The Diverse Evolutionary Histories of Domesticated Metaviral Capsid Genes in Mammals

The Diverse Evolutionary Histories of Domesticated Metaviral Capsid Genes in Mammals

March 20, 2024 | William S. Henriques, Janet M. Young, Artem Nemudryi, Anna Nemudraia, Blake Wiedenheft, and Harmit S. Malik
The study by Henriques et al. investigates the evolutionary trajectories and functional potential of capsid (CA) genes derived from *Metaviridae*, a lineage of retrovirus-like retrotransposons, in mammals. Using a complete human genome assembly and additional vertebrate genomes, the authors re-analyze the domestication events of these genes, finding at least five independent domestication events from diverse *Metaviridae* lineages. These events have led to three universally retained single-copy genes under purifying selection and two gene families unique to placental mammals, with evidence of rapid evolution in some members. The study reveals diverse amino-terminal domains in the SIRH/RTL family, widespread loss of protein-coding capacity in RTL10, and differential utilization of an ancient programmed ribosomal frameshift in RTL3. Additionally, most members of the PNMA family encode a conserved putative RNA-binding domain, which is also present in some *Metaviridae*. The findings correct previous annotations of the essential CDC8 gene and highlight the divergent outcomes of multiple domestication events from diverse *Metaviridae* in the common ancestor of placental mammals.The study by Henriques et al. investigates the evolutionary trajectories and functional potential of capsid (CA) genes derived from *Metaviridae*, a lineage of retrovirus-like retrotransposons, in mammals. Using a complete human genome assembly and additional vertebrate genomes, the authors re-analyze the domestication events of these genes, finding at least five independent domestication events from diverse *Metaviridae* lineages. These events have led to three universally retained single-copy genes under purifying selection and two gene families unique to placental mammals, with evidence of rapid evolution in some members. The study reveals diverse amino-terminal domains in the SIRH/RTL family, widespread loss of protein-coding capacity in RTL10, and differential utilization of an ancient programmed ribosomal frameshift in RTL3. Additionally, most members of the PNMA family encode a conserved putative RNA-binding domain, which is also present in some *Metaviridae*. The findings correct previous annotations of the essential CDC8 gene and highlight the divergent outcomes of multiple domestication events from diverse *Metaviridae* in the common ancestor of placental mammals.
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