Fig. 1

MLV regions sequenced and summary of sequence cluster information. The structure of the MLV genome is shown between two data tables, with the locations of retroviral regions that were amplified and sequenced indicated by the thick lines. The numbers with which these regions are labeled (1, 2,3, 5, 6) indicate the positions of the regions targeted by PCR, which covered 5 of the 6 recombination sites that created XMRV from PreXMRV-1 and PreXMRV-2 [5]. The target region labeled “2,3” was a single PCR product that included recombination sites 2 and 3. Note that there is no line segment numbered 4, since the PCR targeting the fourth recombination region yielded far fewer reads for all mice tested and was therefore excluded from further analyses. Block arrows point from the analyzed MLV regions to the corresponding table summarizing the clusters identified and analyzed for that genome region. Within the tables, each row represents one cluster of related sequences. A cluster is defined as sequences sharing sufficient identity with each other and with the chosen reference sequences to form a group distinct from other sequences. The first five columns in each table represent the number of sequences in a given cluster for the samples from inbred laboratory mouse strains C3H, LP/J, SJL and two wild caught mice Mmd1 (Corsica) and Mmd2 (mainland France). Shading of these cells correspond to the number of sequences per cluster that were identified per mouse: white for no sequences matching a cluster, light gray for 1-6 sequences, dark gray for more than 6 sequences. Cells shaded in intermediate gray indicates that a cluster was unique to a single mouse. The last four table columns list four different types of MLV (Xmv, XMRV, Pmv or Mpmv), each of which was compared to the mouse sequences generated by the current study. An “X” in these table cells indicates that one or more of the corresponding reference sequences were assigned to the given cluster. When only a single type of MLV reference sequence was assigned to the cluster, the “X” is underlined