The Earth BioGenome Project Phase II: illuminating the eukaryotic tree of life.

The Earth BioGenome Project (EBP) aims to "sequence life for the future of life" by generating high-quality reference genome sequences for all recognized eukaryotic species, thereby building a rich knowledge base to inform conservation, inspire bioindustry, ensure food security, advance medicine, and establish a deeper understanding of biodiversity. As the EBP works toward completing the original Phase I goal-a reference genome for each of the approximately 10,000 taxonomic families of eukaryotes-milestone publications have demonstrated the transformative potential of the project. The EBP has promoted global collaboration and established core methods and standards. By the end of 2024, EBP-affiliated projects had publicly released 2,000 high-quality genome assemblies, representing more than 500 eukaryotic families. In this article, we present a revised set of goals for Phases I and II of the EBP. For Phase II, we propose generating reference genomes for 150,000 species over 4 years, including representative genomes for at least 50% of all accepted genera and for additional species of biological and economic importance. To deliver Phase II, EBP-affiliated projects will have to release over 3,000 new genomes per month. We review the magnitude of the tasks in sourcing, sequencing, assembling, annotating, and analyzing genomes at this scale, and explore the scientific, technical, social, legal, ethical, and funding challenges associated with them. Success in Phase II will set the stage for sequencing the remaining ~1.5 million named species of Eukaryota and establishing the knowledge platforms necessary for understanding, preserving, and utilizing Earth's biodiversity in an era of rapid environmental change. Key points: The ongoing success of Phase I of the Earth Biogenome Project (EBP) demonstrates the feasibility of producing reference-quality genomes at scale, enabling the project to achieve its overarching goal: to sequence 1.67 million eukaryotic species in 10 years.Using knowledge from Phase I projects, we propose a revised strategy for Phase II: collecting specimens for 300,000 species and sequencing 150,000 species, representing at least half of the eukaryotic genera, in 4 years.Technical advances in DNA sequencing, genome assembly, and genome annotation have reduced costs and increased throughput to the point that we envisage globally distributed production of reference-quality genomes for most eukaryotic species for a total cost of about US$3.9 billion-US$800 million less than initially envisioned.Key challenges remain, including enhancing global coordination and building communities of users and interested parties; creating an inclusive, global biodiversity genomics workforce; developing effective access and benefit-sharing methodologies; facilitating collection at scale of vouchered specimens; sequencing reference genomes from single-celled and very small organisms; enhancing functional annotation; and building large-scale toolkits for comparative genomics.Technological and operational innovations, such as a "sequencing lab in a box," have the potential to radically transform the global capacity for biodiversity genome sequencing, facilitating national benefit-sharing agreements and the realization of societal impacts on Indigenous peoples and local communities.We propose the establishment of a US$0.5 billion Foundational Impact Project (FIF) fund to support the immediate use of the genome sequences in conservation, agriculture, biodiversity monitoring, biotechnology, and basic sciences, focused on supporting initiatives in the Global South.