SPECIAL FEATURE: SPECIAL FEATURE: INTRODUCTION INTRODUCTION The Earth BioGenome Project 2020: Starting the clock Harris A. Lewina,b,1 , Stephen Richardsc , Erez Lieberman Aidend, Miguel L. Allendee,f , John M. Archibaldg, Miklo s Ba linth,i, Katharine B. Barkerj, Bridget Baumgartnerk, Katherine Belovl, Giorgio Bertorellem, Mark L. Blaxtern , Jing Caio, Nicolette D. Caperelloc, Keith Carlsonp, Juan Carlos Castilla-Rubioq, Shu-Miaw Chawr, Lei Cheno, Anna K. Childerss, Jonathan A. Coddingtont , Dalia A. Condeu,v , Montserrat Corominasw,x , Keith A. Crandally,z , Andrew J. Crawfordaa, Federica DiPalmabb, Richard Durbincc,dd , ThankGod E. Ebenezeree, Scott V. Edwardsff,gg , Olivier Fedrigohh, Paul Flicekdd,ii, Giulio Formentijj, Richard A. Gibbskk, M. Thomas P. Gilbertll,mm , Melissa M. Goldsteinnn, Jennifer Marshall Gravesoo,pp , Henry T. Greelyqq , Igor V. Grigorievrr,ss , Kevin J. Hacketttt, Neil Halluu, David Hausslervv,ww, Kristofer M. Helgenxx, Carolyn J. Hoggl , Sachiko Isobeyy, Kjetill Sigurd Jakobsenzz , Axel Jankeh , Erich D. Jarvishh,ww, Warren E. Johnsonaaa,bbb , Steven J. M. Jonesccc, Elinor K. Karlssonddd,eee , Paul J. Kerseyfff, Jin-Hyoung Kimggg, W. John Kresshhh , Shigehiro Kurakuiii,jjj, Mara K. N. Lawniczakn, James H. Leebens-Mackkkk , Xueyan Lilll, Kerstin Lindblad-Toheee,mmm , Xin Liunnn, Jose V. Lopezooo,ppp, Tomas Marques-Bonetqqq,rrr,sss,ttt , Sophie Mazarduuu, Jonna A. K. Mazetvvv , Camila J. Mazzoniwww,xxx, Eugene W. Myersyyy , Rachel J. O’Neillzzz,aaaa, Sadye Paezhh, Hyun Parkbbbb, Gene E. Robinsoncccc , Cristina Roquetdddd,eeee , Oliver A. Ryderffff,gggg , Jamal S. M. Sabirhhhh,iiii , H. Bradley Shafferjjjj,kkkk , Timothy M. Shankllll, Jacob S. Sherkowcccc,mmmm , Pamela S. Soltisnnnn,oooo , Boping Tangpppp , Leho Tedersooqqqq,rrrr, Marcela Uliano-Silvan, Kun Wango, Xiaofeng Weinnn, Regina Wetzerssss,tttt, Julia L. Wilsondd, Xun Xunnn, Huanming Yangnnn, Anne D. Yoderuuuu,vvvv , and Guojie Zhanglll,nnn,wwww,xxxx November 2020 marked 2 y since the launch of the ecosystems (2). The International Union for Conser- Earth BioGenome Project (EBP), which aims to vation of Nature now counts more than 35,000 sequence all known eukaryotic species in a 10-y (28%) of all surveyed species of plants and animals timeframe. Since then, significant progress has been as threatened with extinction (3). The Earth may lose made across all aspects of the EBP roadmap, as out- 50% of its biodiversity by the end of this century if lined in the 2018 article describing the project’s nothing is done to mitigate the anthropogenic fac- goals, strategies, and challenges (1). The launch tors that drive species to extinction and destroy the phase has ended and the clock has started on reach- health of global ecosystems that sustain human exis- ing the EBP’s major milestones. This Special Feature tence (2). Degradation of aquatic and terrestrial eco- explores the many facets of the EBP, including a systems has continued unabated, and we may soon review of progress, a description of major scientific face the possibility of massive ecosystem collapse goals, exemplar projects, ethical legal and social on a global scale. issues, and applications of biodiversity genomics. In Such a collapse would have an enormous impact this Introduction, we summarize the current status of not only on biodiversity, but also on global political the EBP, held virtually October 5 to 9, 2020, includ- stability, and might ultimately affect the survival of ing recent updates through February 2021. Referen- our own species. Biological diversity underpins eco- ces to the nine Perspective articles included in this system services: that is, those services provided by Special Feature are cited to guide the reader toward nature that generate food, clean air and water, regu- deeper understanding of the goals and challenges lation of critical environmental processes and facing the EBP. biogeochemical cycles, and are the basis for deep It is urgent that the EBP move forward. The year cultural and esthetic ties between humans and the 2020 marked a global failure in meeting any of the natural world. Biodiversity is also foundational for the 20 “Aichi goals” for the preservation of wildlife and rapidly growing global bioeconomy that exceeds Author contributions: H.A.L. and S.R. analyzed data; and H.A.L., S.R., E.L.A., M.L.A., J.M.A., M.B., K.B.B., B.B., K.B., G.B., M.L.B., J.C., N.D.C., K.C., J.C.C-R., S.-M.C., L.C., A.K.C., J.A.C., D.A.C., M.C., K.A.C., A.J.C., F.D., R.D., T.E.E., S.V.E., O.F., P.F., G.F., R.A.G., M.T.P.G., M.M.G., J.M.G., H.T.G., I.V.G., K.J.H., N.H., D.H., K.M.H., C.J.H., S.I., K.S.J., A.J., E.D.J., W.E.J., S.J.M.J., E.K.K., P.J.K., J.-H.K., W.J.K., S.K., M.K.N.L., J.H.L.-M., X. Li, K.L.-T., X. Liu, J.V.L., T.M.-B., S.M., J.A.K.M., C.J.M., E.W.M., R.J.O., S.P., H.P., G.E.R., C.R., O.A.R., J.S.M.S., H.B.S., T.M.S., J.S.S., P.S.S., B.T., L.T., M.U.-S., K.W., X.W., R.W., J.L.W., X.X., H.Y., A.D.Y., and G.Z. wrote the paper. The authors declare no competing interest. This article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND). 1 To whom correspondence may be addressed. Email: lewin@ucdavis.edu. Downloaded by guest on January 20, 2022 This article contains supporting information online at http://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2115635118/-/DCSupplemental. Published January 18, 2022. PNAS 2022 Vol. 119 No. 4 e2115635118 https://doi.org/10.1073/pnas.2115635118 j 1 of 7 $500 billion each year in just the United States and European (15)], and promotes programs for diversity, equity, inclusion, and Union (4, 5), and it is essential for sustainable food security (6). If justice among the project’s participants. The EBP Member Institu- biodiversity disappears, so too will the potential for a new inclu- tions and Affiliated Projects are committed to open data access sive bioeconomy that is possible through a combination of geno- and compliance with the principles of Access and Benefits Sharing mics, computational biology, and synthetic biology, identified by under the Convention on Biological Diversity and the Nagoya Pro- the World Economic Forum as key to the fourth Industrial Revolu- tocol (16). The EBP communicates progress and information about tion (7) and estimated to be worth up to US $3 to 5 trillion per the project through its website (https://www.earthbiogenome.org), annum (8). its Twitter handle (@EBPgenome), and other social media The year 2020 will also be remembered in history as the accounts, currently with more than 2,000 followers. beginning of the COVID-19 pandemic. The virus that causes The EBP Secretariat is located at the University of California, COVID-19, SARS-CoV-2, evolved from a bat betacoronavirus Davis, and operates under a Memorandum of Understanding (9), possibly finding its way into the human population through between participating institutions available at the EBP website, an intermediate host that has yet to be identified (10). Spillover https://www.earthbiogenome.org. The representatives of mem- of SARS-CoV-2 infection to wildlife, pets, and captive-bred ber institutions have adopted an interim governance structure animals demonstrates the interconnectedness of life on Earth, (SI Appendix, Fig. 1). reinforcing the One Health concept that all organisms are inter- An interim governance committee is in place, The Earth Bio- dependent: the health of one impacts the health of all (11). A Genome Project Working Group, which as of February 2021 One Health approach to addressing the biodiversity crisis criti- consists of one representative of each of the 43 Memorandum cally relies on supporting infrastructures, such as the genomic of Understanding-signing institutions (see list on the EBP web- infrastructure that can be provided by the EBP and affiliated site, https://www.earthbiogenome.org) and 44 affiliated proj- projects. The economic disaster and devastating human death ects (Dataset S1; brief summaries of 21 affiliated projects can be toll caused by the pandemic illustrate just how critical it is to found in SI Appendix), with membership up 121% and 153%, have knowledge of potential human pathogens and their hosts respectively, since 2018. The Chair of the EBP Working Group before such events arise (12). Clearly, DNA sequence informa- coordinates the activities of all the working committees and tion on the virus and its potential hosts has helped the world to conducts extensive international outreach for promoting collab- manage and hopefully soon contain COVID-19. Similarly, creat- oration between member institutions and affiliated projects, ing a library of DNA sequences for all known eukaryotic life can implementation of standards, assisting the formation of national contribute critical data necessary to generate effective tools for and regional projects, and coordination of activities across the preventing biodiversity loss and pathogen spread, monitoring EBP network-of-networks. The International Science Committee and protecting ecosystems, and enhancing ecosystem services consists of a chairperson and five subcommittees that are [see The Darwin Tree of Life Project Consortium, this issue (13)]. responsible for standards development in the following areas: The EBP’s proactive stance on understanding the ethical, legal, sample collection and processing, sequencing and assembly, and social issues surrounding the project will also inform recom- annotation, information technology and informatics, and data mendations on access and commercial benefit sharing, equity, analyses. Committee reports are available on the EBP website and inclusion in the biodiversity genomics community and in (https://www.earthbiogenome.org) and summarized in this issue. indigenous communities within the world’s most biodiverse The EBP plans to formally adopt a permanent governance struc- countries [see McCartney et al., this issue (14)]. ture in 2021. Those institutions and projects that are interested in joining the EBP should contact the Secretariat using the EBP website for further information. Organization and Governance The EBP’s Committee on Ethical, Legal, and Social Issues A critical role of the EBP organization is to: develop and pro- (ELSI), established in 2020, makes recommendations to the EBP mote standards for the scalable production of reference-quality Working Group on legal obligations relating to the Nagoya Pro- genomes; dissemination of best practices; coordination of tocol on Access and Benefit Sharing; ethical considerations sequencing, annotation, data analysis, and training activities; relating to collection of samples, societal concerns, and biose- public accessibility of data; and communications about the proj- curity; and collaboration standards (e.g., sample information, ect’s progress. To accomplish these goals, the EBP was estab- digital sequence information, intellectual property, authorship lished as an international network-of-networks: organizations and publication guidelines). The committee’s outline of the ELSI that specialize in sample acquisition and vouchering; technol- issues facing the EBP can be found in this issue (15). A Commit- ogy centers for sequencing, assembly, and annotation; and affil- tee on Diversity, Equity, Inclusion, and Justice (DEIJ) was iated projects with deep expertise with specific taxonomic approved recently by the EBP Working Group. DEIJ recommen- groups, biomes, and ecosystems (Box 1). In addition, the EBP dations will be based on participatory approaches with fair develops ethical standards for project participation, data shar- treatment and meaningful involvement of all people to define ing, access and benefit sharing of intellectual property derived processes and practices for creating a welcoming, inclusive, and from whole-genome sequencing [see Sherkow et al., this issue supportive biodiversity genomics community. Box 1. The EBP international network-of-networks functions to support the three proposed phases of the EBP Phase I: An annotated reference genome for one representative of each taxonomic family of eukaryotes (∼9,400 species) in 3 y. Phase II: Reference genomes for one representative of each genus (∼180,000 species) in years 4 to 7. Downloaded by guest on January 20, 2022 Phase III: Reference genomes for remaining ∼1.65 million known eukaryotic species in the final 3 y of the project. 2 of 7 j PNAS Lewin et al. https://doi.org/10.1073/pnas.2115635118 The Earth BioGenome Project 2020: Starting the clock Global Status of Biodiversity Sequencing of the meeting is available (20). The EBP is also developing new Our current ability to investigate the diversity and evolution of initiatives in training, broadening diversity and inclusion in pro- Earth’s biota is severely constrained by the absence of high- ject leadership, and building support for project funding from quality genome sequences for most of the species on the government agencies and private foundations around the eukaryotic tree of life. There are now ∼1.84 million taxonomi- world. cally classified eukaryotic species, but the estimated number of The current line-up of 43 EBP-affiliated projects cover most eukaryotic species is 12 to 15 million, including 8.1 million of the major groups of eukaryotic taxa and represent access to plants and animals (17). The EBP aims to sequence all classified tens of thousands of high-quality samples in museum collections species and to facilitate the discovery and classification of new and those from field biologists. The geographic diversity of the species. As of March 4, 2021, the International Nucleotide institutional members and affiliated projects cover 21 countries Sequence Database Collaboration (INSDC) contained whole- across all continents except Antarctica. The first African nodes genome DNA sequence information on 6,480 unique species, have recently come on line in 2021 as part of the Africa BioGe- representing 81.4% of eukaryotic phyla, 64.7% of classes, nome Project. The EBP also aims to expand member institutions 40.1% of orders, 15.5% of families, 2.3% of genera, and just and affiliated projects across additional biodiverse regions of 0.43% of all species (Fig. 1). the world, including the Indian subcontinent, Southeast Asia, However, the assembly quality of these 6,480 species’ and South America [for example, see Huddart et al. (21), this genomes varies greatly (SI Appendix, Fig. 1). A majority (63.1%) issue]. With high endemism concentrated in these regions, the of the assemblies falls into the short-read draft category, with ultimate success of the EBP requires building scientific capacity contig N50 < 100 kb and scaffold N50 < 10 Mb. A relatively in developing nations and respecting national laws for access small number of the draft-quality assemblies have achieved and benefit sharing. greater contiguity using scaffolding methods, such as Hi-C, EBP-affiliated projects, such as the Darwin Tree of Life Pro- linked-reads, and optical maps (19). The number of unique ject [see The Darwin Tree of Life Project Consortium, this issue eukaryotic species with whole-genome assemblies has more (22)], The Vertebrate Genomes Project, 1000 Fungal Genomes than doubled since 2018 (Fig. 2), most of which are short-read Project, B10K (sequencing 10,000 bird species), and others draft quality. The number of reference-quality chromosome- have led the way in producing publicly accessible high-quality scale assemblies of unique species representing taxonomic fam- genomes (Table 1 and SI Appendix). A Perspective on sequenc- ilies nearly tripled since 2018, from 210 to 583. EBP-affiliated ing of plant genomes is included in this special issue (23). EBP- projects produced about half of these new reference-quality affiliated sequencing centers around the world are now coming assemblies (see below), demonstrating the efficacy of shared online for the production of reference genomes using a simpli- goals and standards. fied pipeline consisting of long reads and Hi-C (or equivalent), and other scaffolding methods, such as optical mapping, and Progress of the EBP toward Phase I Goals public domain assembly tools, such as the recently developed The past 2 y represent the start-up phase of the EBP. The major hifiasm for generating long-read–based contigs (24) and SALSA activities of the international EBP network-of-networks include: for generating Hi-C scaffolds (25). This simplified approach, the development of standards; the evaluation of strategies for within the reach of most EBP-affiliated laboratories, yields producing reference genomes; organizing regional, national, chromosome-scale assemblies that meet the EBP standard (see and transnational projects; and building communities through above). regular working committee meetings and an annual conference. The EBP-affiliated projects have sequenced the genomes of The “Biodiversity Genomics 2020” conference was held virtually 1,719 eukaryotic species, all of which have assemblies deposited and had 3,000 registrants from 89 countries. The full recording in public domain databases (Table 1 and Dataset S1). Of these, Downloaded by guest on January 20, 2022 Fig. 1. Global progress in whole-genome sequencing across all eukaryotic taxonomic levels. Data source: National Center for Biotechnology Information, March 4, 2021 (18). Lewin et al. PNAS j 3 of 7 The Earth BioGenome Project 2020: Starting the clock https://doi.org/10.1073/pnas.2115635118 Fig. 2. Year-over-year progress in whole genome sequencing for all eukaryotic taxa (Upper) and family-level (Lower) eukaryotic taxa, 2010 to March 4, 2021. The metrics for draft and reference quality assemblies are given in the text. 316 are reference-quality genomes, constituting ∼50% of all the viruses linked with their host species and for codevelopment of genomes in the INSDC that meet the EBP reference standard. biosurveillance strategies (12). Integrated high-level coordina- Furthermore, these already represent more than 200 taxonomi- tion between these projects will have synergistic effects on bio- cally distinct nonredundant families. Thus, in the start-up phase, diversity science and societal outcomes. A broad perspective EBP-affiliated projects have sequenced ∼2% of extant eukaryotic on the scientific challenges and opportunities enabled by large- families to reference-level quality. There are 3,021 family-level scale comparative genomics is provided by Stephan et al., this reference genomes expected to be completed in 2021. Thus, by issue (28). the end of 2021, the first full year of the project, we project that ∼3,200 taxonomic families will have been sampled with at least The Challenges Ahead one reference genome, corresponding to 34% completion of the Although the number of reference-quality genomes at the fam- EBP Phase I goal. ily level tripled from 2018 to March 4, 2021 (Fig. 2), the EBP will Other large-scale initiatives with complementary goals have have to produce nearly 3,000 genomes per year to meet the joined EBP as affiliated projects. These include BIOSCAN (26) EBP Phase I goal of producing at least one reference genome and the Global Virome Project (27). BIOSCAN aims to DNA bar- from all ∼9,400 eukaryotic families in 3 y. The main challenges code every eukaryotic species on Earth, which will be critical to in meeting this target are given in Box 2. the EBP sample vouchering process and for accessing rare sam- To meet the EBP Phase I goal, the EBP network-of-networks ples for sequencing. Partnership with the Global Virome Project will need to produce nine genomes per day, 365 d/y. Is this feasi- creates an exciting avenue to identify potentially pathogenic ble? The Wellcome Sanger Institute alone plans to produce 1,500 Table 1. Progress of EBP affiliated projects in whole-genome sequencing and the production of reference genomes Project name No. of species No. of references No. of families with reference No. of references 2021 No. of drafts 2021 1000 Fungal Genomes 663 20 10 10 100 B10K (birds) 400 32 29 0 400 Zoonomia (mammals) 130 0 0 0 0 VGP (vertebrates) 128 129 119 200 0 i5K (arthropods) 86 2 2 2 8 Darwin Tree of Life 71 71 14 1,500 0 Tree of Life, Sanger 50 50 50 300 0 LOEWE Center 43 43 43 84 95 Ungulates Genome Project 41 0 0 4 6 CanSeq150 36 21 0 0 0 10KP (plants) 21 2 2 16 42 All other 80 42 30 905 1,505 Total 1,719 412 316 3,021 2,156 All tabulated genomes in the first three columns have been submitted to the INSDC or other public domain databases. Numbers in the last two columns are Downloaded by guest on January 20, 2022 projected additional species genomes for 2021. A complete table with INSDC project identifiers can be found in Dataset S1. Totals include some species that overlap between projects. 4 of 7 j PNAS Lewin et al. https://doi.org/10.1073/pnas.2115635118 The Earth BioGenome Project 2020: Starting the clock of ∼165,000 genera in 4 y will require an increase in the Box 2. Challenges in meeting EBP goals throughput of genomes from 9 per day to 123 per day, or • Sourcing, vouchering, and permitting thousands of speci- 14-fold above the Phase I target. Phase III will require another mens globally 10-fold increase above the Phase II target in order to complete • High molecular weight DNA and RNA isolation at scale the project in 10 y. We are optimistic that within 5 y, sample • Sequencing capacity and throughput processing and sequencing technology will improve and costs • Assembly and curation at scale will be reduced so that reference-quality genomes can be pro- • Annotation at scale duced for all species for under USD $1,000 for a 2-Gb genome. • Managing data flows in the context of international cur- We note that the cost, accuracy, and contiguity of assemblies rent and future data access and sharing regulations produced today with long reads were not available 2 y ago. • Whole genome alignments at scale High-quality draft assemblies based on long reads can already • Comparative genomic analysis, population genomics, be produced for ∼$2,000 in reagents and compute per 1-Gb and data visualization at scale genome average, getting closer to the $800 originally envi- sioned for short-read draft-quality genomes (1). Sequencing done for Phases II and III should meet or exceed the minimum reference-quality genomes in 2021 as part of the Darwin Tree of standards for short-read–based draft assemblies: contig N50 > Life Project, corresponding to four genomes per day. As pre- 100 Kb, scaffold N50 > 1 Mbp (or chromosome scale for smaller sented in Table 1, the Institute is already well on its way to achiev- genomes), QV30. Although the EBP aspires to produce ing this goal in the coming year. The Vertebrate Genomes Project chromosome-level assemblies for all species, for uncultured aims to produce six genomes per week to complete its goal of microbial eukaryotes and highly repetitive genomes, the project producing high-quality assemblies for species representing 260 will sacrifice perfection for progress in the near term. vertebrate lineages separated by 50 million y or more from a com- In 2018, we estimated a total EBP cost of USD $4.7 billion. mon ancestor (19), by the end of 2021. With current technology This is significantly less than the original USD $2.7 billion (1991 and funded commitments for 2021 by EBP-affiliated sequencing dollars) cost of sequencing the human genome, comparable centers, reaching the goal of 9 genomes per day globally, or with USD $5.2 billion today. We note that producing complete nearly 3,000 annually, is anticipated (Table 1). The main challenge telomere-to-telomere assemblies for all human chromosomes is will be sourcing high-quality taxonomically identified samples for a mission that is now being realized (32), and that the true cost the isolation of high molecular weight DNA and RNA required for of sequencing the human genome is significantly higher than long-read DNA sequencing, scaffolding, and annotation. Separate the original USD $2.7 billion price tag. Reference-quality from the current commitments above, about 50% of the taxo- genomes currently being produced by the EBP’s sequencing nomic families could be obtained today from existing collections nodes are of far greater quality (i.e., continuity, completeness, in the Global Genome Biodiversity Network (SI Appendix) (29). phasing) than the original “complete” human genome Obtaining samples from many countries may require diverse per- sequence [e.g., Rhie et al. (19)], and can now be produced for mit processes that can last weeks to years. The EBP is working to about USD $10,000 per 2-Gb genome, including transcriptome develop long-term collaborations to facilitate sample access across data for annotation. This amount is 20% of the cost of a similar the world. quality assembly only 3 y ago when the original estimates were Another critical challenge will be obtaining reference-quality made. The project will save about USD $186 million in Phase I assemblies from small organisms, single-cell eukaryotes, and due to these improvements, bringing the total cost of Phase I some green plants. New low-DNA input methods (30) have down to $414 million from $600 million. essentially solved the problem for most metazoans, but not for The EBP has embraced the strategy of supporting funding single-cell eukaryotes that cannot be cultured. Producing efforts by states and nations: for example, the California Con- reference-quality genomes thus remains a significant challenge servation Genomics Project and 1000 Chilean Genomes (SI for a large part of the eukaryotic tree of life. Setting standards for Appendix), and EBP-Colombia (21). This effort has proven the generation and storage of the complex set of genomes that highly successful as it allows for local and regional concerns to characterize green plants will need to accommodate the be addressed in the funding drive. For example, in Australia immense variation in their size, transposable element content, there is great interest in conserving endangered marsupial spe- and structure, while enabling research into the molecular and cies [see Hogg, this issue (33)]. This has led to a funded project evolutionary processes that have resulted in this enormous geno- that will produce five new marsupial reference genomes in mic variation (23). Recommendations for sample collection and 2021 (Table 1). Other examples include the Catalan Initiative processing are included in this issue. Accelerating the annotation for the Earth BioGenome Project, which aims to prioritize pipeline will also present major challenges as the production of sequencing of endemic species with the goal of eventually genomes scales up. Planned 2021 annotation throughput is 300, sequencing all species in the Catalan territories (SI Appendix). 400, and 500 species for the National Center for Biotechnology National funding also provides an inherent mechanism for com- Information, Joint Genome Institute, and European Molecular pliance with national laws on access and benefit sharing, which Biology Laboratory–European Bioinformatics Institute, respec- may prove essential for building trust, and ultimately obtaining tively, which remains short of what will be necessary. This issue all taxonomically classified species for sequencing. Capacity can be addressed by expanding capacity and creating more effi- building in developing countries will be a direct benefit of cient genome annotation tools (31). Current recommendations participation. for genome annotation are provided in this issue . To achieve the outputs required for Phase II and Phase III, Conclusions Downloaded by guest on January 20, 2022 dramatic increases in genome sequence production and effi- The past year has been one of great progress for the EBP, mark- ciency will be required. Sequencing one representative for each ing the start of the clock for completing Phase I of the project. Lewin et al. PNAS j 5 of 7 The Earth BioGenome Project 2020: Starting the clock https://doi.org/10.1073/pnas.2115635118 There are many challenges ahead in meeting Phase II and Phase tremendous passion and energy among the project’s partici- III goals. Clearly, the ultimate aim of sequencing 1.84 million pants, particularly its younger generation of scientists and the eukaryotes cannot be achieved by a single country or private general public. entity. The coordinated efforts of thousands of scientists and Given the precarious condition of Earth’s biodiversity, it is institutions around the world are needed to produce ∼9,400 essential that the EBP and its affiliated projects achieve their family reference genomes in 3 y. The project needs significant ambitious goals. In the words of David Attenborough, amounts of new funding, but the investments required on a “Extinction is forever—so our action must be immediate.” global scale should be obtainable given the importance of the Every eukaryotic species is the product of millions of years of project to conserving and enhancing ecosystem services in the evolution. Recorded in their genomes are secrets that can fun- context of climate change and promoting a new bioeconomy. damentally change our understanding of the evolution of life Despite limited financial resources for coordination, the EBP on Earth—its very existence and essence—and may lead to international network-of-networks has matured as the world’s radical new approaches for mitigating the effects of climate most technically advanced organization to tackle the grand change on biodiversity, improving agriculture, growing a sus- challenge of sequencing all known eukaryotes, identifying their tainable global bioeconomy, saving species and repairing eco- genes and functions, advancing our understanding of the evolu- systems, and preventing future pandemics. Let us go forth and tion of life on Earth, and developing a complete genomic char- sequence! acterization of Earth’s critical ecosystems. Based on a survey of institutional members and affiliates, the EBP now includes more Acknowledgments than 5,000 scientists and technical staff around the world who We thank Prof. Beth Shapiro and Fritz J. Sedlazeck for their editorial comments are dedicated to EBP’s mission. The EBP has unleashed on the manuscript. a Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, CA 95616; b Department of Population Health and Reproduction, University of California, Davis, CA 95616; c University of California Davis Genome Center, University of California, Davis, CA 95616; d DNA Zoo and The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030; e Center for Genome Regulation, Universidad de Chile 3425 Santiago, Chile; f Facultad de Ciencias, Universidad de Chile 3425 Santiago, Chile; g Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4H7, Canada; h LOEWE Centre of Translational Biodiversity Genomics, Senckenberg Leibniz Institution for Biodiversity and Earth System Research 60325 Frankfurt am Main, Germany; i Institute for Insect Biotechnology, Justus-Liebig University 35392 Giessen, Germany; j Global Genome Biodiversity Network Secretariat, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560; k Revive & Restore, Sausalito, CA 94965; l School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia; m Department of Life Sciences and Biotechnology, University of Ferrara 44121 Ferrara, Italy; n Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom; o School of Ecology and Environment, Northwestern Polytechnical University 710072 Xi’an, China; p The Novim Group, University of California, Santa Barbara, CA 93106; q Spacetime Ventures 05449- 050 S~ ao Paulo, Brazil; r Biodiversity Research Center, Academia Sinica 11529 Taipei, Taiwan; s Bee Research Laboratory, Beltsville Agricultural Research Center, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705; t Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560; u Conservation Science, Species360 Conservation Science Alliance, Bloomington, MN 55425; v Department of Biology, University of Southern Denmark 5230 Odense M, Denmark; w Department of Genetics, Microbiology, and Statistics, Universitat de Barcelona 08028 Barcelona, Spain; x Catalan Society for Biology, Institute for Catalan Studies 08001 Barcelona, Spain; y Department of Biostatistics & Bioinformatics, Computational Biology Institute, George Washington University, Washington, DC 20052; z Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052; aa Department of Biological Sciences, Universidad de los Andes 111711 Bogot a, Colombia; bb Genome British Columbia, Vancouver, BC V5Z 0C4, Canada; cc Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom; dd Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom; ee UniProt, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom; ff Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138; gg Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138; hh Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065; ii European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, United Kingdom; jj Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065; kk Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030; ll GLOBE Institute, University of Copenhagen 1350 Copenhagen, Denmark; mm University Museum, Norwegian University of Science and Technology 7491 Trondheim, Norway; nn Department of Health Policy and Management, George Washington University, Washington, DC 20052; oo School of Life Sciences, La Trobe University, Bundoora, VIC 3086, Australia; pp Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia; qq Stanford Law School, Stanford University, Stanford, CA 94305; rr US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; ss Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720; tt Office of National Programs, US Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705; uu Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom; vv Genome Institute, University of California, Santa Cruz, CA 95060; ww HHMI, Chevy Chase, MD 20815; xx Australian Museum Research Institute, Australian Museum, Sydney, NSW 2000, Australia; yy Department of Frontier Research and Development, Kazusa DNA Research Institute, Chiba 292-0818, Japan; zz Department of Biosciences, University of Oslo, Oslo 0316, Norway; aaa Walter Reed Biosystematics Unit, Smithsonian Institution, Suitland, MD 20746; bbb Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630; ccc Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada; ddd Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605; eee Broad Institute of MIT and Harvard, Cambridge, MA 02142; fff Royal Botanic Gardens, Kew, Richmond TW9 3AE, United Kingdom; ggg Division of Life Sciences, Korea Polar Research Institute 21990 Incheon, South Korea; hhh Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012; iii Department of Genomics and Evolutionary Biology, National Institute of Genetics 411- 8540 Shizuoka, Japan; jjj Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research 650-0047 Hyogo, Japan; kkk Department of Plant Biology, University of Georgia, Athens, GA 30602; lll State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences 650223 Yunnan, China; mmm Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University 752 36 Uppsala, Sweden; nnn BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China; ooo Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University, Dania Beach, FL 33004; ppp Guy Harvey Oceanographic Center, Dania Beach, FL 33004; qqq Institute of Evolutionary Biology, Pompeu Fabra University, Consejo Superior de Investigaciones Cientificas, Parc de Recerca Biomedica de Barcelona 08003 Barcelona, Spain; rrr Catalan Institute of Research and Advanced Studies 08010 Barcelona, Spain; sss Centre Nacional d'An alisi Gen omica, Centre for Genomic Regulation, Barcelona Institute of Science and Technology 08028 Barcelona, Spain; ttt Institut Catal a de Paleontologia Miquel Crusafont, uuu vvv Universitat Aut onoma de Barcelona 08193 Barcelona, Spain; Bioplatforms Australia, Macquarie University, Sydney, NSW 2109, Australia; One Health Institute, University of California Davis, CA 95616; www Berlin Center for Genomics in Biodiversity Research 14195 Berlin, Germany; xxx Evolutionary Genetics Department, Leibniz Institute for Zoo and Wildlife Research 10315 Berlin, Germany; yyy Max Planck Institute for Molecular Cell Biology and Genetics 01307 Dresden, Germany; zzz Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269; aaaa Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269; bbbb Division of Biotechnology, Korea University 02841 Seoul, Korea; cccc Department of Entomology, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801; dddd Systematics and Evolution of Vascular Plants Associated Unit to Consejo Superior de Investigaciones Cientificas, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Aut onoma de Barcelona 08193 Bellaterra, Spain; eeee Laboratoire d’Ecologie Alpine, University Grenoble Alpes, University Savoie Mont Blanc, CNRS 38000 Grenoble, France; ffff Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027; gggg Division of Biology, Department of Evolution, Behavior, and Ecology, University of California, San Diego, La Jolla, CA 92039; hhhh Department of Biological Sciences, Faculty of Science, King Abdulaziz University 21589 Jeddah, Saudi Arabia; iiii Centre of Excellence in Bionanoscience Research, King Abdulaziz University 21589 Jeddah, Saudi Arabia; jjjj La Kretz Center for California Conservation Science, Institute of Environment and Sustainability, University of California, Los Angeles, CA 90024; kkkk Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095; llll Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543; mmmm College of Law, University of Illinois at Urbana–Champaign, Champaign, IL 61820; nnnn Florida Museum of Natural History, University of Florida, Gainesville, FL 32611; oooo Biodiversity Institute, University of Florida, Gainesville, FL 32611; pppp Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetlands, Yancheng Teachers University 224002 Yancheng, China; qqqq Center of Mycology and Microbiology, University of Tartu 50411 Tartu, Estonia; rrrr College of Science, King Saud University 11451 Riyadh, Saudi Arabia; ssss Research and Collections, Natural History Museum of Los Angeles County, Los Angeles, CA 90007; tttt Biological Sciences, University of Southern California, Los Angeles, CA 90089; uuuu Department of Biology, Duke University, Durham, NC 27708; vvvv Duke Center for Genomic and Computational Biology, Duke University, Durham, NC 27708; wwww Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Downloaded by guest on January 20, 2022 Department of Biology, University of Copenhagen 2100 Copenhagen, Denmark; and xxxx China National Genebank, Beijing Genomics Institute 51803 Shenzhen, China 6 of 7 j PNAS Lewin et al. https://doi.org/10.1073/pnas.2115635118 The Earth BioGenome Project 2020: Starting the clock 1 H. A. Lewin et al., Earth BioGenome Project: Sequencing life for the future of life. Proc. Natl. Acad. Sci. U.S.A. 115, 4325–4333 (2018). 2 S. Dıaz et al., Summary for Policymakers of the Global Assessment Report on Biodiversity and Ecosystem Services of the Intergovernmental Science-Policy Plat- form on Biodiversity and Ecosystem Services (Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services, 2019). 3 International Union for Conservation of Nature, The IUCN Red List of Threatened Species. Version 2020-3. https://www.iucnredlist.org. Accessed 1 April 2021. 4 Bioeconomy Capital, Bioeconomy dashboard: Economic metrics. http://www.bioeconomycapital.com/bioeconomy-dashboard. Accessed 1 April 2021. 5 Natural Resources Institute Finland, Finnish bioeconomy in numbers. https://www.luke.fi/en/natural-resources/finnish-bioeconomy-in-numbers/. Accessed 1 April 2021. 6 National Academy of Sciences, The Challenge of Feeding the World Sustainably: Summary of the US-UK Scientific Forum on Sustainable Agriculture (National Academies Press, Washington, DC, 2021). 7 World Economic Forum, The Global Risks Report 2021, ed. 16. https://www3.weforum.org/docs/WEF_The_Global_Risks_Report_2021.pdf. Accessed 1 April 2021. 8 McKinsey Global Institute, The Bio Revolution—Innovations transforming economies, societies, and our lives. https://www.mckinsey.com/∼/media/McKinsey/ Industries/Pharmaceuticals%20and%20Medical%20Products/Our%20Insights/The%20Bio%20Revolution%20Innovations%20transforming%20economies%20 societies%20and%20our%20lives/May_2020_MGI_Bio_Revolution_Report.pdf. Accessed 1 April 2021. 9 P. Zhou et al., A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579, 270–273 (2020). 10 J. Damas et al., Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates. Proc. Natl. Acad. Sci. U.S.A. 117, 22311–22322 (2020). 11 G. Hansen, J. Mazet, J. Rushton, C. Stroud, What happens after disease X: Using One Health to prevent the next pandemic. NAM Perspectives, 10.31478/ 202011c (2020). 12 W. J. Kress, J. A. K. Mazet, P. D. N. Hebert, Opinion: Intercepting pandemics through genomics. Proc. Natl. Acad. Sci. U.S.A. 117, 13852–13855 (2020). 13 M. L. Blaxter, et al., Why sequence all eukaryotes? Proc. Natl. Acad. Sci. U.S.A., 10.1073/pnas.2115636118 (2021). 14 S. A. McCartney et al., Balancing openness with indigenous data sovereignty: An opportunity to leave no one behind in the journey to sequence all life. Proc. Natl. Acad. Sci. U.S.A., 10.1073/pnas.2115860118 (2021). 15 J. S. Sherkow et al., Ethical, legal, and social issues in the Earth BioGenome Project. Proc. Natl. Acad. Sci. U.S.A., 10.1073/pnas.2115859118 (2021). 16 Secretariat of the Convention on Biological Diversity, Text and Annex of the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Shar- ing of Benefits Arising from Their Utilization to the Convention on Biological Diversity (United Nations, Montreal, ed. 1, 2011). https://www.cbd.int/abs/text/ default.shtml. Accessed 21 February 2015. 17 Y. Roskov et al., Eds., Species 2000 & ITIS Catalogue of Life, 2020-12-01 (Species 2000: Naturalis, Leiden, the Netherlands, 2020). https://www.catalogueoflife. org. 18 National Center for Biotechnology Information, Data from “Eukaryota.” NCBI. https://www.ncbi.nlm.nih.gov/assembly?term=eucaryotes. Accessed 4 March 2021. 19 A. Rhie et al., Towards complete and error-free genome assemblies of all vertebrate species. Nature 592, 737–746 (2021). 20 C. Leech, “Biodiversity Genomics 2020” (video recording, 2020). https://www.youtube.com/playlist?list=PLpziXi8KUFQXTq6YeIpmBCicIRA1KB6eU. Accessed 3 December 2021. 21 J. Huddart, A. J. Crawford, A. L. Luna Tapia, S. Restrepo, F. DiPalma, EBP-Colombia and the bioeconomy: Genomics in the service of biodiversity conservation and sustainable development. Proc. Natl. Acad. Sci. U.S.A., 10.1073/pnas.2115641118 (2021). 22 The Darwin Tree of Life Project Consortium, Sequence locally, think globally: The Darwin Tree of Life Project. Proc. Natl. Acad. Sci. U.S.A., 10.1073/pnas. 2115642118 (2021). 23 W. J. Kress et al., Green plant genomes: What we know in an era of rapidly expanding opportunities. Proc. Natl. Acad. Sci. U.S.A., 10.1073/pnas.2115640118 (2021). 24 H. Cheng, G. T. Concepcion, X. Feng, H. Zhang, H. Li, Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods 18, 170–175 (2021). 25 J. Ghurye et al., Integrating Hi-C links with assembly graphs for chromosome-scale assembly. PLoS Comput. Biol. 15, e1007273 (2019). 26 D. Hobern, BIOSCAN: DNA barcoding to accelerate taxonomy and biogeography for conservation and sustainability. Genome 64, 161–164 (2021). 27 D. Carroll et al., The Global Virome Project. Science 359, 872–874 (2018). 28 T. Stephan et al., Darwinian genomics and diversity in the Tree of Life. Proc. Natl. Acad. Sci. U.S.A., 10.1073/pnas.2115644118 (2021). 29 G. Droege et al., The Global Genome Biodiversity Network (GGBN) data portal. Nucleic Acids Res. 42, D607–D612 (2014). 30 S. B. Kingan et al., A high-quality de novo genome assembly from a single mosquito using PacBio sequencing. Genes (Basel) 10, 62 (2019). 31 K. L. Howe et al., Ensembl 2021. Nucleic Acids Res. 49, D884–D891 (2021). 32 K. H. Miga et al., Telomere-to-telomere assembly of a complete human X chromosome. Nature 585, 79–84 (2020). 33 C. J. Hogg et al., Threatened Species Initiative: Empowering conservation action using genomic resources. Proc. Natl. Acad. Sci. U.S.A., 10.1073/pnas. 2115643118 (2021). Downloaded by guest on January 20, 2022 Lewin et al. PNAS j 7 of 7 The Earth BioGenome Project 2020: Starting the clock https://doi.org/10.1073/pnas.2115635118