“Earth BioGenome Project” enters new phase in cataloguing DNA of 1.8 million species

Sequencing the genomes of all plants, animals, fungi and other microbial life on Earth is a strategy to foster better understanding, management and restoration of biodiversity and ecosystem services.

Biodiversity and Earth BioGenome Project | (photos: J.Zwilling/O.Krone/unsplash/EBP)

The Leibniz Institute for Zoo and Wildlife Research (Leibniz-IZW) and scientists working on the European Reference Genome Atlas (ERGA) work hand in hand with the Earth BioGenome Project (EBP) on this mission – building a global network of scientists as well as strengthening sequencing expertise and capacity. The EBP is now entering a new phase as it moves from pilot projects to full scale “production” sequencing. This new phase is marked with a collection of papers published this week in the “Proceedings of the National Academy of Sciences of the USA” (PNAS), describing the project’s goals, achievements to date and next steps.

All over the world, scientists are currently setting up genomic consortia to generate high-quality, error-free genome sequences of all species. These resources can be essential to address fundamental questions in biology, one health and disease research, and biological conservation. “Genomics is a fast-evolving discipline that aims to study the entire genetic repertoire of species as well as differences and interactions among individuals, populations and communities. Genomic-associated technology has the capacity to generate large amounts of data in a short-time for any given specimen and therefore can be used as a dynamic and multi-purpose tool to support actions against the ongoing mass extinction crisis” says Leibniz-IZW scientist Dr Camila Mazzoni, the chairperson of ERGA. “Generating reference genomes of the entire eukaryotic biodiversity is a moonshot endeavour that can only be approached via a large collaborative and well-coordinated worldwide effort. Major and minor projects – under the umbrella of EBP – such as the Vertebrate Genomes Project (VGP), Darwin Tree of Life (DToL), European Reference Genome Atlas (ERGA) and Africa BioGenome Project (AfricaBP) will together change the tools currently existing for analysing biodiversity and hence provide the way for a deeper understanding.”

The Earth BioGenome Project functions as an international network of networks, coordinating numerous group-specific, regional and national-scale efforts, such as the California Conservation Genome Project (U.S.), the Darwin Tree of Life (Great Britain and Ireland) or the ERGA (Europe). “The special feature of the EBP captures the essence and excitement of the largest-scale coordinated effort in the history of biology,” said Harris Lewin, chair of the EBP Working Group and Distinguished Professor of Evolution and Ecology at the University of California, Davis. “Earth is forecast to lose 50% of its biodiversity by the end of this century without action to curb climate change and protect the health of global ecosystems. Creating a digital library of DNA sequences for all known eukaryotic life can help generate effective tools for preventing biodiversity loss and pathogen spread, monitoring and protecting ecosystems, and enhancing ecosystem services. Achieving the ultimate goal of sequencing all eukaryotic life now seems within our reach.”

Launched in November 2018, the goal of the EBP is to provide a complete DNA sequence catalogue of all 1.8 million species of plants, animals and fungi as well as single-celled microbial eukaryotes. The EBP has now surpassed the start-up phase and enters phase 1 (through 2023) with the ambitious goal to produce reference genomes representing about 9,400 taxonomic families. So far, affiliated projects have produced about 200 such reference genomes, with sequencing, assembly and annotation of another 3,021 expected to be completed by the end of 2022, representing 34% of the phase 1 goal.

As of December 2021, the project includes 5,000 scientists and technical staff at 44 member institutions in 22 countries on every continent except Antarctica. There are 49 affiliated projects covering most major taxonomic groups of eukaryotes, representing access to tens of thousands of high-quality samples from museum collections and field biologists. Most recently, a group of African institutions in 22 countries came together as the Africa BioGenome Project. BIOSCAN, which is implementing DNA barcode technology for discovering and identifying species, and the Global Virome Project, an effort to discover new viruses that might pose pandemic threats, have also joined as affiliates.

Major activities of the first three years have included developing and evaluating scientific quality standards and strategies, organising regional, national, and transnational projects, and building communities through regular working committee meetings and an annual conference.

In addition to the International Scientific Committee, which develops standards for the project, the EBP has also formed committees on Ethics, Legal and Social Issues (ELSI) and Justice, Equity, Diversity and Inclusion (JEDI). EBP’s proactive stance on understanding ethical, legal, and social issues surrounding the project will inform recommendations on access and commercial benefit sharing, equity and inclusion in the biodiversity genomics community and in indigenous communities within the world’s most biodiverse countries.

About ERGA

The European Reference Genome Atlas (ERGA) initiative is a pan-European scientific response to current threats to biodiversity. Reference genomes provide the most complete insight into the genetic basis that forms each species and represent a powerful resource in understanding how biodiversity functions. The ERGA initiative includes, among others, the Leibniz Institute for Zoo and Wildlife Research (Leibniz-IZW), the Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) and the Museum of Natural History (MfN), which together with the Botanical Garden/Botanic Museum of the Freie Universität Berlin, the Biology department of FU Berlin and the Institute of Biochemistry and Biology of the University of Potsdam founded the Berlin Center for Genomics in Biodiversity Research (BeGenDiv) in 2011. In 2021, ERGA has elected Dr Camila Mazzoni as its first chairperson.

Publication

Lewin HA, Richards S, Aiden EL, Allende ML, Archibald JM, Bálint M, Barker KB, Baumgartner B, Belov K, Bertorelle G, Blaxter ML, Cai J, Caperello ND, Carlson K, Castilla-Rubio JC, Chaw SM, Chen L, Childers AK, Coddington JA, Conde DA, Corominas M, Crandall KA, Crawford AJ, DiPalma F, Durbin R, Ebenezer TGE, Edwards SV, Fedrigo O, Flicek P, Formenti G, Gibbs RA, Gilbert MTP, Goldstein MM, Graves JM, Greely HT, Grigoriev IV, Hackett KJ, Hall N, Haussler D, Helgen KM, Hogg CJ, Isobe S, Jakobsen KS, Janke A, Jarvis ED, Johnson WE, Jones SJM, Karlsson EK, Kersey PJ, Kim JM, KressWJ, Kuraku S, Lawniczak MKN, Leebens-Mack JH, Li X, Lindblad-Toh K, Liu X, Lopez JV, Marques-Bonet T, Mazard S, Mazet JAK, Mazzoni CJ, Myers EW, O’Neill RJ, Paez S, Park H, Robinson GE, Roquet C, Ryder OA, Sabir JSM, Shaffer HB, Shank TM, Sherkow JS, Soltis PS, Tang B, Tedersoo L, Uliano-Silva M, Wang K, Wei X, Wetzer R, Wilson JL, Xu X, Yang H, Yoder AD, Zhang G (2022): The Earth BioGenome Project 2020: Starting the clock.

PNAS 119, e2115635118. doi:10.1073/pnas.2115635118.

/Public Release. This material from the originating organization/author(s) may be of a point-in-time nature, edited for clarity, style and length. The views and opinions expressed are those of the author(s).View in full here.