Genomes making waves for marine life.
Why do EBP-affiliated scientists want to sequence all Eukaryotic life in the global oceans? As Mark Blaxter, Head of the Tree of Life Programme at the Wellcome Sanger Institute, put it:
“From space, the planet is blue—70% of Earth’s surface area is water. And by depth, there is far more depth to the planet than there is height. The oceans are where all phyla can be found, and where most of life exists.”
Despite this immense biological richness, we still understand very little about how most marine species grow, behave, and interact. EBP-affiliated scientists are leveraging genomics to pave the way for transformative discoveries. We won’t appreciate the full range of insights that marine genomes can unlock—insights into agriculture and aquaculture, pathogens and disease, climate resilience, growth rates, regenerative biology, and extreme adaptations—until we build a comprehensive catalog of high-quality, near-complete genomes.
These genomes will serve as a launchpad into uncharted scientific frontiers, allowing scientists worldwide to ask new questions, make unexpected discoveries, and illuminate the hidden blueprint of life in Earth’s oceans.
🌍 Travel through the oceans and see how genomes unravel the mysteries of the deepest depths
Genomics of the largest kind
How Big Is Too Big?
Critically Endangered Marine Mammals
Underwater Sight
The Whale Shark (Rhincodon typus)
Genomics of the largest kind
The blue whale (Balaenoptera musculus) is Earth’s largest known animal, surpassing even the biggest dinosaurs in length and mass. To sustain their size, they filter up to six tons of krill daily. Once decimated by commercial whaling, blue whale populations are slowly recovering but remain threatened by climate change, prey decline, ship strikes, and fishing gear entanglement. These giants are also exceptionally long-lived, reaching 80–90 years.
The Vertebrate Genomes Project, in collaboration with G10K, recently produced the first chromosome-level reference genome for the species (Bukhman et al., 2024). Genomic insights from blue whales have profound implications for human health: despite trillions of cells and decades of replication, they show remarkable resistance to cancer. Studying their tumor-suppressing mechanisms and genome stability could shed light on cancer and aging. Because many aging-related genes lie in hard-to-sequence chromosome telomeres, near-complete genomes, like this one, are essential to unlocking these mysteries.
How Big Is Too Big? The Mega-Genome of Tiny Krill
The Fish10K consortium, known for generating genomes of marine and freshwater fish, has recently achieved a milestone: assembling a chromosome-level genome for the Antarctic krill. Despite their tiny size, Antarctic krill (Euphausia superba) are among the most abundant animals on Earth—an estimated 300–500 million tons of biomass, the largest of any wild animal species (Shoa et al., 2023). They form the foundation of the Southern Ocean food web, sustaining predators from seabirds to the massive blue whale.
But this small marine crustacean hides a remarkable secret: the largest genome of any animal on Earth. To tackle this challenge, Fish10K scientists deployed every sequencing and assembly technology available. It took the combined efforts of 6 scientists and more than 13,140 hours to unravel this genome. Minwen Zhang “By comparison, this process was about 100 times more time-consuming [for our team] than assembling a 1 Gb fish genome.” Why was such an effort required for such a tiny creature?
Antarctic krill have evolved extraordinary adaptations to survive in an environment of highly variable light, temperature, and sea ice. Their genomes hold clues to how these animals thrive in extreme conditions while sustaining their massive populations. Adding another layer of difficulty, the krill genome is exceptionally repetitive, which the scientists note made genome assembly “particularly challenging.”
Coral Reef Ecosystems: some of the most biodiverse
Sea fan.
Genomes making waves for Critically Endangered Marine Mammals
Recently, the Cetacean Genomes Project, Darwin Tree of Life, and the Vertebrate Genomes Project joined forces to publish a paper highlighting 18 high-quality whale and dolphin genomes (Morin et al., 2025). The authors took advantage of chance strandings of these marine giants to obtain samples from hard-to-find species like the critically endangered Rice’s whale, North Atlantic right whale, and vaquita porpoise. Reference genomes from threatened species like these are the jumping off point for downstream population genomics studies, which can identify potential for inbreeding depression and help to develop appropriate conservation strategies for the species most at risk of extinction. For example, the team leveraged the genome of the vaquita porpoise—one of the most endangered mammals globally with fewer than 10 mature adults in the wild—to determine that, surprisingly, the species has an extremely low mutational load. Recently, conservation planning models indicated that inbreeding depression, a common risk for very small or bottlenecked populations, is unlikely to pose a major concern for vaquita conservation and recovery (Robinson et al., 2022). Unfortunately, accidental bycatch and the purposeful targeting for the illegal wildlife trade remain significant threats to the species’ survival. Additionally, with only 10 adult individuals remaining, their risk of extinction remains extremely high and is further compounded by the population’s reduced resilience to additional stressors such as emerging diseases, ongoing climate change, and limited available resources.
Phillip Morin, head of the EBP-affiliated Cetacean Genomes Project, emphasized the importance of rapid access to reference genomes for advancing conservation efforts to protect marine mammals at risk of extinction:
“Availability of the genomic resources from these species is catalyzing diverse studies, including health, evolution, taxonomy, adaptation, and critical vulnerabilities of these and other whale, dolphin, and porpoise species.”
Squalomix dives into underwater sight.
The Whale Shark (Rhincodon typus) exhibits a strikingly unique method of underwater vision, enabling it to exploit habitats throughout the entire water column. This lifestyle requires its eyes to function across very different light conditions. Researchers from Squalomix analyzed complete shark genomes and identified gene mutations that help the species adjust to low-light environments. Their findings suggest that whale shark vision shifts in response to water temperature: in colder, deeper waters, blue light–sensing pigments important for dim-light vision are activated, while in warmer surface waters, these pigments are switched off. This temperature-sensitive molecular mechanism reflects how evolution has fine-tuned sensory systems to support survival across a range of marine habitats.
Diversity around a coral reef.
Written by: Anna Bramucci (Earth BioGenome Project: Genomic Insights Coordinator)
Acknowledgements
Thank you to all EBP-affiliated projects and downstream researchers using these EBP reference genomes who submitted valuable contributions to this newsletter. And thank you to all of the funders supporting these monumental research efforts around the world.