Summary: This publication argues that scaling biodiversity genomics in Phase II will require not only much higher sequencing throughput, but also coordinated global sampling, distributed regional capacity, equitable partnerships, robust metadata and biobanking systems, scalable annotation and informatics, workforce development, stronger governance, and sustained funding.
Key aspects this publication says EBP must address to scale biodiversity genomics
A massive increase in throughput is required: Phase II would require more than 3,000 new genomes per month. That is a major jump from current output and means scaling every step of the pipeline, not just sequencing.
Sampling is a central bottleneck: EBP would need to collect and biobank 300,000 species in 4 years. Scaling depends on coordinated global sampling, legal and ethical collection, voucher-linked specimens, strong metadata, and better systems for prioritization and avoiding duplication. The paper argues for adaptive sampling rather than rigidly following a species list.
Regional nodes are essential: The paper proposes roughly 25 regional nodes. These nodes should not only collect locally, but also sequence, assemble, annotate, and analyze locally. This is presented as necessary for both throughput and equity.
Equity and Global South leadership are core requirements: One of the paper’s three main pillars is equitable global partnerships. It argues that much of Phase II must be carried out in the Global South, especially in highly biodiverse countries. That includes local sequencing capacity, local training, local data generation and analysis, and fair benefit-sharing.
Access and benefit-sharing must be solved in practice: The publication emphasizes the need to work within the Nagoya Protocol, CARE principles, and the rights and interests of Indigenous peoples and local communities. Scaling will require clear, trusted systems for permissions, consent, provenance, attribution, and benefit-sharing.
High-quality standards must be maintained at scale: The paper argues that Phase II should still target reference-quality genomes, not lower-quality drafts. That means scaling while preserving standards for contiguity, chromosomal scaffolding, base accuracy, and annotation quality.
Small-bodied, single-celled, and difficult taxa remain a major technical barrier: The publication is clear that many of the hardest species are still hard for technical reasons. Key challenges include tiny DNA inputs, single-celled eukaryotes, polyploid genomes, and contamination or cobionts. Scaling biodiversity genomics means solving the hard genomes problem, not just accelerating easy taxa.
Annotation is a major bottleneck: Producing assemblies is not enough. The paper stresses that annotating 150,000 genomes will require major improvement in methods, including scalable orthology-based annotation, AI-assisted gene prediction, transcriptome generation at scale, and better quality metrics.
Metadata, vouchering, and biobanking are foundational: The publication repeatedly stresses the need for Darwin Core-compliant metadata, specimen imaging and digital vouchers, biobanking infrastructure, and interoperable data systems. Scaling is not just about reads and assemblies; it requires a reliable specimen-data backbone.
Informatics must be interoperable, open, and more efficient: The paper highlights the need for trusted metadata frameworks, interoperable databases, shared workflows, open standards, and real-time coordination systems like GoaT. It also stresses “compute once, reuse many” to reduce duplicated computation and carbon cost.
Automation and standardized workflows are critical: The paper points to workflow optimization, automation in laboratory steps, automation in assembly and QC, and open workflow systems. Scaling will depend on reducing manual, bespoke processing across the pipeline.
Workforce development is a core scaling requirement: The paper treats workforce capacity as a major limiting factor. EBP will need a much larger global workforce across collection, taxonomy, molecular lab work, bioinformatics, annotation, ethics, and governance. This includes training, mentoring, leadership development, and reciprocal knowledge exchange.
Stronger coordination and Secretariat support are needed: The publication explicitly says Phase II requires an enhanced Secretariat. Scaling depends on better coordination across member projects, regional nodes, standards, training, policy engagement, and overlap resolution.
Funding remains one of the biggest limiting factors: The paper states that funding has been the main factor limiting output so far. It estimates about US$1.1 billion for Phase II, including a proposed Foundational Impact Fund. Scaling depends not only on more money, but on funding that supports infrastructure, equitable participation, R&D, downstream impact, and stable coordination.
EBP must show real-world impact, not just produce genomes: The paper argues that scaling will be easier to justify if genomes are translated into conservation, agriculture, biodiversity monitoring, biotechnology, and comparative genomics. This is why it proposes the Foundational Impact Fund.