Cross-Species Transmission and Differential Fate of an Endogenous Retrovirus in Three Mammal Lineages
(a) dN/dS ratio (ω) of each coding domain in FcERV_γ6, MLERV1_2 and MLERV1_3. MA, CA, PRO, RT, RH, INT and TM denote matrix, capsid, aspartyl protease, reverse transcriptase, RnaseH, integrase and envelope transmembrane domain, respectively. Asterisks denote the level of significance of departure from ω = 1 (likelihood ratio test, see Methods) with * = p<0.05; ** = p<0.01; *** = p<0.001. NS = not significant (p>0.05); NA = not applicable (domain deleted). (b) Shared breakpoints at the site of envelope deletion in a subset of FcERV_γ6 elements. A schematic of the prototypical proviral coding regions showing the approximate position of the envelope deletion in 29 FcERV_γ6 elements marked with blue triangles in Fig 4 and (below) an alignment with a subset of envelope-containing FcERV_γ6 elements, showing that they share the same deletion breakpoints. These data indicate that these 29 elements likely arose from amplification of a progenitor copy that had suffered a large deletion in the envelope region.