Mark Blaxter
Aquatic Symbiosis Genomics


The Tree of Life programme at the Sanger Institute has embarked on an ambitious programme to sequence the genomes of species involved in a wide range of symbioses in marine and freshwater ecosystems.

Funded by the Gordon and Betty Moore Foundation’s Symbiosis in Aquatic Systems Initiative and working with global partners, we will collect a wide range of symbiotic organisms (protists, plants and animals in the main), focused on specific scientific questions and generate reference-quality genomes for all species in each symbiosis.

We will collaborate with ten Hubs, experts in the field of symbiosis, and they will nominate the species we will sequence. The sequencing will follow the lead of our Darwin Tree of Life project, using long read and long range data, but the assembly process will be focused on delivering multiple independent genomes from the same sample. Using transcriptome data our partners at EMBL-EBI will annotate the genomes, and release these openly through the European Nucleotide Archive, who are developing a dedicated data portal for the project. Sanger and EBI staff will also work together to provide training opportunities to members of the hubs.

In collaboration with all project partners we will analyse the genomes to answer long-standing questions in symbiosis biology. To build the symbiosis genomics community we will develop and deliver a collaborative programme of training in genomics and bioinformatics for early career researchers to build capacity to fully exploit the genome sequences.

Just as the symbiotic corals are the essential foundations of flourishing reef ecosystems, we intend that these new genome resources will be the lasting foundation of a new, flourishing ecosystem of functional genomics and population genomics of aquatic symbioses.

Phase 1 - Four Pilot Aquatic Symbiosis Hubs

Phase One of the Aquatic Symbiosis Genomics project will create the essential research infrastructure and capacity of the scientific community to analyse genomic information in relation to the development and adaptation symbiosis.

Four international teams of collaborators with expert knowledge in symbiosis (see below) are working with the Sanger Institute’s Tree of Life Programme to generate reference genomes, develop new laboratory techniques and bioinformatic approaches.

Each collaborating hub will submit samples for around 100 genomes for sequencing and analysis by Sanger Institute scientists.

The first four Hubs are:

Sponges as symbiont communities

Ute Hentschel Humeida (GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany) and colleagues study sponges and their diverse associations with microbes, often based on mutual nutritional support. Genome sequencing will define the different sets of organisms involved in sponge-microbe symbiosis, and help understand how the collaborations have arisen, how they are maintained and how they contribute to major geochemical cycles in the oceans.

Photosymbiosis in marine animals

Jose Victor Lopez (Nova Southeastern University, Florida, USA) is the nucleus of a group interested in how animals have established symbiosis with light-harvesting algae and other microbes – photosymbiosis. Working on corals, molluscs, flatworms and others, they will use the complete genome sequences of these astonishing “plant-animals” to show how the animals have rearranged the way they live to rely on food directly from their partners.

Coral symbiosis sensitivity to environmental change

Michael Sweet (University of Derby, UK) and colleagues work on the sensitivity of corals to environmental change, in particular the global phenomenon of “bleaching”, where the coral loses its photosynthetic algal partner. The coral then turns bright white, and may ultimately die. Mass bleaching events are threatening the future of reef ecosystems worldwide. The Hub will compare bleaching-resistant colonies to those which are more sensitive from the same species, with the goal of shining some light onto symbiotic processes which occur and allow for this natural variation in the response of corals facing the same stress. A greater understanding may allow mitigation of the effects of climate change and assist reefs to evolve in the face of continuing  and increasing stressors.

Evolution of new symbioses in single-celled eukaryotes

John Archibald (Dalhousie University, Canada) brings together a team working on symbioses between different kinds of single celled organisms. The symbionts cooperate through photosymbiosis and nutritional or metabolic symbiosis. Understanding how these organisms work together will both illuminate dark areas of the tree of life and reveal how symbiosis can evolve multiple times.

Phase 2 - Six Additional Hubs

Following a very competitive open call for applications to form one of the Phase 2 hubs, we are delighted to welcome 6 new collaborations to the project.

The Phase 2 hubs are:

Ciliates as models for symbiosis: Using genomic analyses of functionally diverse symbiotic associations with parallel origins to gain insights into basic evolutionary principles of symbiosis

Led by Patrick Keeling at the University of British Columbia

Genomic signatures behind the origin of multiple cephalopod symbiotic organs

Led by Oleg Simakov at the University of Vienna

Bacterial symbiosis as an adaptation to extreme environments in annelid worms

Led by José M. Martín-Durán at Queen Mary University of London

What makes a lichen? Evolution and ecology of fungal-algal symbioses across marine and freshwater environments

Led by Nick Talbot at the Sainsbury Laboratory

Symbiosis as a driver for molluscan diversity

Led jointly by Jillian Petersen (University of Vienna), Roxanne Beinart (University of Rhode Island) and Julia Sigwart (Senckenberg Research Institute)

Symbioses in 3D: diversity and dynamics in pelagic symbioses across the tree of life

Led jointly by Anne Thompson (Portland State University), Kelly Sutherland (University of Oregon) and Michael N Dawson (University of California, Merced)

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