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 1
Simplified phylogeny of gammaretroviruses based on over 2000 gammaretrovirus-like sequences with one zinc finger in Gag, from selected vertebrate genomes (in a first version of RetroBank) and reference gammaretroviruses. Retroviral groups which occur in phylogenetically distant vertebrate hosts, indicating cross-species transmission events, are shown in red. The neighbor-joining tree was based on an alignment of 105 reference and consensus Pol amino acid sequences. Only the major branches are shown. As explained in the text, they were provisionally named after the cosegregating HERV group. The group of “MLV-like viruses,” MLLVs, at least 60% similar in Pol, is boxed in. The similarity is calculated from the inverted ratio of the BLASTP score of the sequence against itself to another sequence, or to a consensus Pol sequence. Some two-zinc finger sequences (ERV-HF, containing HERV-H and HERV-F) were included as a reference. Although the clustering included several genomes, the groups were named from the human sequence representative. MuERV: mouse endogenous retrovirus. MmERV is from Bromham et al. [13], and MdERV is Mus dunni ERV from Wolgamot et al. [14]. GLN MuERV is from Ribet et al. [15]. Symbols: position of XMRV/HMRV, § recombinant MuERV Sp496-5Sb [16] from Mus spretus, ¤ hortulanus endogenous murine virus, HEMV, from Mus spicilegus [17], # MuRRS [18], and MuERVC [19]. An ERV-S sequence [20] was used to root the tree. It came from HERV-S, a sequence intermediate to spuma-, epsilon-, and gammaretroviruses. It belongs to the so-called “ERV3 family” according to the RepBase nomenclature [21]. This large clade is also called “Class III ERVs.” It should not be confused with the ERV3 group shown in the figure. The hand symbols denote proviruses with one and two zinc fingers in Gag, respectively. The murine gammaretroviral groups G1-G3 are described in greater detail in a forthcoming paper (Elfaitouri et al., accepted, Plos One).
