New project aims to sequence all known eukaryotic species

The Earth BioGenome Project, launched in November 2018, is an ambitious undertaking with the goal of sequencing all the existing, named eukaryotes—about 2 million species of fungi, plants, and animals—in a 10-year timeframe. The project was highlighted in “The Earth BioGenome Project: The Launch of a Moonshot for Biology Special Feature” in the Proceedings of the National Academy of Sciences. It includes a collection of papers covering a range of issues such as international law, intellectual property, biosecurity and biosafety concerns, the rights of Indigenous Peoples and Local Communities, and animal welfare and data rights. Together, the articles describe the progress, major goals, and applications of the EBP.

All life evolved from bacteria and archaea, which have a “simpler” cellular makeup compared to the complexity exhibited by eukaryotes. Although the diverse metabolic capabilities of these microbes are well known, there is much to learn about eukaryotic genomes.

Historically, genome sequencing has been a laborious process, requiring years of human effort. The development of new high-quality techniques has now made it possible to sequence genomes in a timely fashion. Since sequencing 2 million species is no small matter, there are several smaller projects that are looking at different subsets: The Vertebrate Genomes Project aims to sequence all 70,000 vertebrate species, the Darwin Tree of Life project will sequence all 70,000 species in Britain and Ireland, and other projects will focus on species that are important for conservation.   

EBP has three proposed phases. In Phase 1 the research groups aim to have a reference genome for one representative species of each family of eukaryotes (about 9,400 species) in three years. Phase 2 aims to sequence reference genomes for one representative species of each genus (about 180,000 species) in the next three years. Finally, Phase 3 includes having reference genomes for the remaining 1.5-2 million known eukaryotic species.

In the past two years of the start-up phase, there have been 43 EBP-affiliated projects that have included high-quality samples from 21 countries across all continents except Antarctica. So far, they have sequenced 1,719 species and are well on their way to meet their Phase 1 goal. The project will also continue to expand the number of institutions and projects to biodiverse regions, including the Indian subcontinent, Southeast Asia, and South America.

“We are very pleased with the progress being made by the EBP, especially at the international level, and anticipate explosive growth in the next couple of years,” said Gene Robinson (GNDP), IGB Director.

EBP’s goal of sequencing so many species also raises a number of international and national legal challenges, according to Jacob Sherkow (GSP), a professor of law and lead author of one of the papers in the Special Feature. Some are related to proper sample collection, where the researchers will have to collect them in one country’s jurisdiction and sequence them in another, or if the collected species presents issues to national biosecurity. Other more complex issues include ensuring a fair distribution of the benefits that will arise from using these genetic resources, intellectual property rights, using resources from the land of native peoples, and focusing equally on all the vulnerable species instead of just those that command the most public attention.

Nevertheless, sequencing the genomes of all eukaryotic species will transform our understating of the world we live in. To date, researchers have largely focused on human genome sequencing, which though very important for human health, fails to look at the interconnectedness of life on Earth. For example, SARS-Cov-2 evolved from a bat coronavirus that found its way into the human population and, concerningly, the infection can spread to other wildlife, pets, and captive animals. Creating a library of DNA sequences for all eukaryotic life can give us data that can help predict and possibly prevent such pathogen spreads.

There are several other fundamental questions we can answer including how the eukaryotic tree of life is arranged, how eukaryotes evolved, and what are all the eukaryotic genes. Most importantly, the efforts of EBP will go a long way in understanding the Earth’s biodiversity. Every species is the result of millions of years of evolution, with important information etched in their genomes. Sequencing and analyzing their genomes can potentially lead to new knowledge that can be used to alleviate the effects of climate change on biodiversity; improve agriculture; grow a sustainable global bioeconomy, where biological resources are used to provide products; and repair ecosystems by saving species.