Earth BioGenome Project: Sequencing life for the future of life

Abstract

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.

Keywords: access and benefit sharing; biodiversity; data science; genome sequencing; genomics.

Fig. 1.

Current status of the sequencing of life. Open Tree of Life (opentreeoflife.org) synthesis of phylogeny for all of life with resolution to the genus level, and showing phylogenetic information for Archaea (red), Bacteria (purple), Fungi (orange), Plantae (blue), Protista (brown), and Animalia (green). The current state of genomic information available from NCBI’s GenBank is shown in the inner circle, with complete genomes colored in red, chromosome level in blue, scaffolds in dark gray, and contigs in light gray. The second circle shows the transcriptomes available from the NCBI Transcriptome Shotgun Assembly Sequence Database (https://www.ncbi.nlm.nih.gov/genbank/tsa/). Genome size as C value is displayed in bars around the outer circle. Data for animals were extracted from the Animal Genome Size Database (www.genomesize.com/), data for plants were extracted from the Royal Botanic Gardens, Kew (data.kew.org/cvalues/), and data for fungi were extracted from the Fungal Genome Size Database (www.zbi.ee/fungal-genomesize/).

Fig. 2.

Proposed roadmap for the EBP.

Fig. 3.

The EBP organizational model. The schematic shows the main features of the proposed organizational model for the EBP as a global network of communities. The outer ring shows a global network of interacting nodes involved in DNA sequencing and informatics. The geographical locations are representative and are not intended to be completely inclusive of all participating countries or political entities. The communities in the inner ring are also representative and are not intended to be inclusive of all taxon-related communities and organizations that are supporting the goals of the EBP. The EBP Coordinating Council will have representation from all participating nodes, communities, and organizations as well as representation from the public and private sectors. 1KP, Initiative to Sequence 1000 Plant Genomes; GGI, Global Genome Initiative.