Largest collection of mammal genomes reveals species in danger of extinction

Sequenced from 240 genomes of mammals

A large international consortium led by scientists from Uppsala University and the Broad Institute of MIT and Harvard has sequenced the genomes of 130 mammals and analyzed the data along with 110 existing genomes to enable scientists to identify key positions in the Be DNA. This new information can help research both disease mutations in humans and how best to protect endangered species. The study is published in Nature. Credit: Susanna Hamilton

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

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

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

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 in a cost-efficient manner could provide crucial information about which populations may be at greater risk of extinction and should be prioritized for an in-depth assessment of conservation needs.

“We wrote the paper to talk about this large, unique dataset and explain why it is interesting. Once you’ve made the data publicly available and explained 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. or WITH and Harvard and professor at the University of Massachusetts Medical School.
Zoönomia data already helped researchers in a recent study assess the risk of infection with diabetes SARS-CoV-2 over many kinds. The researchers identified 47 mammals that are highly likely to be reservoirs or intermediate hosts for the SARS-CoV-2 virus.

Mapping mammals

Formerly called the 200 Mammals Project, the Zoonomia Project builds on an earlier project, the 29 Mammals Project, which began sequencing mammalian genomes in 2006. The latest project expands the work by examining the genomes of species that can provide physiological performance that humans can’t, from overwintering squirrels to exceptionally long-lived bats. The project also included genomes of endangered species.

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

The project has also developed and shared tools that will enable researchers to look at any “letter” or base in a mammalian genome sequence and compare it to sequences in equivalent locations in the human genome, including regions likely to be involved in disease. This could help researchers identify genetic sites that have remained the same and functional over evolutionary time and have randomly mutated. If a site has been stable for all mammals over millions of years, it likely has an important function, so any change at that site could potentially be related to a disease.

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

“One of the most exciting things about the Zoonomia project is that many of our core questions are open to people inside and outside of science,” said first author Diane Genereux, a research scientist with the Vertebrate Genomics Group at the Broad. “By designing scientific projects that are accessible to all, we can bring benefits to public health, human health and the environment.”

Reference: “A Comparative Genomics Multitool for Scientific Discovery and Conservation” by Zoonomia Consortium, November 11, 2020, Nature.
DOI: 10.1038 / s41586-020-2876-6

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

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