Review Article

Phylogeny-Directed Search for Murine Leukemia Virus-Like Retroviruses in Vertebrate Genomes and in Patients Suffering from Myalgic Encephalomyelitis/Chronic Fatigue Syndrome and Prostate Cancer

Figure 3

Neighbor-joining (NJ) tree based on Pol amino acid sequences of 300 high ReTe scoring MLLVs, the same as in Figure 4. The three high-scoring murine gamma groups (G1–G3) segregate in a similar way as in a gag nt-based tree (Figure 4). Bootstrap values are shown to the left of each branch. Structurally intact proviruses are marked with green arrows. GLN virus [15], MmERV, Mus dunni ERV (MdERV), AKV MLV, and XMRV (VP62 clone) are marked with magenta arrows. Murine MLLVs occur from the black arrow in the tree and upwards. The branch labels are either ERV host genus, chromosomal position, ReTe score, provisional genus, “po” for Pol, PBS, and number of stops and frame shifts (“z 0/0” means 0 stops and 0 shifts in pol), or a reference Pol name. PBS assignments are made by the 1.01 version of RetroTector. A more complete interpretation of PBS sequences of the G1-G3 groups is given in a forthcoming publication (Elfaitouri et al., accepted in Plos One). The major one zinc finger branch is indicated by the hand symbol. Nonmurine gammaretroviral ERV sequences were taken from the prototype of RetroBank. Further information on which assemblies were used can be found in [47].
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