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Open Access Methodology article

Microarray estimation of genomic inter-strain variability in the genus Ectocarpus (Phaeophyceae)

Simon M Dittami123, Caroline Proux4, Sylvie Rousvoal12, Akira F Peters56, J Mark Cock12, Jean-Yves Coppée4, Catherine Boyen12 and Thierry Tonon12*

Author Affiliations

1 UPMC Univ Paris 6, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680 Roscoff, France

2 CNRS, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680 Roscoff, France

3 Current Address: Department of Biology, University of Oslo, P.O. Box 1066 Blindern, N-0316 Oslo, Norway

4 Institut Pasteur, Plate-Forme 2- Puces à ADN, 25 rue du docteur Roux, 75724 Paris Cedex 15, France

5 BEZHIN ROSKO, 40 rue des pêcheurs, 29250 Santec, France

6 MBA Laboratory, Citadel Hill, Plymouth PL1 2PB, UK

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BMC Molecular Biology 2011, 12:2  doi:10.1186/1471-2199-12-2

Published: 13 January 2011

Abstract

Background

Brown algae of the genus Ectocarpus exhibit high levels of genetic diversity and variability in morphological and physiological characteristics. With the establishment of E. siliculosus as a model and the availability of a complete genome sequence, it is now of interest to analyze variability among different species, ecotypes, and strains of the genus Ectocarpus both at the genome and the transcriptome level.

Results

We used an E. siliculosus gene expression microarray based on EST sequences from the genome-sequenced strain (reference strain) to carry out comparative genome hybridizations for five Ectocarpus strains: four E. siliculosus isolates (the male genome strain, a female strain used for outcrosses with the genome strain, a strain isolated from freshwater, and a highly copper-tolerant strain), as well as one strain of the sister species E. fasciculatus. Our results revealed significant genomic differences between ecotypes of the same species, and enable the selection of conserved probes for future microarray experiments with these strains. In the two closely related strains (a male and a female strain used for crosses), genomic differences were also detected, but concentrated in two smaller genomic regions, one of which corresponds to a viral insertion site.

Conclusion

The high variability between strains supports the concept of E. siliculosus as a complex of cryptic species. Moreover, our data suggest that several parts of the Ectocarpus genome may have evolved at different rates: high variability was detected particularly in transposable elements and fucoxanthin chlorophyll a/c binding proteins.