Team AG - Algal Genetics

The brown algae (Phaeophyceae) are an ecologically and economically important group of organisms that constitute the third most complex lineage of multicellular organisms on the planet¹. These seaweeds have been evolving independently of land plants and animals for over a billion years and, as a result, have acquired many unique biological characteristics. Over the past two decades, the Algal Genetics Group has been developing key tools and resources for brown algal research and has been applying these resources to understand some of these unique features of brown algal biology. Resource development has included the establishment of the filamentous brown alga Ectocarpus as a model system² (including deployment of CRISPR-Cas9 methodology³) and large-scale generation of genomic data, from the initial publication of the Ectocarpus genome sequence¹, which was the first macroalgal genome to be assembled, up until the recent generation of 67 brown algal genomes by the Phaeoexplorer project⁴. This latter resource provides a comprehensive genome-based view of the evolutionary history of the brown algal lineage. Important advances towards understanding brown algal biology have included the identification of master regulators of the Ectocarpus life cycle⁵, cloning of the first macroalgal developmental gene by forward genetics⁶, the description of brown algal sex chromosomes⁷ and the first analysis of histone modifications in a macroalga⁸. Current research in the Algal Genetics Group combines laboratory-based functional genomic approaches with population genetics and field ecology, allowing investigations to scale from molecules to ecosystems. The specific aims of the different research axes within the group are i) to identify the factors that influence the evolution of reproductive barriers and underlie speciation in the brown algae, including the roles of the haploid-diploid life cycle and sexual systems, ii) to understand how brown algae defend themselves against pathogens, and iii) to investigate genetic and epigenetic control of life-cycle-related developmental processes. Building on resources generated by these fundamental research projects, we are also implementing a breeding program for the cultivated kelp Saccharina latissima. 
 

Reproductive isolation and speciation 

Research axis leader: Agnieszka Lipinska

Reproductive barriers play a crucial role in maintaining species boundaries by limiting gene exchange between diverging species. While numerous studies have explored the genomic landscape of speciation in select organisms from the plant and animal kingdoms, our objective is to shed light on the genetic bases of reproductive isolation in another major eukaryotic supergroup – the brown algae (Phaeophyceae). Brown algae possess a distinctive haploid–diploid life cycle with U/V sex determination, featuring independent, free-living multicellular gametophyte and sporophyte stages. This alternation of generations provides a powerful framework for studying how selection acts differently on haploid versus diploid genomes, shaping patterns of adaptation and speciation. A complementary focus is the evolution of haploid U/V sex chromosomes⁹, which offer a unique opportunity to test long-standing theories about how sex chromosomes influence reproductive isolation and drive speciation. We investigate how genomic changes contribute to reproductive isolation—from chromosomal rearrangements that suppress recombination to subtle genetic incompatibilities that reduce hybrid fitness. By generating high-quality, chromosome-level genome assemblies across species with varying degrees of divergence, we aim to uncover the genomic architecture of both pre- and post-zygotic barriers. Through comparative genomics, population studies, and controlled laboratory crosses, we seek to identify the specific genes and mutations underlying hybrid incompatibilities, including reduced fertility and developmental abnormalities. Together, these efforts will advance our understanding of how genetic divergence gives rise to new species in this ecologically and evolutionarily important group.

Lipinska website: https://www.lipinska-lab.com/

Evolutionary ecology and speciation genomics in the intertidal zone

Research axis leader: Alan Le Moan

Speciation is often conceptualized as a continuum along which divergent lineages gradually accumulate reproductive barriers. Yet this process is not unidirectional: reproductive barriers can erode when gene flow is sufficiently strong, such as during secondary contact, potentially reversing speciation. We aim to understand the genetic and ecological mechanisms that shape the speciation dynamic using the brown algal genera Fucus and Dictyota and marine invertebrates of the genus Littorina as study systems. The approach centres on studying lineages with partial reproductive isolation that interact and hybridize in natural settings, forming hybrid zones that serve as natural laboratories for speciation research.

A major focus of this research is ecotype evolution. Ecotypes are populations within a species that exhibit heritable morphological, physiological, and/or behavioural differences consistently associated with specific environmental conditions. We aim to uncover both the evolutionary history and genetic architecture underlying divergence between ecotypes. This work extends to examining how human activities interfere with speciation, as anthropogenic disturbances create unique natural experiments for studying evolutionary forces at different stages along the speciation continuum. The research also explores suture zones—geographic regions marking boundaries between distinct species assemblages. These zones are particularly valuable because they represent contact points for divergent lineages across multiple species simultaneously. This feature makes them ideal for comparative genomics approaches, enabling us to understand how different species evolve under shared environmental pressures and to identify the genetic basis of recent transitions in life-history traits associated with local adaptation.

Immunity to pathogens

Research axis leader: Yacine Badis

Macroalgal immunity is poorly understood compared with the equivalent systems of land plants, for example, but the former is not only important because of pathogen threats to seaweed aquaculture but also because macroalgal host-pathogen relationships often exhibit unusual and novel features. For example, the major seaweed oomycete pathogens are derived from poorly-characterised, early-branching clades within the oomycete phylogenetic tree such as the Eurychasmatales and the Anisolpidales¹⁰ and, although they are obligate biotrophic pathogens, they have remarkably broad host ranges^10,11. This latter characteristic is surprising for pathogens that interact very intimately with their hosts, entering and growing within the host cells. The strategy that is being employed in the group to characterise brown algal immune responses to oomycete pathogens is to search for algal proteins that interact with so-called parasite-secreted effectors (PSEs), i.e. proteins that are secreted by the oomycete pathogen and target host cellular component to mediate pathogenicity. Recent unpublished work indicates that brown algal oomycete pathogens lack major PSEs of plant-pathogenic oomycetes, such as the RxLRs and CRNs, but has identified a panel of secreted proteins that represent potential PSEs either because they are predicted to have cytosolic or nuclear function (the host cytosol and nucleus being outside the pathogens plasma membrane) or because they are predicted to encode short peptides. The current strategy is to select the best candidate PSEs based on multiple criteria and to search for interacting Ectocarpus proteins using the yeast two-hybrid system.

Life cycles and development

Research axis leader: J. Mark Cock

We previously showed that the TALE homeodomain transcription factors OUROBOROS and SAMSARA control the deployment of the sporophyte generation of the Ectocarpus life cycle⁵. Current work is aimed at investigating the events that occur downstream of these master regulators during the progression of the sporophyte developmental program. We recently identified clusters of genes with coordinated patterns of expression during sporophyte development and detected a marked change in transcriptome composition during very early sporophyte development. Current work is not only focused on these changes in protein-coding gene expression but is also investigating the role of long non-coding RNA transcripts (ANR project BrownLincs) and epigenetic processes such as the expression of different histone variants during the life cycle (ANR project His2Avar).

Kelp breeding

Research axis leader: J. Mark Cock

In Europe, seaweed mariculture is still an emerging sector and cultivated strains are currently derived directly from wild populations. There is therefore considerable scope for improvement through the application of breeding approaches. We are focusing our efforts on the sugar kelp Saccharina latissima, which is the most common mariculture species in Europe. Working within the national project Idealg and the European projects Genialg and SeaMark, and in collaboration with other groups at the Roscoff Biological Station, we have established a number of resources for this species, including a chromosome-scale genome assembly, a genetic map and a large collection of clonal gametophyte strains. We are also developing CRISPR-based gene editing within the context of the Kelprime project. Using these resources, we have initiated a breeding program based on the generation and phenotyping of F1 hybrids and on the analysis of F2 families that segregate for several phenotypes of economic interest. 

References

1. Cock, J. M. et al. (2010). The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature 465, 617–621

2. Cock, J. M. (2023). The model system Ectocarpus: Integrating functional genomics into brown algal research. J. Phycol. 59, 4–8

3. Badis, Y., Scornet, D., Harada, M., Caillard, C., Godfroy, O., Raphalen, M., Gachon, C. M. M., Coelho, S. M., Motomura, T., Nagasato, C. & Cock, J. M. (2021). Targeted CRISPR-Cas9-based gene knockouts in the model brown alga Ectocarpus. New Phytol. 231, 2077–2091

4. Denoeud, F. et al. (2024). Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems. Cell 187, 6943–6965

5. Arun, A., Coelho, S. M., Peters, A. F., Bourdareau, S., Pérès, L., Scornet, D., Strittmatter, M., Lipinska, A. P., Yao, H., Godfroy, O., Montecinos, G. J., Avia, K., Macaisne, N., Troadec, C., Bendahmane, A. & Cock, J. M. (2019). Convergent recruitment of TALE homeodomain life cycle regulators to direct sporophyte development in land plants and brown algae. eLife 8, e43101

6. Macaisne, N., Liu, F., Scornet, D., Peters, A. F., Lipinska, A., Perrineau, M.-M., Henry, A., Strittmatter, M., Coelho, S. M. & Cock, J. M. (2017). The Ectocarpus IMMEDIATE UPRIGHT gene encodes a member of a novel family of cysteine-rich proteins with an unusual distribution across the eukaryotes. Development 144, 409–418

7. Ahmed, S., Cock, J. M., Pessia, E., Luthringer, R., Cormier, A., Robuchon, M., Sterck, L., Peters, A. F., Dittami, S. M., Corre, E., Valero, M., Aury, J. M., Roze, D., Van de Peer, Y., Bothwell, J., Marais, G. A. & Coelho, S. M. (2014). A Haploid System of Sex Determination in the Brown Alga Ectocarpus sp. Curr Biol 24, 1945–1957

8. Bourdareau, S., Tirichine, L., Lombard, B., Loew, D., Scornet, D., Wu, Y., Coelho, S. M. & Cock, J. M. (2021). Histone modifications during the life cycle of the brown alga Ectocarpus. Genome Biol. 22, 12

9. Barrera-Redondo, J. et al. (2025). Origin and evolutionary trajectories of brown algal sex chromosomes. Nat. Ecol. Evol. 1–18 doi:10.1038/s41559-025-02838-w

10. Gachon, C. M. M., Strittmatter, M., Badis, Y., Fletcher, K. I., West, P. V. & Müller, D. G. (2017). Pathogens of brown algae: culture studies of Anisolpidium ectocarpii and A. rosenvingei reveal that the Anisolpidiales are uniflagellated oomycetes. Eur. J. Phycol. 52, 133–148

11. Müller, D. G., Küpper, F. C. & Küpper, H. (1999). Infection experiments reveal broad host ranges of Eurychasma dicksonii (Oomycota) and Chytridium polysiphoniae (Chytridiomycota), two eukaryotic parasites in marine brown algae (Phaeophyceae). Phycol Res 47, 217–223