Dynamic evolution of retroviral envelope-derived sequences in primates
DOI:
https://doi.org/10.51094/jxiv.2051Keywords:
endogenous retrovirus, de novo genes, co-option, primate evolutionAbstract
It is known that several endogenous retroviruses (ERVs), remnants of ancient retroviral integrations, retain envelope (env) genes encoding fusogenic proteins in primates. While most env genes are degraded, a few have been co-opted by hosts, yet the entire evolutionary dynamics of env sequences remain poorly understood. To explore this, we screened and compared env open-reading frames (ORFs) from 247 primate genomes. In total, 8,683 nearly intact env-ORFs encoding over 400 amino acids were identified, and their copy numbers ranged from 3 to 429 across primate species. By conducting sequence similarity clustering, we found that the reported functional env-derived genes tend to have low copy numbers and to be retained across primate lineages. Notably, an evolutionary conserved env ortholog with low sequence similarity to other env-ORFs was identified in tarsiers, which exhibited cell fusion activity in vitro, suggesting a potential fusogenic function in tarsiers. Further, we found that certain co-opted env-derived genes may have lost their functions due to nonsense or indel mutations within specific primate lineages. Considering that many env genes tend to be maintained at low copy numbers and reported to be under natural selection, such dynamic evolutionary turnover of env-derived genes may be driven by host-virus arms races, as viruses and endogenous retroviruses often share cell-surface receptors.
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Published: 2025-12-01 09:27:55 UTC
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Koichi Kitao
Kirill Kryukov
Lihua Jin
Yuta Shintaku
Takashi Hayakawa
So Nakagawa
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