Figure 1 Saccharomyces cerevisiae Ty1 virus (SceTy1V) 1-381 virions; surface structure of two forms (T = 3, left; T = 4, right) determined by cryo-electron microscopy, with the corresponding diagrammatic models.
(Courtesy of H. Saibil, adapted from J. Virol., 71, 6863–6868.)
Figure 2 The genomic organization of Saccharomyces cerevisiae Ty1 virus (SceTy1V) (5.9 kb) and Drosophila melanogaster copia virus (DmeCopV) (5.1 kb). Black boxes within the LTRs depict sequences repeated at the 5’ and 3’ ends of the virus’s transcripts (R regions); sequences 5’ of R represent U3, and sequences 3’ of R represent U5. Open boxes below the viruses indicate gag and pol. Conserved aa sequences in pol that identify protease (PR), integrase (IN) and reverse transcriptase/RNAse H (RT) are labeled. Individual mRNAs are depicted as arrows. Arrowhead indicates site of ribosomal frameshifting.
Figure 3 Examples of variability in the genome organization of members of the genus Sirevirus. Variability can be observed by the presence or absence of an env-like ORF, the organization of the env-like ORF relative to pol, and the organization of gag and pol.
Figure 4 Phylogenetic tree based on the amino acid sequences of the reverse transcriptase domain of members of the family Pseudoviridae. The Pfam HMM reverse transcriptase model for Pseudoviridae retrotransposons (RVT_2 PF07727.6) was used to scan and locate the respective domain in each element. After the alignment, MEGA4 was used to construct the phylogenetic tree using the neighbor-joining distance method. Bootstrap support was calculated based on 1000 replicates (values shown where >50%) and the evolutionary distances were computed using the Poisson correction model. Members of the genus Pseudovirus are shown in red, Hemivirus in blue and Sirevirus in green. Tpv2-6 is an unassigned species and Osr7 and Osr8 have not yet been classified but clearly belong with the sireviruses.
(Courtesy of A. Bousios, Institute of Agrobiotechnology, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece.)
Figure 5 Unrooted phylogenetic tree of all class of reverse transcriptase containing viruses. While over 100 reverse transcriptase sequence were used to generate this phylogeny, to simplify visual comparison of the major topologies of the tree, viruses from the same class that are located on the same branch of the tree are indicated by an oval. The length of the oval corresponds to the most divergent viruses within that oval. The arrow indicates a possible root of the tree using RNA polymerase sequences.