Earth BioGenome Project: Sequencing life for the future of life

Increasing our understanding of Earth’s biodiversity and responsibly stewarding its resources are among the most crucial scientific and social challenges of the new millennium. These challenges require fundamental new knowledge of the organization, evolution, functions, and interactions among millions of the planet’s organisms. Herein, we present a perspective on the Earth BioGenome Project (EBP), a moonshot for biology that aims to sequence, catalog, and characterize the genomes of all of Earth’s eukaryotic biodiversity over a period of 10 years. The outcomes of the EBP will inform a broad range of major issues facing humanity, such as the impact of climate change on biodiversity, the conservation of endangered species and ecosystems, and the preservation and enhancement of ecosystem services. We describe hurdles that the project faces, including data-sharing policies that ensure a permanent, freely available resource for future scientific discovery while respecting access and benefit sharing guidelines of the Nagoya Protocol. We also describe scientific and organizational challenges in executing such an ambitious project, and the structure proposed to achieve the project’s goals. The far-reaching potential benefits of creating an open digital repository of genomic information for life on Earth can be realized only by a coordinated international effort.

[1]  R. Mounce,et al.  Ex situ conservation of plant diversity in the world’s botanic gardens , 2017, Nature Plants.

[2]  Jerome H. Reichman,et al.  The U.S. Culture Collection Network Responding to the Requirements of the Nagoya Protocol on Access and Benefit Sharing , 2017, mBio.

[3]  R. Dirzo,et al.  Biological annihilation via the ongoing sixth mass extinction signaled by vertebrate population losses and declines , 2017, Proceedings of the National Academy of Sciences.

[4]  H. Lewin,et al.  Reconstruction and evolutionary history of eutherian chromosomes , 2017, Proceedings of the National Academy of Sciences.

[5]  Sean P. Jungbluth,et al.  Opinion: Telepresence is a potentially transformative tool for field science , 2017, Proceedings of the National Academy of Sciences.

[6]  Brett R. Scheffers,et al.  Biodiversity redistribution under climate change: Impacts on ecosystems and human well-being , 2017, Science.

[7]  A. Rokas,et al.  Contentious relationships in phylogenomic studies can be driven by a handful of genes , 2017, Nature Ecology &Evolution.

[8]  E. Pennisi Sequencing all life captivates biologists. , 2017, Science.

[9]  Sònia Casillas,et al.  Molecular Population Genetics , 2017, Genetics.

[10]  Xin Zhou,et al.  The Global Genome Biodiversity Network (GGBN) Data Standard specification , 2016, Database J. Biol. Databases Curation.

[11]  Juan Carlos Castilla-Rubio,et al.  Land-use and climate change risks in the Amazon and the need of a novel sustainable development paradigm , 2016, Proceedings of the National Academy of Sciences.

[12]  Tatiana Saksina The International Union for Conservation of Nature's (IUCN) 2016 Observer Review report , 2016 .

[13]  Morgan R. Gostel,et al.  Global Genome Biodiversity Network: saving a blueprint of the Tree of Life – a botanical perspective , 2016, Annals of botany.

[14]  Aaron Bouchie,et al.  White House unveils National Microbiome Initiative , 2016, Nature Biotechnology.

[15]  Robert Carlson Estimating the biotech sector's contribution to the US economy , 2016, Nature Biotechnology.

[16]  E. Jarvis Perspectives from the Avian Phylogenomics Project: Questions that Can Be Answered with Sequencing All Genomes of a Vertebrate Class. , 2016, Annual review of animal biosciences.

[17]  S. Richards,et al.  It's more than stamp collecting: how genome sequencing can unify biological research. , 2015, Trends in genetics : TIG.

[18]  M. Schatz,et al.  Big Data: Astronomical or Genomical? , 2015, PLoS biology.

[19]  N. Stork,et al.  New approaches narrow global species estimates for beetles, insects, and terrestrial arthropods , 2015, Proceedings of the National Academy of Sciences.

[20]  S. O’Brien,et al.  The Genome 10K Project: a way forward. , 2015, Annual review of animal biosciences.

[21]  Sudhir Kumar,et al.  Tree of Life Reveals Clock-Like Speciation and Diversification , 2014, Molecular biology and evolution.

[22]  J. G. Burleigh,et al.  Synthesis of phylogeny and taxonomy into a comprehensive tree of life , 2014, Proceedings of the National Academy of Sciences.

[23]  R. Knight,et al.  The Earth Microbiome project: successes and aspirations , 2014, BMC Biology.

[24]  Fabien Burki The eukaryotic tree of life from a global phylogenomic perspective. , 2014, Cold Spring Harbor perspectives in biology.

[25]  Tanja Woyke,et al.  Obtaining genomes from uncultivated environmental microorganisms using FACS–based single-cell genomics , 2014, Nature Protocols.

[26]  Éamonn Ó Tuama,et al.  The Global Genome Biodiversity Network (GGBN) Data Portal , 2013, Nucleic Acids Res..

[27]  Susan J. Brown,et al.  The i5K Initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment. , 2013, The Journal of heredity.

[28]  Natalia N. Ivanova,et al.  Insights into the phylogeny and coding potential of microbial dark matter , 2013, Nature.

[29]  Indra Neil Sarkar,et al.  Research and applications: Leveraging biodiversity knowledge for potential phyto-therapeutic applications , 2013, J. Am. Medical Informatics Assoc..

[30]  Meredith Wadman,et al.  Economic return from Human Genome Project grows , 2013, Nature.

[31]  David Haussler,et al.  A unifying model of genome evolution under parsimony , 2013, BMC Bioinformatics.

[32]  O. Ryder,et al.  Conservation genomics of threatened animal species. , 2013, Annual review of animal biosciences.

[33]  Loretta Auvil,et al.  Reference-assisted chromosome assembly , 2013, Proceedings of the National Academy of Sciences.

[34]  J. Dudley,et al.  Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations. , 2011, Trends in genetics : TIG.

[35]  L. Redd,et al.  International Union for Conservation of Nature , 2010, Permanent Missions to the United Nations, No. 309.

[36]  S. O’Brien,et al.  Every genome sequence needs a good map. , 2009, Genome research.

[37]  Jay D Keasling,et al.  Induction of multiple pleiotropic drug resistance genes in yeast engineered to produce an increased level of anti-malarial drug precursor, artemisinic acid , 2008, BMC biotechnology.

[38]  Laureana Rebordinos,et al.  Genome-wide amplifications caused by chromosomal rearrangements play a major role in the adaptive evolution of natural yeast. , 2003, Genetics.

[39]  M. Bailey Mainstreaming agrobiodiversity in sustainable food systems: Scientific foundations for an agrobiodiversity index - Summary , 2016 .

[40]  Jose V. Lopez,et al.  The Global Invertebrate Genomics Alliance (GIGA): Developing community resources to study diverse invertebrate genomes , 2014 .

[41]  S. Pomponi,et al.  The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes. , 2013, The Journal of heredity.

[42]  David L. Erickson,et al.  DNA barcodes: methods and protocols. , 2012, Methods in molecular biology.

[43]  Paul Medvedev,et al.  Genome Graphs , 2010 .

[44]  E. Wilson,et al.  The Diversity of Life , 1993, Politics and the Life Sciences.