Revealing the genome organization of the first common ancestor of all mammals

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From the platypus to the blue whale, all mammals alive today are descendants of a single ancestor that existed approximately 180 million years ago. However, less is known about this animal.

Now, an international team has computer-reconstructed the organization of its genome. The reconstructed ancestral genome could help understand the evolution of mammals and the conservation of modern animals. The reconstructed ancestral genome could help understand the evolution of mammals and the conservation of modern animals.

The first mammalian ancestor probably resembled the fossil animal “Morganucodon”, which lived about 200 million years ago.

Harris Lewin, Distinguished Professor of Evolution and Ecology at the University of California, Davis, said: “Our findings have important implications for understanding mammalian evolution and conservation efforts.”

The scientists relied on high-quality genomic sequences from 32 living species representing 23 of the 26 known orders of mammals. They included chimpanzees, humans, wombats, domestic cattle, rhinos, bats, pangolins and manatees. The genomes of chicken and Chinese alligators were also analyzed as comparison samples. The Earth BioGenome Project and other biodiversity genome sequencing initiatives are producing some of these genomes. The Earth BioGenome Project Working Group is chaired by Lewin.

Joana Damas, the study‘s first author and postdoctoral researcher at the UC Davis Genome Center, said: “The reconstruction shows that the mammalian ancestor had 19 autosomal chromosomes, which control the inheritance of characteristics of an organism apart from those controlled by sex-linked chromosomes (these are paired in most cells, either 38 in total) plus two sex chromosomes. The team identified 1,215 gene blocks that consistently appear on the same chromosome in the same order in all 32 genomes. These building blocks of all mammalian genomes contain genes essential to the development of a normal embryo.

Scientists have found nine whole chromosomes or chromosome fragments in the mammalian ancestor whose genetic arrangement is similar to the chromosomes of modern birds.

Levin said, “This remarkable finding shows the evolutionary stability of the order and orientation of genes on chromosomes over an extended evolutionary period of more than 320 million years. In contrast, the regions between these conserved blocks contained more repetitive sequences and were more prone to sequence breaks, rearrangements and duplications, which are the main drivers of genome evolution.

Professor William Murphy, Texas A&M University, who was not one of the paper’s authors, said: “Ancestral genome reconstructions are essential for interpreting where and why selective pressures vary across genomes. This study establishes a clear relationship between chromatin architecture, gene regulation and bond conservation. This provides the basis for assessing the role of natural selection in the evolution of chromosomes through the mammalian tree of life.

Scientists could track ancestral chromosomes back in time from the common ancestor. Scientists, over time, could trace ancestral chromosomes from the same ancestor. They found that there were variations in the rates of chromosomal rearrangement between mammalian lineages. For example, when an asteroid impact 66 million years ago wiped out the dinosaurs and gave rise to mammals, the process of rearrangement in the ruminant lineage – which gave rise to contemporary cattle, sheep and deer – accelerated.

Co-author Dr Camilla Mazzoni said: “The results will help understand the genetics behind the adaptations that allowed mammals to thrive on a changing planet over the past 180 million years.”

Journal reference:

  1. Damas J, Corbo M, Kim J, et al. Evolution of ancestral mammalian karyotype and syntenic regions. PNAS 119, e2209139119. DOI: 10.1073/pnas.2209139119
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