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Earth BioGenome Project begins genome sequencing in earnest

WHOI deep-sea biologist Tim Shank will help lead the Deep-Ocean Genomes Project as part of the Earth BioGenome Project. (Photo by Luis Lamar)

January 19, 2022

WHOI to co-lead Deep-Ocean Genome Project with University of Connecticut as part of global effort

A global effort to map the genomes of all plants, animals, fungi and other eukaryotic life (organisms with a cellular nucleus) on Earth is entering a new phase as it moves from pilot projects to full-scale production sequencing. This new phase of the The Earth BioGenome Project (EBP) is marked with a collection of papers published January 17 in Proceedings of the National Academies of Science describing the project’s goals, achievements to date, and next steps. Included among these are an ambitious effort co-led by the Woods Hole Oceanographic Institution (WHOI) and the University of Connecticut (UConn) to obtain fundamental new knowledge of the organization, evolution, functions, and interactions of life in one of Earth’s least-understood regions: the deep ocean.

“The special feature on the EBP captures the essence and excitement of the largest-scale coordinated effort in the history of biology,” said Harris Lewin, chair of the EBP Working Group and Distinguished Professor of Evolution and Ecology at the University of California, Davis, which will serve as the project’s administrative center. “From fundamental science to breakthrough applications across a wide range of pressing global problems, such as preventing biodiversity loss and adapting food crops to climate change, the EBP’s progress in sequencing eukaryotic life is humbling and inspiring. Achieving the ultimate goal of sequencing all eukaryotic life now seems within our reach.”

Earth is forecast to lose 50% of its biodiversity by the end of this century without action to curb climate change and protect the health of global ecosystems. Creating a digital library of DNA sequences for all known eukaryotic life can help generate effective tools for preventing biodiversity loss and pathogen spread, monitoring and protecting ecosystems, and enhancing the natural services that healthy ecosystems provide the planet.

Of these, the ocean is the largest and most biodiverse ecosystem on Earth, hosting 33 known phyla from the tree of life comprising roughly 410,000 named species, with estimates of the total number of species exceeding 100 million. In addition, the deep sea hosts a wide range of unique habitats that present remarkably diverse and seemingly extreme living conditions, including immense pressures, near-freezing to beyond-boiling temperatures, absence of sunlight, and chemicals toxic to almost all other life forms on Earth.

“Deep-sea life has overcome some incredible challenges, but it has been able to thrive and diversify,” said WHOI deep-sea biologist Tim Shank, who will co-lead the Deep-Ocean Genomes Project with Rachel O’Neill, Director of UConn’s Center for Genome Innovation. “Learning more about the deep ocean could revolutionize our understanding of biology and evolution on Earth in ways that stand to benefit both society and the environment.”


Network of networks

EBP functions as an international network of networks, coordinating numerous group-specific, regional, and national-scale efforts. These include programs such as the California Conservation Genome Project, Darwin Tree of Life Project, the Vertebrate Genome Project, and the Deep-Ocean Genomes Project.

Although far removed from human activity on land, deep-sea life is considered to be more vulnerable than ever to the spread of ocean acidification, ocean warming, oxygen minimum zones, extractive industries, and pollution from chemical waste and plastics. The Deep-Ocean Genomes Project will use comparative sequencing methods to identify genes that are essential to life in the deep sea and to trace the evolution of life in the ocean. This is expected to provide fundamental insights into life on Earth, help inform conservation and management efforts, and even spur novel technologies and applications in human and environmental health.

“Even though it seems remote and even alien, this overlooked part of our planet plays a vital role in making our planet habitable,” said Shank. “We need to learn as much as we can before humanity changes the deep ocean forever.”


About Woods Hole Oceanographic Institution
The Woods Hole Oceanographic Institution (WHOI) is a private, non-profit organization on Cape Cod, Massachusetts, dedicated to marine research, engineering, and higher education. Established in 1930, its primary mission is to understand the ocean and its interaction with the Earth as a whole, and to communicate an understanding of the ocean’s role in the changing global environment. WHOI’s pioneering discoveries stem from an ideal combination of science and engineering—one that has made it one of the most trusted and technically advanced leaders in basic and applied ocean research and exploration anywhere. WHOI is known for its multidisciplinary approach, superior ship operations, and unparalleled deep-sea robotics capabilities. We play a leading role in ocean observation and operate the most extensive suite of data-gathering platforms in the world. Top scientists, engineers, and students collaborate on more than 800 concurrent projects worldwide—both above and below the waves—pushing the boundaries of knowledge and possibility. For more information, please visit

Key Takeaways

  • WHOI and University of Connecticut will co-lead the Deep-Ocean Genomes Project as part of the Earth BioGenome Project to map the genomes of all plants, animals, fungi and other eukaryotic life (organisms with a cellular nucleus) on Earth.
  • The ocean is among the most biodiverse, ecosystem on Earth, hosting 33 known phyla comprising roughly 410,000 named species, and an estimated 100 million species yet to be named.
  • The deep ocean one of the most under-studied regions within the ocean, containing many unique habitats that present a variety of challenges that life has evolved to overcome.
  • The Deep-Ocean Genomes Project will apply comparative genomic sequencing methods to improve understanding of life on Earth, inform conservation and management, and drive new innovation in human and environmental health.

More information

Shank Lab (WHOI)

Center for Genome Innovation (UConn)

Earth BioGenome Project (UC Davis)

EBP Phase 2 Announcement (UC Davis)