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The Zoonomia Project: Investigating 240 Mammalian Genomes




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  • The Zoonomia Project: Investigating 240 Mammalian Genomes

    An international collaboration including more than 50 different institutions investigated the genomes of 240 mammals. The efforts were part of the Zoonomia Project, which was created to identify genomic segments that have remained unchanged over millions of years across a wide range of animals. The researchers leading the study are hopeful that understanding these unchanged segments will allow for the advancement of human medicine and support conservation efforts.

    This week, a collection of articles from the Zoonomia Project were released in a special edition of Science. Each one demonstrates how analyzing these different genomes can help understand mammalian evolution, diversity, and human health.

    Results from this project have led to the largest comparative mammalian genomics resource to date. “One of the biggest problems in genomics is that humans have a really big genome and we don’t know what all of it does,” said Elinor Karlsson, one of the study’s leaders and Director of the Vertebrate Genomics group at the Broad Institute of MIT and Harvard and a professor at the UMass Chan Medical School. “This package of papers really shows the range of what you can do with this kind of data, and how much we can learn from studying the genomes of other mammals.”

    In each of the studies, the scientists were able to identify conserved regions of the genomes and in some cases, single bases that remain unchanged despite millions of years of evolution. This work also elucidated the genetic basis for specific traits like the ability to detect distant scents and the ability to hibernate.

    Additionally, the researchers were able to identify variants likely to have a role in human disease and detect species more susceptible to extinction. The project was supported through DNA samples donated by various institutions, such as the San Diego Wildlife Alliance, which provided samples for threatened and endangered species.

    Conserved regions
    One of the studies highlighted in the release showed that at least 10 percent of the human genome is highly conserved across various species, including many regions that occur outside of the usual protein-coding genes. The researchers found that more than 4,500 elements are highly conserved across more than 98 percent of the studied species.

    Most of those conserved regions are involved with important processes like embryonic development and regulation of RNA expression, and their changes have been slower over time than the expected random variations in the genome. The regions found to change more often were those associated with the mammal’s environmental interactions, like those responsible for immune responses and skin development.
    The study also focused on preserving biodiversity, during which the researchers observed that mammals with fewer changes at conserved regions in the genome were actually at greater risk for extinction. Authors from the study have explained the need for available reference genomes for each species to help identify more at-risk animals, as currently, less than 5 percent of all mammalian species have reference genomes.

    Human disease
    Another study from the package investigated the different mammalian genomes to better understand human disease. Focusing on highly conserved genomic regions discussed in the first publication, the researchers compared these regions to previously identified genetic variants linked to disease. The comparison showed that the genome annotations built based on evolutionary conservation exposed more links between genetic variants and their function than previously utilized methods. Furthermore, the group identified mutations likely to cause different types of disease, highlighting the possibility of identifying disease-related mutations by investigating genetic conservation.

    Additional highlights
    Some of the other publications included in the release:
    • Examined over 10,000 genetic deletions in humans and linked several to neuron functions
    • Discovered that mammals diversified prior to the mass dinosaur extinction
    • Used genetics to explain why the famous sled dog Balto could survive Alaska’s brutal conditions
    • Uncovered changes specific to human genome organization
    • Applied machine learning techniques to find genomic regions associated with brain size
    • Showed the evolution of regulatory sequences within the human genome
    • Investigated transposable elements
    • Determined that species with small population sizes are generally at higher risk of extinction
    • Evaluated genes from almost 500 species of mammals
    Many of the project’s researchers, like Kerstin Lindblad-Toh, Scientific Director of Vertebrate Genomics at the Broad and a professor at Uppsala University, are optimistic about what will come from these results.
    “We’re very enthusiastic about sequencing mammalian species,” said Lindblad-Toh. “And we’re excited to see how we and other researchers can work with this data in new ways to understand both genome evolution and human disease.”

    For more information, read the publications released in this week’s edition of Science.

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