Convergent Co-option of the Retroviral Gene during the Early Evolution of Mammals.

Endogenous retroviruses, records of past retroviral infections, are ubiquitous in vertebrate genomes. On occasion, vertebrate hosts have co-opted retroviral genes for their own biological functions. Here, we perform a phylogenomic survey of retroviral gene homologs within vertebrate genomes and identify two ancient co-opted retroviral genes, designated () and (), in mammals. Conserved synteny and evolutionary analyses suggest that the and co-options occurred before the origin of modern placental mammals (∼100 million years ago) and before the origin of modern marsupials (∼80 million years ago), respectively. We found that the genes were lost or pseudogenized multiple times during the evolutionary course of mammals. While the gene is mainly subject to negative selection in placental mammals (except in Perissodactyla), the gene underwent positive selection in marsupials. Moreover, analyses of transcriptome-sequencing (RNA-seq) data suggest that the and the genes are expressed in a wide range of tissues. The convergent co-option in mammals implies the retroviral gene might have been repurposed more frequently than previously thought. Retroviruses occasionally can infect host germ lines, forming endogenous retroviruses. Vertebrates, in turn, recruited retroviral genes for their own biological functions, a process formally known as co-option or exaptation. To date, co-opted retroviral genes have rarely been reported. In this study, we identified two co-opted retroviral genes, designated () and (), in mammals. The co-option of and occurred before the origin of modern placentals and before the origin of modern marsupials, respectively. Our study indicates that retroviral gene co-option might have occurred more frequently than previously thought during the evolutionary course of vertebrates.