Sibelle Torres Vilaça, Alexandre Aleixo, Juliana A. Vianna
The biodiversity crisis is accelerating, with recent IUCN Red List confirming multiple recent species extinctions (IUCN, 2025). 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 nine of the megadiverse countries. Generating knowledge for 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 and understanding genome-wide variation can help estimate important biological variables essential for species conservation, understanding adaptation to climate change, and predicting populations' long-term resilience (Vilaça et al., 2024).Genome sequencing has ramped up in the last decade as the costs drop and technology advances (Wetterstrand et al, 2025). The Earth BioGenome Project (EBP) is capitalizing on this in its aim to sequencing the genomes of all known eukaryotic species. The lead article by Blaxter et al., (2025) 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 3 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 do 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 policy makers.Sequencing life on Earth requires global participation, especially in biodiversity-rich regions. A solution proposed by Blaxter et al., (2025) involves the creation of decentralized laboratories (gBox) established at 25 regional nodes. This model is based on the approach used in outbreak response for pathogen detection like COVID-19. While laboratories for rapid response to disease outbreaks require a Biosecurity Level 3/4, the general infrastructure (Affara et al., 2021) is typically simpler in terms of equipment than the laboratories required for sequencing reference genomes. In our experience, maintaining sequencers in countries where few 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 (Vilaça et al., 2024). The current limitations in technology, maintenance, importing reagents, and keeping 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 USD$9.2 billion in vaccine development (Tortorice et al., 2024) generating trillions in social, health, economic revenue. The same model is needed for biodiversity. With an estimated global cost of €14 trillion in ecosystem services associated with biodiversity loss until 2050 (ten Brink et al., 2009), this 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 (Catanzaro et al., 2014;Angelo, 2017). Environmental expenditures by governments decrease in times of recession with some countries failing to include biodiversity agendas in their post-COVID economy recovery packages (McElwee et al., 2020). 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 its conservation and recovery. The creation of a global public-private co-funding mechanism similar to the recently established Tropical Forests Forever Facility (TFFF) -aimed at compensating financially countries that commit to preserving their tropical forests (https://www.wri.org/insights/financing-nature-conservation-tropical-forest-forever-facility) -could be explored as an alternative to support sequencing efforts in megadiverse countries. Under such a co-funding mechanism, Global South countries would find mechanisms for matching at least some percentage of the external funding that is brought into the country for biodiversity genomics in several alternative ways.We view this as an important step to root perennial biodiversity initiatives in their Global South countries' own territories. These 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.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 (Vilaça et al., 2024), but need to be embedded in decision-making, generate data locally, and contribute as skilled personnel.Therefore, it is important that EBP-Phase II -in addition to direct efforts to reference genome sequencing proper -also include the training of local researchers in genome sequencing, assembly, curation, and annotation to overcome the capacitation 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 (Vilaça et al., 2024;Povill et al., 2025). 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 financing support. Brazil and Chile began coordinating meetings with scientists from Argentina, Colombia, and Mexico. 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, like the 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 from politically-bound research agendas are crucial for the EBP hubs to dictate research direction 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 EBP's Phase II 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 like 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, boosting their confidence in becoming equitable partners in biodiversity genomics initiatives, rather than adopting a defensive attitude to avoid any undue use of the 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 as "stakeholders". They must become active partners in the co-creation of genomic initiatives (see Vilaça et al. 2024). 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, the EBP Phase II can become not only a global sequencing effort but a transformative movement toward a more inclusive, resilient, and strategically valuable model of biodiversity science.Author contribution