Identification and characterization of an ancient conserved retroviral envelope gene in Afrotheria

Abstract Background Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections that became permanently integrated into host germline genomes. Although most ERV sequences accumulate mutations and lose coding potential over evolutionary time, some have been co-opted by the host for important physiological functions, particularly in placental development and antiviral defense. Despite the availability of high-quality genome assemblies, the genomes of elephants have not been systematically screened for conserved ERV envelope (env) genes. Here, we performed a comprehensive computational and evolutionary analysis to identify intact retroviral env open reading frames (ORFs) in elephant genomes and investigate their conservation across Afrotheria. Results A genome-wide screen of the African elephant ( Loxodonta africana ) and Asian elephant ( Elephas maximus ) identified 59 independently acquired intact retroviral env ORFs. Most represented recent lineage-specific integrations; however, one env gene, termed AFRenv, was conserved at the same orthologous genomic position across multiple Afrotherian orders, including Proboscidea, Sirenia, and Afrosoricida, indicating that the progenitor retrovirus became fixed in the common ancestor of extant Afrotherians at least 79 million years ago. AFRenv retains a full-length ORF in several Afrotherian lineages and preserves key structural features characteristic of gamma-type retroviral Env proteins, including a signal peptide, furin cleavage site, conserved cysteine motif, and transmembrane domain. Simulations of neutral sequence evolution demonstrated that long-term preservation of the AFRenv ORF is highly unlikely in the absence of selective pressure. Codon-based maximum likelihood analyses confirmed that AFRenv has evolved under purifying selection, with a substantial proportion of codons under negative selection and no evidence of diversifying selection. Transcriptomic analysis further revealed that AFRenv is transcriptionally active in elephants and exhibits placenta-enriched expression in the African elephant. Conclusions Our findings identify AFRenv as one of the oldest intact retroviral env genes described in placental mammals. The remarkable preservation of its coding capacity, structural motifs in multiple lineages, and its placenta-enriched expression in the African elephant suggest that AFRenv has been maintained to fulfill a host physiological function in Afrotheria. These findings provide new insight into the long-term evolutionary impact of ancient retroviral integrations on mammalian genome evolution.