Sequencing life on Earth, one eukaryote at a time

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The Human Genome Project, an international and collaborative research effort to sequence the entire human genome, was completed in 2003, two years ahead of schedule. This marked the birth of the “genomic era,” a period in which next-generation sequencing (NGS) technologies would dramatically increase in capacity and speed, while reducing costs.

Nearly 20 years after the completion of the HGP, the impact of the genomic era is visible in today’s society and scientific research. Genomic sequencing has become an integral part of agricultural research, personalized medicine, the study of human history, and more recently, navigating our response to the COVID-19 pandemic.

Fifteen years after the completion of the HGP, scientists have set their sights on a new goal: the Earth BioGenome Project (EBP). Described as a ‘moonshot’ project for biology, it aims to sequence, catalog and characterize the genomes of the 1.8 million named species of plants, animals and fungi – and unicellular eukaryotes – on Earth, in 10 years.

“The idea for EBP was pioneered by me, Professor Gene Robinson and Professor John Kress in 2015,” says Harris Lewin, Robert and Rosabel Osborne Endowed Chair and Emeritus Professor of Evolution and Ecology. at the University of California Davis, in an interview. with Technological networks. “The main motivating factor was that we all encountered obstacles in our research due to the lack of high-quality genomic sequences of eukaryotic species.”

Why is EBP necessary?

The trio held an exploratory meeting at The Smithsonian Institution in 2015, in the presence of some of the most renowned genome scientists in the world and representatives of the main American funding agencies, to study the feasibility of the project.

The meeting concluded that a global initiative, like the EBP, is imperative to preserve biodiversity and sustain human society, and it must happen now. Lewin explains: “Threats to global biodiversity, ecosystems, agriculture and energy supply from climate change, habitat destruction and other anthropogenic factors are now of paramount importance. .

Understanding the biodiversity crisis

The amount of biodiversity on Earth is rapidly decreasing – this is called the biodiversity crisis. Some scientists argue that conserving biodiversity is an even greater challenge than combating climate change.

According to the United Nations, the average abundance of native species in terrestrial habitats has declined by more than 20% since 1900. More than 40% of amphibian species, 33% of reef-forming corals and more than a third of all marine mammals are threatened. . At least 680 species of vertebrates have disappeared since the 16and century, and more than 9% of domesticated breeds of mammals used for food and agriculture were extinct by 2016.

Before the start of the project, only 0.6% of known eukaryotes had sequenced genomes. As such, the basic knowledge and biological infrastructure to solve these global problems is lacking. An easily accessible DNA library for all eukaryotic life would greatly aid conservation efforts around the world, says Lewin: “Conservation genomics is a relatively new discipline that generates and uses genomic information from endangered species and endangered for conservation purposes. Understanding the genomic diversity of remnant populations facilitates the development of species management plans. He notes the California Conservation Genomics Project as an excellent example of such a management plan.

The birth of EBP

Over the next two years, a series of meetings followed the initial discussion at the Smithsonian Institution – including the first International Conference on Biodiversity Genomics in 2017 – and a blueprint for sequencing all eukaryotes was developed. In the summer of 2018, a manifesto for the EBP has been published in the Proceedings of the National Academies of Sciences (PNAS) review. Shortly after, the project was officially launched at the Wellcome Trust in London in the fall.

The manifesto outlines key performance indicators and strict timelines for EBP. “We must lay the foundation for the future by completing this project in 10 years, as we have proposed, before it is too late to safeguard the genomic information of up to 50% of terrestrial biodiversity that could be lost in the current sixth mass extinction. life on earth,” says Lewin.

Key performance indicators and timelines for EBP. Credit: The Earth BioGenome Project.

The manifesto also outlines EBP’s logic for sequencing each species – as opposed to a representative member of each family or genus. EBP leaders argue that sampling a species by genus or family would not provide a realistic assessment of the evolutionary complexity of these groups. “While acknowledging that it may not be possible to obtain samples for every species, pragmatism does not negate the primary scientific and societal need to try to do so,” the manifesto states.

Current progress and future prospects

EBP was officially launched at the Wellcome Trust in London in the fall of 2018. From 2018 to 2020 the project was in a “start-up” phase, during which the focus was on developing standards , strategies, organizing transnational and transnational translation projects and building communities.

“EBP will revolutionize the field of evolution and will have major impacts on agriculture, medicine and environmental science”, – Harris Lewin.

The EBP consists of an international “network of networks” where it forms the central core of other “megaprojects” such as the Darwin’s tree of life. To date, 43 institutions and 49 affiliated projects are working on eukaryotic taxa, and individual scientists are involved in several projects. Harris explains, “We have approximately 5,000 scientists in 100 countries currently involved in EBP activities. This global community is actively engaged in all aspects of the project, from sample collection, genome generation and assembly, and data analysis. He predicts that many of the collaborations born out of the networks will continue well beyond the sequencing of the latest genome.

In January 2022, EBP announced that it had entered a new phase, moving from pilot projects to full-scale production sequencing. The statement was accompanied by a series of articles published in PNAS outlining some of the main achievements of the project to date.

The wealth of data generated will be made freely available, Lewin points out: “To be a member of the EBP, each institution and each project must commit to free and open access to the data and are required to make the raw data and the genome assemblies in public databases, such as GenBank. Members must also commit to respecting the Convention on Biological Diversity, a multilateral treaty with three objectives: the conservation of biological diversity, the sustainable use of its components, and the fair and equitable sharing of the benefits arising from genetic resources.

The objective of the current stage – Phase I – is to create reference genomes for approximately 9,400 taxonomic families, of which 200 have already been produced. It is expected that by the end of 2022, over 3,000 sequences will be completed. Lewin is convinced that advances in EBP over the coming years will “revolutionize” the study of evolution, having “major impacts on agriculture, medicine, and environmental science”, concludes- he.

This article appeared in issue 12 of The Scientific Observer, Technological networks’ monthly. To download your copy of this issue, click the link below.

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