, 2021 - 11:40:59 AM Last modification on : Friday, August 5, 2022 - 10:43:47 AM Long-term archiving on: : Friday, August 27, 2021 - 7:09:32 PM
Cyril Dégletagne, 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⟩