The Diverse Evolutionary Histories of Domesticated Metaviral Capsid Genes in Mammals
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Abstract
Selfish genetic elements comprise significant fractions of mammalian genomes. In rare instances, host genomes domesticate segments of these elements for function. Using a complete human genome assembly and 25 additional vertebrate genomes, we re-analyzed the evolutionary trajectories and functional potential of capsid (CA) genes domesticated from Metaviridae, a lineage of retrovirus-like retrotransposons. Our study expands on previous analyses to unearth several new insights about the evolutionary histories of these ancient genes. We find that at least five independent domestication events occurred from diverse Metaviridae, giving rise to three universally retained single-copy genes evolving under purifying selection and two gene families unique to placental mammals, with multiple members showing evidence of rapid evolution. In the SIRH/RTL family, we find diverse amino-terminal domains, widespread loss of protein-coding capacity in RTL10 despite its retention in several mammalian lineages, and differential utilization of an ancient programmed ribosomal frameshift in RTL3 between the domesticated CA and protease domains. Our analyses also reveal that most members of the PNMA family in mammalian genomes encode a conserved putative amino-terminal RNA-binding domain (RBD) both adjoining and independent from domesticated CA domains. Our analyses lead to a significant correction of previous annotations of the essential CCDC8 gene. We show that this putative RBD is also present in several extant Metaviridae, revealing a novel protein domain configuration in retrotransposons. Collectively, our study reveals the divergent outcomes of multiple domestication events from diverse Metaviridae in the common ancestor of placental mammals.
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N-terminal regions
If you seeded sequence- or structure-based searches with only these regions, do you ever see them fused to other known functional domains besides this family?
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Diverse N-terminal structures
This is so interesting!
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glires
I learned a new word today!
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function is not universally required in mammals
Could it be that they had essential functions in now-extinct mammals? No idea how one would answer this, but I always wonder in these instances.
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17 additional representative mammalian genomes
Curious how these were chosen? Was it based primarily on availability or was there something specific about the particular ones you chose? Would have been cool to see more marsupials or monotremes represented, but I assume it was challenging to find high quality genomes that were amenable to your analyses?
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including reproduction
I've always found this fascinating. Did ERV gene domestication happen at a particularly interesting moment in natural history for these animals with regard to reproduction? Something major that was changing in the environment that benefited from domestication events to accelerate change?
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