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

Abstract

BackgroundBrown 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.ResultsWe 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.ConclusionThe 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.

Towards deciphering dynamic changes and evolutionary mechanisms involved in the adaptation to low salinities in Ectocarpus (brown algae)

“…Raw expression data were obtained directly from Roche NimbleGen. Only well conserved probes based on our previous comparative genome hybridization (CGH) experiments (Dittami et al. , 2011a) were considered for further analysis (i.e.…”

“…, 2009), have become available. Furthermore, the suitability of comparative microarray studies between strains that include the freshwater strain isolated by West and Kraft (FWS) was assessed (Dittami et al. , 2011a), making Ectocarpus an excellent model to study the adaptation of a primarily marine photosynthetic organism to freshwater.…”

Host–microbe interactions as a driver of acclimation to salinity gradients in brown algal cultures

“…The transition from marine environments to freshwater is a particularly rare event in brown algae, and only about 1% of brown algal species have colonized this habitat (Bold and Wynne, 1985). Although the exact taxonomic position of the freshwater strain and its relatives remains to be established, they do not belong to the genome-sequenced Ectocarpus siliculosus but constitute a sister species (Dittami et al, 2011) that has separated from E. siliculosus roughly 16 million years ago (Dittami et al, 2012).…”

Toward Systems Biology in Brown Algae to Explore Acclimation and Adaptation to the Shore Environment

“…Analysis of these ecotypes by different omics approaches, including sequencing of their genomes, should provide strong support for comparative analysis and insights into the mechanisms driving adaptation of these strains to diverse aquatic conditions. Studies on these ecotypes is also relevant in the actual context where species concept is changing in Ectocarpus (Dittami et al, 2011b;Peters et al, 2010aPeters et al, , 2010b, with this genus possibly containing more species than it is currently acknowledged. In parallel, highthroughput sequencing of new Ectocarpus, and hopefully other brown algal genomes, represents a method of choice to detect small noncoding RNAs (including miRNAs and antisense transcript RNAs), in relation with the importance of these molecules in the regulation of some mechanisms underlying abiotic stress response.…”