One Eukaryote at a Time, Sequencing Life on Earth

One Eukaryote at a Time, Sequencing Life on Earth ...

The Human Genome Project, a worldwide and collaborative research effort to sequence the entire human genome, was completed in 2003, two years ahead of schedule. It marked the birth of the genomic era, a time in which next-generation sequencing technologies (NGS) would drastically increase in capability and speed, while reducing in cost.

The impact of the genomic era is now visible across modern-day society and scientific research. Genomic sequencing is now an integral part of agricultural research, personalized medicine, studying the history of humanity, and most recently in helping us navigate our response to the COVID-19 epidemic.

In ten years, scientists decided to pursue a new goal: The Earth BioGenome Project (EBP) a moonshot experiment for biology. It is aimed at assembling, cataloging, and characterizing the genomes of the 1.8 million previously identified species of plants, animals, and fungi and single-celled eukaryotes on Earth.

Why is the EBP necessary?

In 2015, the trio had an exploratory meeting at The Smithsonian Institution, attended by some of the world''s most famous genome scientists and representatives from major US funding agencies, to examine the feasibility of projects.

The meeting concluded that a global effort, like the EBP, is essential for protecting biodiversity and protecting human society, and it must happen now. Lewin warns: Climate change, habitat destruction, and other anthropogenic factors have all led to significant threats.

Understanding the biodiversity crisis

The amount of biodiversity on Earth is rapidly declining, which is now known as the biodiversity crisis. Several scientists argue that conserving biodiversity poses an even greater challenge than combating climate change.

According to the United Nations, the average abundance of native species in land-based habitats has decreased by >20% since 1900. Over 40% of amphibian species, 33% of reef-forming corals, and over one third of all marine mammals are at danger. At least 680 vertebrate species have gone extinct since the 16th century, and over 9% of domesticated breeds of mammals were extinct by 2016.

Prior to the start of the projects, only 0.6% of known eukaryotes had sequenced genomes. Consequently, basic knowledge and biological infrastructure to address these global challenges is lacking. Conservation genomics is a relatively new discipline that allows for and utilizes genomic information from endangered and endangered species to make conservation decisions. The California Conservation Genomics Project is a key example of such a management strategy.

The birth of the EBP

Following the first discussion at The Smithsonian Institution in 2017 and a plan for sequencing all eukaryotes was developed. A manifesto for the EBP was published in the Proceedings of the National Academies of Sciences (NAP) journal in the summer of 2018. Shortly after, the project was officially launched at the Wellcome Trust in London in the fall.

The manifesto outlines key performance indicators and timeframes for the EBP. Lastly, we must execute this project in ten years, as we have proposed, before it is too late to save genomic information for up to 50% of earth''s biodiversity that might be lost during the ongoing sixth mass extinction of life on Earth.

The EBP''s key performance indicators and time frames. Credit: The Earth BioGenome Project.

The manifesto explains the EBP''s logic for sequencing every species instead of a representative member of each family or genus. The leadership behind the EBP argue that sampling one species per genus or family would not provide a realistic assessment of the evolutionary complexity of such groups. However, pragmatism does not negate the primary scientific and societal need for doing so.

Current progress and future perspectives

In the fall of 2018, the EBP was officially launched at the Wellcome Trust in London, whereby the project was in a startup phase, whereby focus was placed on developing standards, strategies, organizing cross-regional and national translational initiatives, and forming communities.

The EBP consists of a multi-billion-dollar network, which includes an entire network of networks which acts as the predominant foundation for other Darwin Tree of Life projects. To date, 43 institutions and 49 affiliated projects have completed the eukaryotic taxa, and individual scientists are participating in multiple projects. Harris explains that many of the networks that have originated will continue beyond the sequencing of the previous genome.

The EBP announced in January 2022 that it had entered a different phase, transitioning from pilot projects to full-scale production sequencing. The statement was accompanied by a series of papers published in PNAS that highlight some of the previously significant initiatives.

Why not sequence all eukaryotes?

The Earth BioGenome Project''s Standards Project is being developed as a result of the Earth BioGenome Project''s Standards.

What we know in an era of rapidly expanding possibilities in green plant genomes

Genomics in the service of biodiversity conservation and sustainable development, according to EBP-Colombia and the bioeconomy.

The Darwin Tree of Life Project focuses on seminating locality and thinking globally.

Lewin emphasises that each institution and project must ensure the data''s free and open access, as well as that the raw data and genome assemblies must be put into public databases, such as GenBank. Members must also commit to complying with the Convention on Biodiversity, a multilateral treaty with three objectives: conservation of biological diversity, sustainable use of its components, and the equitable and equitable sharing of benefits.

The aim of the current phase I is to make reference genomes for 9,400 taxonomic families, of which 200 have already been created. It is anticipated that by the end of 2022, over 3,000 sequences will be complete. Lewin is optimistic that progress over the years ahead of the EBPs will revolutionize the study of evolution, which has major implications on agriculture, medicine, and environmental sciences.

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