The choice of Ectocarpus as a genetic and genomic model organism for the brown algae (Peters et al., J. Phycol. 2004) was based on a number of features:
- its small size (several centimetres)
- the fact that its life cycle can be completed in culture in less than 3 months
- genetic analysis (crosses, complementation) is possible
- large scale mutant screens are possible (several hundred individuals can be screened in a single petri dish for example)
- it is highly fertile
- it has a relatively small genome
The Ectocarpus genome project
The 214 million base pair genome of Ectocarpus was sequenced by Genoscope and analysed by an international consortium coordinated by the Algal Genetics Group (Cock et al., 2010). Analysis of the genome sequence provided important insights into how the brown algae have adapted to the intertidal environment and identified a number of genes that were linked with the evolution of multicellularity in this lineage. The genome sequence has recently been re-annotated to improve the gene models and add information about various classes of non-protein-coding loci (Cormier et al. 2017).
The Ectocarpus genome can be browsed at the Orcae website (http://bioinformatics.psb.ugent.be/orcae/overview/EctsiV2).
In addition to the genome sequence itself, the Ectocarpus genome project generated a number of tools that are of interest for the future exploitation of this alga as a model organism. These include a large expressed sequence tag (EST and RNA-seq) collection, a large collection of small RNA sequencing reads and genetic maps (Heesch et al., 2010, Avia et al., 2017).
Additional genetic tools available include protocols for UV mutagenesis, phenotypic screening methods, genetic crosses, methods for handling large populations, a large number of genetic markers, defined strains for genetic mapping and protocols for epigenetic analyses (histone PTM ChIP-seq, Hi-C).
Cultures of a wide range of Ectocarpus ecotypes are available in the Roscoff collection. You can find protocols for Ectocarpus cultivation in our publication list.
Current work includes the development of protocols for RNA interference (Macaisne et al., 2017) and CRISPR-Cas9 knockouts for the analysis of gene function.
Recent work carried out in the context of the ANR project IDEALG aims to develop additional, classical genetic approaches for Ectocarpus such as the identification of quantitative trait loci (Avia et al., 2017). This is a collaborative project between our laboratory, the EBEA (Evolutionary Biology and Ecology of Algae) laboratory, also in Roscoff, and the Laboratoire des Sciences de l'Environement Marin, in Brest, France.