Fig. 1
From: Reconstruction of a replication-competent ancestral murine endogenous retrovirus-L
Structure and distribution of MuERV-L elements in the mouse genome and reconstruction of an ancestral ~ 2MY old MuERV-L sequence. a Schematic representation of the structure of MuERV-L elements. White boxes in gag represent the 33 and 39nt deletions in gag at nucleotide positions 671 and 1597, respectively. b Distribution of distinct MuERV-L structures among mouse chromosomes. YS = Y chromosome short arm, YL = Y chromosome long arm. c Distribution of MuERV-L elements in mouse genomic features (GRCm38/mm10). The fraction of the 2971 elements inside and outside genes is depicted (top chart), as the fraction of elements present in each type of gene or gene feature (bottom chart). d Distribution of MuERV-L elements in genic or intergenic regions relative to random controls. The measured value indicates the percentage of MuERV-L elements in each population divided by that of the random controls (see “Methods”). The horizontal dotted line indicates no difference between the ratio of MuERV-L elements in each population and that of the controls. (*) p value < 0.05. (***) p value < 0.001. P values are based on Chi-squared goodness-of-fit or contingency table tests. e Maximum likelihood phylogenetic tree of 95 LTR–gag–pol–LTR MuERV-L elements in the mouse genome. Arrow denotes the ancestral node reconstructed by baseml (pol and LTR, node 96). f Maximum likelihood phylogenetic tree of 230 gag–pol containing MuERV-L elements in the mouse genome. The monophyletic red clade contains only elements with a 33nt deletion in gag at position 671 with or without an additional 39nt deletion in gag at position 1597. Arrow denotes the ancestral node reconstructed by baseml (gag, node 377)