Sequencing life on Earth: why the Global South must be central

Key points

• Equitable global partnerships in biodiversity genomics require Global South researchers to hold decision-making and leadership roles within governing bodies and affiliated projects, particularly in megadiverse countries.
• The feasibility of decentralized laboratories must be carefully evaluated, as there are recurrent challenges in importing reagents, maintaining equipment, and ensuring reliable cold-chain delivery.
• Producing reference-quality genomes for Earth’s biodiversity requires integration into strategic global and national agendas supported by stable funding mechanisms that are not constrained by short-term or geopolitically driven priorities.

Introduction

The biodiversity crisis is accelerating, with the International Union for Conservation of Nature (IUCN)’s recent Red List confirming multiple recent species extinctions (1). Of the 17 megadiverse countries, which account for ~70% of Earth’s biodiversity, 15 are part of the Global South. Most of the habitat and biodiversity loss is concentrated in 9 of the megadiverse countries. Generating knowledge about all life on Earth is fundamental for bending the curve of biodiversity loss, and genomics has recently emerged as an important component in conservation biology. Mapping genome-wide variation can help estimate important biological variables essential for species conservation, understanding adaptation to climate change, and predicting populations’ long-term resilience (2).

Genome sequencing has ramped up in the last decade as costs drop and technology advances (3). The Earth BioGenome Project (EBP) is capitalizing on this in its aim to sequence the genomes of all known eukaryotic species. The lead article by Blaxter et al. (4) paves the way for Phase II of the EBP, which aims to sequence reference genomes for 150,000 species throughout the tree of life. With an estimated cost of US$1.1 billion (US$4.42 billion for all three phases), Phase II will bring important developments in technology for data production and processing, while establishing sequencing centers worldwide. Although these accomplishments are set to change the way we perform biodiversity genomics research globally, we believe that major challenges need to be overcome for the project to accomplish its goals and truly reach equitable partnerships and effective engagement with the Global South. Bringing our significant experience as researchers involved in EBP-affiliated initiatives based in South America, we address potential blockers for Phase II in the Global South in sequencing infrastructure and technology, funding sources, enabling equitable global participation, and engaging government and policymakers.

Obstacles for Phase II

Sequencing life on Earth requires global participation, especially in biodiversity-rich regions. A solution proposed by Blaxter et al. (4) involves the creation of decentralized laboratories (“genomes from a box”; gBox) established at 25 regional nodes. This model is based on the approach used in outbreak response for pathogen detection, such as COVID-19. While laboratories for rapid response to disease outbreaks require a Biosecurity Level 3/4 (5), the general infrastructure is typically simpler in terms of equipment than what laboratories require for sequencing reference genomes. In our experience, maintaining sequencers in countries where little or no other similar equipment is available is challenging due to the lack of specialized and timely maintenance. The reliance on imported reagents from the Global North can further undermine efforts because of common cold-chain failures that often lead to reagents not arriving at their destination with the required integrity for optimal use (2). The current limitations in technology, maintenance, importing reagents, and sample integrity are important obstacles that need to be overcome for the gBox model to work in countries without a tradition in genomic sequencing.

Securing adequate funding remains a key issue. During the SARS-CoV-2 pandemic, rapid funding availability by governments and the private sector allowed investments of US$9.2 billion in vaccine development (6), generating trillions in social, health, and economic revenue. The same model is needed for biodiversity. With the global cost of lost ecosystem services projected to reach €14 trillion by 2050 (7), biodiversity loss will bring severe impacts on health, economy, and social well-being. Unfortunately, this sense of urgency is not yet instilled in funding priorities and financial investments. In our experience, this is a general pattern of biodiversity-related science funding, as both the Chilean and Brazilian governments have invested in large facilities for astronomy and physics (8). Environmental expenditures by governments decrease in times of recession, with some countries failing to include biodiversity agendas in their post-COVID economic recovery packages (9). Because reference genomic libraries are key for supporting the monitoring of endangered species and developing local bioeconomy initiatives, wider investments focused on biodiversity knowledge are necessary for their conservation and recovery. The creation of a global public–private co-funding mechanism similar to the recently established Tropical Forests Forever Facility (https://tfff.earth/)—aimed at financially compensating countries that commit to preserving their tropical forests—could be explored as an alternative to support sequencing efforts in megadiverse countries. Under such a co-funding mechanism, Global South countries could find mechanisms for matching at least some percentage of the external funding that is brought into the country for biodiversity genomics. Mechanisms could include institutional commitments (e.g., integration into national biodiversity and bioeconomy agendas) and recurrent budget lines supporting the development of local biological collections, biobanks, and molecular biology laboratories in addition to genomics expertise. We view this as an important step to ensure perennial biodiversity initiatives are rooted in the territories of Global South countries themselves.

Moving forward with equitable partnerships

Achieving the goals of Phase II of the EBP will require more than advances in sequencing technologies and expanded reference databases; it will require structural changes that enable equitable global participation and governance. Researchers based in megadiverse countries cannot be relegated to sample providers (2), but need to be embedded in decision-making, generate data locally, and contribute as skilled personnel. Therefore, it is important that Phase II of the EBP—in addition to direct efforts to generate reference genomes—also includes training of local researchers in genome sequencing, assembly, curation, and annotation to overcome the capacity gap in genomics found nowadays in Global South countries.

First, the involvement of Global South scientists within the EBP must extend to decision-making and leadership roles that reflect the contribution of the communities within megadiverse countries. Other critical roles include setting local priorities in terms of species to be sequenced and linking locally generated genomes with national research, development, and innovation agendas, as done in the Genomics of Brazilian Biodiversity (GBB) consortium (2, 10). Recently, Latin American countries started organizing an EBP node (Red de Genomas Neotropicales-BioGenomas) with country representatives sharing experiences, realities, and local models for sequencing projects with reduced financial support. Brazil and Chile began coordinating meetings with scientists from Argentina, Colombia, Uruguay, Ecuador, and Panamá. Since then, Argentina has set the first framework for a national biodiversity genomics consortium. In our model, organizing under nationwide initiatives, followed by a larger network, is the first step to ensure that regional and local realities are represented and considered. Other approaches can also be used as models, such as African BioGenome Project, which started as a continent-wide initiative.

Second, the feasibility of decentralized sequencing infrastructure—such as the proposed gBox—must be carefully evaluated within the context of countries facing recurrent challenges in importing reagents, maintaining equipment, and ensuring reliable cold-chain delivery. These barriers remain major bottlenecks that cannot be overlooked when deploying high-throughput sequencing technology globally. The establishment of the proposed US$0.5 billion Foundational Impact Fund (FIF) in Phase II is therefore essential. By focusing support on capacity development and long-term infrastructure in the Global South, the FIF could catalyze sustainable growth in biodiversity genomics rather than short-term or project-bound grants. Decentralized funding models, unconstrained by politically bound research agendas, are crucial for the EBP hubs to dictate research direction while considering local aspects. In this way, we can focus on local solutions to solve global problems.

In many Global South countries, the acquisition of reagents is hindered by persistent failures in maintaining the required cold chain during importation, customs delays, and the lack of reliable distributor networks. These issues lead to frequent reagent degradation and increased costs that slow down or halt genomic workflows. There is a pressing need for supply chains that support room-temperature reagents to preserve high-quality samples. Legal uncertainties, the absence of standardized national frameworks, and administrative bottlenecks further constrain access and sharing of biological samples. Creating and supporting existing local biodiversity biobanks, possibly associated with natural history collections, is also important for access to high-quality, well-documented samples for genome sequencing. Addressing these challenges requires coordinated technological advances, policy development, and long-term engagement with keystone local institutions.

Third, a critical step toward enabling equitable participation in Phase II of the EBP is transforming how political leaders and policymakers engage with biodiversity science. They must recognize that the biodiversity crisis is as urgent as climate change or future pandemics, and that delaying action will have profound consequences. The ongoing discussions in international policy such as the Convention for Biological Diversity highlight a timely opportunity: biodiversity genomics must be integrated into global and national environmental agendas as a strategic tool for conservation, climate adaptation, and sustainable development. Genomic resources are not only essential for monitoring and protecting biodiversity—they also underpin emerging bioeconomy value chains, biotechnological innovation, and preparedness for future biological emergencies.

Importantly, national public policies for genetic-resource protection—including implementation of the Nagoya Protocol and emerging approaches to Digital Sequence Information (DSI) benefit sharing—are key to enabling local sequencing and ensuring that local researchers remain central. Countries need legislation that not only regulates the use of genetic resources but also actively encourages and funds local sequencing, capacity development, and equitable scientific leadership. This will enable Global South researchers and governments to play active roles in international agreements and participate more confidently as equitable partners in biodiversity genomics initiatives, with safeguards against misuse of their countries’ genomic resources.

As biodiversity loss accelerates, investments in biodiversity genomics should not depend solely on academic enthusiasm; they must be recognized as essential national and global priorities, with clear economic, health, and societal implications. To realize this vision, policymakers should no longer be considered “stakeholders”. They must become active partners in the co-creation of genomic initiatives (2). Co-designing strategies with governments ensures that genomic data are incorporated into national priorities, that legal frameworks evolve in tandem with scientific advances, and that investments in infrastructure and capacity remain stable across political cycles. This shift is especially critical for megadiverse countries, where genomic knowledge can directly inform sustainable resource management, climate resilience, and health surveillance systems. By integrating scientific, political, and community perspectives, Phase II of the EBP can become not only a global sequencing effort but a transformative movement toward a more inclusive, resilient, and strategically valuable model of biodiversity science.

Generative AI statement

The authors declared that generative AI was not used in the creation of this manuscript.

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Footnotes

Edited by: Gane Ka-Shu Wong, University of Alberta, Canada

Reviewed by: Eshchar Mizrachi, University of Pretoria, South Africa