Dive into these EBP publications
Marine taxa remain underrepresented in global reference genome repositories —
EBP-affiliates are actively working to close this critical genome gap.
To date, EBP-affiliated projects have sequenced 4,386 eukaryotic species (EBP progress live), with the pace of genome sequencing and annotation accelerating rapidly. Below are some recent papers from EBP-affiliated projects that highlight the swift scientific breakthroughs made possible by expanding access to the ever-growing digital library of eukaryotic reference genomes.
Genomic infrastructure for cetacean research and conservation: reference genomes for eight families spanning the cetacean tree of life.
“We analyze and compare a set of reference genome assemblies for 18 cetacean species from eight families that include 91% of the 94 recognized species of cetaceans. These reference genomes represent a milestone in creating a cetacean genomic infrastructure for research and conservation, accomplishing four primary goals.”
The Cetacean Genomes Project, the Darwin tree of life project at the Wellcome Sanger Institute, and the Vertebrate Genomes Project
Authors: Morin, P.A., Bein, B., Bortoluzzi, C., Bukhman, Y.V., Hains, T., Heimeier, D., Uliano-Silva, M., Absolon, D.E., Abueg, L., Antosiewicz-Bourget, J. and Balacco, J.R.
Journal: Frontiers in Marine Science
Published: 2025
The orca (Orcinus orca) chromosome-level genome assembly was generated by the Darwin Tree of Life Programme in collaboration with the Wellcome Sanger Institute.
The giant clam (Tridacna maxima), a photosymbiotic species thriving in sunlit tropical waters.
Photosymbiosis shaped animal genome architecture and gene evolution as revealed in giant clams.
“Strikingly, about 70% of the genome is composed of repetitive elements, especially transposable elements, most likely resulting from a symbiosis-adapted immune system.”
Aquatic Symbiosis Genomics Project
Authors: Li, R., Leiva, C., Lemer, S., Kirkendale, L., and Li, J.
Journal: Communications Biology
Published: 2025
Atlantic bonito (Sarda sarda) genomic analysis reveals population differentiation across Northeast Atlantic and Mediterranean locations: Implications for fishery management.
“Our results demonstrate how anthropogenic perturbations impact the dynamics between two well-known ecotypes of Atlantic cod and thus, their genomic signatures.”
Catalan Initiative
Authors: Ollé-Vilanova, J., Hajjej, G., Macias, D., Saber, S., Lino, P.G., Muñoz-Lechuga, R., Baibbat, S.A., Sow, F.N., Diaha, N.C., Araguas, R.M., Sanz, N., and Viñas, J.
Journal: Marine Environmental Research
Published: 2024
Atlantic bonito.
Sea turtle diving gracefully beneath the surface.
Haplotype-resolved reference genomes of the sea turtle clade unveil ultra-syntenic genomes with hotspots of divergence.
“Our analysis reveals remarkable genome synteny and collinearity across all species, despite the clade’s origin dating back more than 60 million years.”
Vertebrate Genomes Project
Authors: Larissa S. Arantes, Tom Brown, Diego De Panis, Scott D. Whiting, Erina J. Young, Erin L. LaCasella, Gabriella A. Carvajal, Adam Kennedy, Deana Edmunds, Blair P. Bentley, Jennifer Balacco, Conor Whelan, Nivesh Jain, Tatiana Tilley, Brian O’Toole, Patrick Traore, Erich D. Jarvis, Oliver Berry, Peter H. Dutton, Lisa M. Komoroske, Camila J. Mazzoni.
Journal: GigaScience.
Published: 2025
Sharks and rays have the oldest vertebrate sex chromosome with unique sex determination mechanisms.
“Sharks and rays share the oldest vertebrate sex chromosomes, dating back approximately 300 My, and employ unique sex determination mechanisms composed of distinct molecules from other vertebrates.”
SQUALOMIX
Authors: Niwa, T., Uno, Y., Ohishi, Y., Kadota, M., Aburatani, N., Kiyatake, I., Katooka, D., Yorozu, M., Tsuzuki, N., Toyoda, A., Takagi, W., Nakamura, M., and Kuraku, S.
Journal: Proceedings of the National Academy of Sciences
Published: 2025
The Corn Earworm Pest (Helicoverpa zea) reference genome was sequenced by the i5k and Ag100Pest Initiatives. Image credit: Brad Coates.
The Brahman cow (hybrid species: Bos indicus x Bos taurus) high-quality reference genome was generated by the Vertebrate Genomes Project (VGP). VGP has generated hundreds of high-quality reference genomes, frequently targeting critically important livestock species such as cow, sheep, rabbit, chicken, and ducks, to name a few.
The Ruminant Telomere-to-Telomere (RT2T) Consortium
“By virtue of both very accurate long and ultralong sequencing technologies, T2T assemblies can resolve repetitive sequence regions that have been collapsed in earlier assembly approaches. Artifactual variants that would have been identified because of these collapsed regions will be reduced in number, and, conversely, more complete assemblies will allow for the identification of variants in previously uncharacterized regions of the genome. The higher accuracy of these new assemblies will also eliminate many artifactual variants that are called because of single-nucleotide and small insertion and deletion (indel) errors in the assembly.”
Ruminant T2T consortium and VGP
Authors: Kalbfleisch T.S., McKay S.D., Murdoch B.M., Adelson D.L., Almansa-Villa D., Becker G., Beckett L.M., Benítez-Galeano M.J., Biase F., Casey T., Chuong E., Clark E., Clarke S., Cockett N., Couldrey C., Davis B.W., Elsik C.G., Faraut T., Gao Y., Genet C., Grady P., Green J., Green R., Guan D., Hagen D., Hartley G.A., Heaton M., Hoyt S.J., Huang W., Jarvis E., et al.
Journal: Nature Genetics
Published: 2024
Occurrence and distribution of two bacterial brood diseases (American and European foulbrood) in US honey bee colonies and resistance to antibiotics from 2015 to 2022
“In the United States alone, the value of pollination services rendered by honey bees is estimated at approximately 17 billion [USD] annually, while the global figure reaches an impressive 215 billion [USD] (Calderone, 2012; Smith et al., 2013). However, the sustainability of these invaluable services is under threat, as evidenced by long-term declines in honey bee colony populations. Specifically, reports indicate a worrying decrease of 25% in European honey bee colonies and an even more concerning 60% reduction in U.S. colonies (Potts et al., 2010; Smith et al., 2013). Among the challenges, diseases present a specific and significant threat to bee health.”
Beenome100
Authors: Alburaki M, Abban SK, Evans JD, and Chen YP.
Journal: Journal of Apicultural Research
Published: 2024
The Buff-tailed Bumblebee (Bombus terrestris) is one of the most numerous bumblebee species in Europe, and is the main species used in greenhouse pollination. The high-quality reference genome for this species and hundreds of other pollinators were generated by Darwin Tree of Life.
