The largest set of mammalian genomes reveals endangered species

The Zoonomia project released this vast dataset to advance both biomedical research and biodiversity conservation.
An international team of researchers with an effort called the Zoonomia Project analyzed and compared the entire genome of more than 80% of all mammalian families, spanning nearly 110 million years of evolution. The genomic dataset, published today (11 November 2020) in Nature, includes genomes from over 120 species that had not previously been sequenced and captures mammalian diversity on an unprecedented scale.

The dataset is intended to advance human health research. Researchers can use the data to compare the genomes of humans and other mammals, which could help identify genomic regions that could be involved in human disease. The authors are also making the dataset available to the scientific community through the website of the Zoonomy Project, without any restrictions on use.

“The central idea of ​​the project was to develop and use this data to help human geneticists understand which mutations cause disease,” said co-senior author Kerstin Lindblad-Toh, scientific director of vertebrate genomics at Broad and professor of comparative genomics at the University of Uppsala.

However, when analyzing the new genomes, the authors also found that mammalian species with high extinction rates have less genetic diversity. The findings suggest that sequencing even a single individual could provide crucial information, in a cost-effective way, about which populations could be at greatest risk of extinction and should be prioritized for a thorough assessment of conservation needs.

“We wrote the paper to talk about this large and unique dataset and explain why it is interesting. Once you make the data widely available and explain its usefulness to the wider research community, you can really change the way science is done, “said co-senior author Elinor Karlsson, director of the Vertebrate Genomics Group. at the Broad Institute of WITH and Harvard and a professor at the University of Massachusetts Medical School.
Zoonomia data have already helped researchers in a recent study assess the risk of infection with SARS-CoV-2 in many species. The researchers identified 47 mammals that have a high probability of being reservoirs or intermediate hosts for the SARS-CoV-2 virus.

Mammalian mapping

The Zoonomia project, formerly called the 200 Mammals Project, builds on an earlier project, the 29 Mammals Project, which began sequencing mammalian genomes in 2006. The latest project extends the work by exploring the genomes of species capable of performing physiological feats that humans can From hibernating squirrels to exceptionally long-lived bats. The project also included genomes of endangered species.

In the new study, the researchers collaborated with 28 different institutions around the world to collect samples for genomic analysis, with the San Diego Global Zoo frozen zoo providing nearly half of the samples. The team focused on species of medical, biological and biodiversity conservation interest and increased the percentage of mammalian families with a representative genome from 49 to 82.

The project has also developed and is sharing tools that will allow researchers to examine every ‘letter’ or base in a mammalian genome sequence and compare it to sequences at equivalent locations in the human genome, including regions that may be involved in the disease. This could help researchers identify genetic sites that have remained the same and functional over evolutionary time and those that have randomly mutated. If a site has been stable among mammals for millions of years, it likely has an important function, so any changes at that site could potentially be disease-related.

In releasing the data, the authors call on the scientific community to support researchers in the field in collecting samples, increasing access to computational resources that enable the analysis of huge genomic datasets, and sharing genomic data quickly and openly.

“One of the most exciting things about the Zoonomy Project is that many of our core questions are accessible to people both inside and outside of science,” said lead author Diane Genomeux, a researcher with the Vertebrate Genomics Group at Broad. “By designing science projects that are accessible to all, we can ensure benefits for public, human and environmental health.”

Reference: “A comparative genomics multitool for scientific discovery and conservation” by Zoonomia Consortium, 11 November 2020, Nature.
DOI: 10.1038 / s41586-020-2876-6

The project was funded in part by the NHGRI, the Swedish Research Council, the Knut and Alice Wallenberg Foundation, Broadnext10 and others.