Project aims to sequence all known species on Earth

To engage the Brazilian scientific community in this major challenge, the founder of the Earth BioGenome Project participated in a Biodiversity & Biobank Workshop held at FAPESP.

By Karina Toledo  |  Agência FAPESP – Sequencing the DNA of all known species on Earth in a period of ten years, from microorganisms invisible to the naked eye to the most complex vertebrates and plants, is the ambitious goal of the Earth BioGenome Project (EBP), an international initiative set to be officially launched in 2018.

With the aim of engaging the Brazilian scientific community in the project, in August 2017, FAPESP and the Brazilian Academy of Sciences (ABC) held a Biodiversity and Biobank Workshop, which was attended by Harris Lewin, a US citizen and one of the EBP’s founders.

“There are 1.5 million species on the planet that have been identified and characterized. But that number represents only 10% of Earth’s total biodiversity, so 90% have yet to be discovered,” said Lewin, who is Professor of Evolution & Ecology at the University of California, Davis.

In Lewin’s opinion, Brazil has an opportunity to make a major contribution to the project because it is home to about 10% of the planet’s biodiversity. Moreover, it has a good scientific infrastructure, a global collaboration network and well-curated biological collections.

“It’s a crucial initiative because many species are disappearing at a very rapid rate,” he said. “In the last 40 years, the vertebrate population has decreased by 42%, and 20,000 species are on the endangered species list. Owing to human activities, the destruction of habitats and the effects of global climate change, the rate of species extinction is 1,000-fold greater than it was a decade ago.”

According to Lewin, with the growing human population, which is set to reach 9 billion by 2050, and the accelerating rate of climate change, “we could find ourselves in a very dangerous and unfortunate situation”.

“Some people have spoken of the sixth mass extinction on this planet. This is a threat not only to these species but to our own survival on Earth,” he said.

By documenting the genetic code for all species before they may disappear, the members of the Earth BioGenome Project plan to create a digital repository of life. This undertaking, in Lewin’s view, will revolutionize biology.

“Such a repository will radically improve our efforts to conserve species and restore degraded habitats,” he said.

So far, around half a dozen countries have joined the project, including the US, France, the UK, Germany and China. Tens of others have signed letters of intent. 

“Participation is voluntary, and the EBP’s role is to establish standards for sample collection, DNA sequencing, the type of information that will accompany samples, and data storage,” Lewin said. “We’ll also pursue the best way to communicate these actions to the general public so that everyone can understand their importance and collaborate. There are 1.5 million known species on the planet, but there aren’t 1.5 million scientists, so society must also be engaged.”

International community of biobanks

Jonathan Coddington, a research scientist at the Smithsonian Institution, which also helped organize the workshop, attended the event representing the Global Genome Biodiversity Network (GGBN), another ambitious international initiative that seeks Brazilian participation.

The GGBN initiative is a global network of biorepositories and biobanks, which are collections of frozen tissues or genetic material (DNA and RNA) from any species in the world, except Homo sapiens sapiens. The initiative began in 2011 and currently comprises 66 participating institutions in 22 countries.

“The purpose of creating this community is so that we can reason globally and set priorities for genome sequencing, conservation of species, environmental monitoring and basic taxonomic studies. For example, of the 11,000 genera that occur in Brazil, which ones is there no genetic information about? We’ll be able to answer questions like that and point to the experts,” Coddington told Agência FAPESP.

Following the advances made possible by the Human Genome Project, he added, the scientific community has used genetic sequencing to answer all kinds of questions that are relevant to human welfare, in areas such as guaranteeing food security, producing energy or finding cures for diseases.

“To be able to do this, we need collections of tissues and DNA that are well preserved, standardized, and representative of global biodiversity. Living beings are divided into about 10,000 families, and 40% of these families occur in Brazil. So, Brazil has unique resources with which to contribute to this initiative. We’ve come here to discuss how it can participate internationally,” Coddington said.

“We’re not talking about exporting genetic resources from Brazil,” he stressed. The idea is for Brazil to set up sequencing centers and biorepositories of its own, to produce Brazilian data. Only information from digitized sequences will be shared internationally.

“The Earth BioGenome Project and the Global Genome Biodiversity Network are complementary initiatives. The EBP is largely made up of experts in genome sequencing, not experts at going out into the forests, rivers and oceans to collect organisms. The GGBN will provide the organization to assemble samples, establish best practices, and ensure access and sharing of benefits and databases,” Coddington said.

Frozen zoo

The conditions established by the Brazilian legislation governing biodiversity data sharing were discussed at the workshop by Manuela da Silva, a researcher at Oswaldo Cruz Foundation (FIOCRUZ) in Rio de Janeiro. One of the problems, she said, is the requirement that data deposited in international data banks be traceable, which experts say is hard to implement.

Oliver Ryder, Director of Genetics at the San Diego Zoo Institute for Conservation Research in the US, presented the Frozen Zoo, a biorepository set up at his institution to store samples of tissue, skin cells and DNA from more than 1,000 animal species.

He said cryopreserved cells are a resource that permits expansion of genetic material in culture, where necessary, as well as sequencing on different platforms, functional studies (in areas such as cell signaling and investigation of disease mechanisms), production of induced pluripotent stem cells, and ultimately genetic rescue of endangered or nearly extinct species.

Other speakers at the event included Eduardo Eizirik (Pontifical Catholic University of Rio Grande do Sul), Luciano Verdade (University of São Paulo and BIOTA-FAPESP Program), Vanderlei Canhos (Environmental Information Reference Center, CRIA), Ana Tereza Vasconcelos (Bioinformatics Lab at the National Scientific Computing Laboratory, LABINFO/LNCC/MCTIC), Isabel Rodrigues Gerhardt (EMBRAPA), and Katherine Barney Barker (GGBN).

In the audience were curators of several Brazilian biological collections, who on the day after the workshop met with the representatives of the EBP and GGBN to discuss requirements for and obstacles to Brazilian participation in these initiatives. Based on this discussion, a document will be produced describing the current situation and the prospects for making Brazil a node of the global project, acknowledged to be one of the planet’s most daunting challenges.

 “This is an opportunity, in these difficult times we live in, to show that science is really important to make Brazil a sustainable country,” said Marie-Anne Van Sluys, a member of FAPESP’s Life Sciences Committee and organizer of the workshop.