Table 1.
Copy number of MLERV1 related proviruses in different species.
Fig 1.
High sequence similarity and taxonomic distribution of MLERV1, FcERV_γ6 and MPERV1.
(a) Sliding window analysis of percent sequence identity along pairwise alignments of entire proviruses. DNA sequence distance is corrected using kimura 2 parameter substitution model. (b) Taxonomic distribution of MLERV1, FcERV_γ6 and MPERV1. A schematic of the phylogenetic relationship of the 55 species from the clade “Scrotifera” currently represented in the NCBI whole genome sequence database, with human and mouse shown as outgroups. The 55 species fall within 6 mammal orders: Pholidota, Carnivora, Cetacea, Artiodactyla, Perissodactyla, Chiroptera. Some of the species are collapsed by order/family with the number of species for each clade indicated into parentheses. The three independent retroviral invasions of MLERV1, FcERV_γ6 and MPERV1 are depicted above each of the mammal lineages affected. The placement of retroviral particles does not imply the timing of corresponding CST.
Fig 2.
Distribution of MLERV1/FcERV_γ6 insertions in vesper bats and felids.
The numbers of ERV insertions detected as orthologous or species-specific are shown as pies above each branch of the phylogeny of the vesper bats and felids examined. Different colors are used to illustrate FcERV_γ6 and the three different MLERV1 subfamilies.
Fig 3.
Dating individual proviral insertions based on LTR-LTR divergence.
(a) Age distribution of proviral insertions inferred from LTR-LTR divergence. The y axis shows the number of insertions for each age class binned in MY on the x axis. Each ERV family is shown as bars of different colors. (b) Evidence of ‘gene’ conversion between 5’ and 3’ LTR of the same provirus. Four LTR trees are shown for four pairs of orthologous proviruses shared by M. lucifugus (MLERV) and M. brandtii (MBERV). Each maximum likelihood tree was built from a multiple alignment of the 5’ and 3’ LTRs from each provirus rooted with a non-orthologous LTR from M. lucifugus (also illustrated in S2 Fig). The support for each node as determined with an approximate likelihood ratio test (aLRT) is shown. The fact that 5’ and 3’ LTR from the same provirus tend to group together rather than by species is indicative of gene conversion between the LTRs along the two species lineages following proviral insertion in their common ancestor.
Fig 4.
Phylogenetic analysis of MLERV1, FcERV_γ6, MPERV1 families.
A maximum likelihood phylogenetic tree built from a multiple alignment of 3’ LTR sequences of 75 proviruses. The support for each node as determined with an approximate likelihood ratio test is shown. Information on the species origin as well as the presence/absence of envelope sequence is labeled at each node. Two independent losses of envelope by deletion are highlighted.
Fig 5.
Selection analysis on coding domains.
(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.