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Monday, February 26, 2024

Earth BioGenome Project plans to sequence genome of every known eukaryotic organism

The project’s administrative office is located at the UC Davis Genome Center, and it will seek to sequence the genomes of 1.8 million species over the course of 10 years

By SONORA SLATER — science@theaggie.org

It took 13 years and three billion dollars to sequence the human genome — but over the next 10 years, the Earth BioGenome Project (EBP) plans to sequence the genome of every other known eukaryotic organism on earth for a fraction of the comparative cost.

EBP was launched in November 2018, and is now entering a new phase, as it shifts from “pilot projects” to beginning the full-scale sequencing of the 1.8 million named plants, animals and fungi that make up Earth’s eukaryotes, according to a recent press release. The information will then be made available in the form of an open-access digital library.

The project’s administrative office is located at the UC Davis Genome Center, and Harris Lewin, a distinguished professor in the Department of Evolution and Ecology at UC Davis, acts as the chair of the EBP Working Group. Lewin also co-authored four papers that were included in a 10-part special feature published in Proceedings of the National Academy of Sciences on Jan. 17 that describe the project’s goals, challenges and future plans. 

“This set of papers, the special feature, represents sort of a series of milestones of where we are, or even where we were one year ago when we started putting these papers together,” Lewin said. “It is a representation of the work that includes 43 institutions around the world.” 

The papers include information about why the project matters, ethical, social and legal challenges that the project has faced, how the genome library will contribute to the conservation of endangered species and reflection on how credit will be attributed, according to Lewin.

“There [are] a lot of ethical issues around […] how the benefits accrue,” Lewin said. “Let’s say there’s Indigenous knowledge about the medicinal properties of a plant. […] how would the benefits be shared with those peoples who might have shared the basic information pointing toward the medicinal qualities of the plant?” 

Jacob Sherkow, a professor of law at the University of Illinois, is the lead author of a paper for the special feature that detailed ethical, legal and social issues in the Earth BioGenome Project. He talked about one of the challenges detailed in the paper.

“The library is going to be open-access, and open-access usually means free,” Sherkow said. “But we also have to make sure that we’re compensating countries for their work sequencing genomes. What we’ve learned in the last 20 years is that the value of genetic data is improved the more that it’s shared, […] so even though it’s a very complex and difficult issue, it’s worth solving, and I believe that the EBP will find a solution to allow open-access.”

Carolyn Hogg, the science lead for the Threatened Species Initiative in Australia and the lead author of the EBP paper investigating how genomic resources can empower conservation action, described how the genomic work they’re doing is especially important when it comes to endangered species.

“Some of our animals are technically extinct in the wild, they’re only found in captivity,” Hogg said. “So the value of those samples is exceedingly high. And the sequencing guys have one chance to get it right. If somebody makes a misstep, there’s no other opportunity to get more samples.” 

Katherine Belov, a professor of comparative genomics at the University of Sydney and one of the co-authors of the same paper, elaborated on the value of gaining genomic information on endangered species. 

“In the worst case – the project will provide us with a blueprint of the genetic diversity that existed in species that are now extinct,” Belov said via email. “I hope it won’t come to that. In the best case, we will find ways to use the EBP genomes to better lobby for conservation of species that are at risk of extinction. Having their genome sequence won’t save them – only preservation of habitats will. But genomes provide information [that can] directly inform economically sound management decisions using scarce conservation dollars.”

This kind of translation from information to action is being incorporated into the goals of the EBP, as they build partnerships between academia and those who work in policy and management spaces, according to Belov.

“The critical step that cannot be forgotten is the importance of empowering conservation managers to be able to use this data to manage animals on the ground,” Belov said via email. “Otherwise, the data just sits in the cloud and gathers dust.” 

The benefits of the EBP aren’t only given to those species being sequenced for the first time. There are also direct benefits to humans, as it relates to agriculture, human health, renewable energy technologies in the form of biofuels and more, according to Hogg.

“Genomes are an exceedingly powerful tool,” Hogg said. “If you think about human medicine, we published the human genome back in 2001. Think about the changes in human medicine back in 2001 versus now — we can do targeted cancer therapy, work against Alzheimers.” 

Hogg said that the foundation of most pharmaceuticals — such as Advil — is found in nature, from plants with medicinal qualities or the venom of certain animals, before they’re synthesized and made more active. Additionally, the productivity and the type of food available in supermarkets is also dependent on biodiversity.

“People [need] to understand that losing biodiversity is not just losing the nice stuff in the forests,” Hogg said. “It’s all interrelated. It’s not just a bunch of scientists trying to shoot for the moon.”

Elaborating on the moon analogy, Hogg referenced a photograph called “Earthrise” taken in 1968 by Bill Anders from Apollo 8. 

“It’s been declared as one of the most environmentally significant photos of all time, because it was the first time we saw our planet from space,” Hogg said. “So part of what Harris and the people who set up Earth BioGenome wanted to do is a ‘moonshot.’ This is the next greatest moonshot.” 

Lewin offered some final thoughts on what the impact of this moonshot could be.

“This is going to be the basis of advances in agriculture, in human health, in animal health, in environmental health and how climate change influences biodiversity,” Lewin said. “Having this knowledge is going to give us the fundamental scientific knowledge to make further advances and decisions and develop policies that are going to be effective in dealing with the major problems that are facing the world today.”

EBP has been built on collaboration, with work being done in 22 countries on every continent except Antarctica. Hogg explained how essential she believes this is to the project’s hopeful success. 

“I think the global challenges we face today are unsolvable by any one person, or any one research group, or any one university,” Hogg said. “I think we will only be able to address the challenges that we face as a species and that the planet faces by working collaboratively and cooperatively. So I think that EBP really is a testament to what can be achieved when everyone comes to the table with the same mindset of what is for the greater good.” 

Written by: Sonora Slater — science@theaggie.org

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