title: Microarray estimation of genomic inter-strain variability in the genus Ectocarpus (Phaeophyceae).
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: UPMC Univ Paris 6, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680 Roscoff, France.
authors.forename: Simon M
authors.initials: SM
authors.lastname: Dittami
authors.forename: Caroline
authors.initials: C
authors.lastname: Proux
authors.forename: Sylvie
authors.initials: S
authors.lastname: Rousvoal
authors.forename: Akira F
authors.initials: AF
authors.lastname: Peters
authors.forename: J Mark
authors.initials: JM
authors.lastname: Cock
authors.forename: Jean-Yves
authors.initials: JY
authors.lastname: Coppée
authors.forename: Catherine
authors.initials: C
authors.lastname: Boyen
authors.forename: Thierry
authors.initials: T
authors.lastname: Tonon
mesh_terms: D002734:Chlorophyll / Q000378:metabolism; D000077194:Chlorophyll A; D055028:Comparative Genomic Hybridization; D017124:Conserved Sequence; D018744:DNA, Plant / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation; D018745:Genome, Plant; D046228:Microarray Analysis / Q000379:methods*; D000459:Phaeophyceae / Q000145:classification / Q000235:genetics*; D010802:Phylogeny
chemical_list: D018744:DNA, Plant; D021903:DNA, Ribosomal Spacer; D002734:Chlorophyll; C064041:chlorophyll c; D000077194:Chlorophyll A