Biology Moonshot, Earth BioGenome Project, Encompasses Earth’s Eukaryotes

Man is not the measure of all things, at least not all thing genomic. Otherwise, we could have sequenced the human genome and called it a day. No, we’re widening our genomic vision so far that we just sequence the DNA of every eukaryotic organism on the planet. It would be a huge undertaking, but well worth the effort, insist the advocates of the Earth BioGenome Project (EBP), a moonshot for biology that would complete its task in 10 years.

To date, the genomes of less than 0.2% of eukaryotic species—that is, all nonbacterial and nonarchaeal species—have been sequenced. That leaves a lot of work for the EBP, an international initiative that proposes to sequence and functionally annotate the genomes of 1.5 million known species of eukaryotes, a massive group that includes plants, animals, fungi, and other organisms whose cells have a nucleus that houses their chromosomal DNA. The EBP also seeks to reveal some of the estimated 10 to 15 million unknown species of eukaryotes, most of which are single-cell organisms, insects, and small animals in the oceans.

Details of the EBP appeared April 23 in the Proceedings of the National Academy of Sciences (PNAS), in an article entitled “Earth BioGenome Project: Sequencing Life for the Future of Life.” The article, which was contributed by 24 interdisciplinary experts, argues that a comprehensive understanding of Earth’s biodiversity would improve humanity’s stewardship of its resources.

“Genomics has helped scientists develop new medicines and new sources of renewable energy, feed a growing population, protect the environment, and support human survival and well-being,” said Gene Robinson, Ph.D., a leader of the proposed effort, a professor of entomology and the director of the Carl R. Woese Institute for Genomic Biology at the University of Illinois. “The Earth BioGenome Project will give us insight into the history and diversity of life and help us better understand how to conserve it.”

In the PNAS article, the EBP’s leaders acknowledged the challenges that would have to be overcome: “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 EBP’s leaders also sounded hopeful, citing how the project would make use of existing resources and institutions whose mission is to procure and preserve the world’s biodiversity. “For example, the world's botanical garden collections hold more than a third of all plant species,” noted Dr. Robinson.”

The authors of the PNAS paper also pointed to the hugely successful precedent of the Human Genome Project. Launched in 1990 and completed in 2003, the U.S. and funding agencies in other countries invested approximately $3 billion to sequence the entire human genome. The resulting “genomic revolution” has had an enormous impact not only on human medicine but also on veterinary medicine, agricultural bioscience, biotechnology, environmental science, renewable energy, forensics, and industrial biotechnology. A 2013 report by the Battelle Memorial Institute estimated the financial benefit of the Human Genome Project to the U.S. economy to be nearly $1 trillion.

The lead author of the paper, Harris A. Lewin, Ph.D., a distinguished professor of evolution and ecology at UC Davis, sees the the EBP as providing even greater opportunities for generating scientific and societal benefits.

“The EBP,” he asserted, “will lay the scientific foundation for a new bioeconomy that has the potential to bring innovative solutions to health, environmental, economic, and social problems to people across the globe, especially in underdeveloped countries that have significant biodiversity assets.”

Advances in technology have made the project feasible. The cost of whole-genome sequencing has declined to about $1000 for a draft-quality sequence of human genome size and about $30,000 for a reference-quality assembly of the chromosomes of an average eukaryotic genome.

With advances in high-performance computing, data storage, and bioinformatics, high-throughput assembly and characterization of genomes is now feasible, although innovations in algorithms for aligning, interpreting, and visualizing the massive amounts of data will be necessary. The completed project is expected to require about one exabyte (one billion gigabytes) of digital storage capacity.