Figure 1 Saccharomyces cerevisiae Ty1 virus (SceTy1V) 1-381 virions; surface structure of two forms (T = 3, left; T = 4, right) determined by cryoelectron microscopy (Courtesy of H. Saibil, adapted from J. Virol. 71; 6863-6868.) The bar represents 100 nm.
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 element transcripts (R regions); sequences 5 of R represent U3, and sequences 3 of R represent U5. Open boxes below the elements indicate gag and pol. Conserved amino acid 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 Phylogenetic relationships of the members of the family Pseudoviridae. The phylogenetic relationship of the elements were determined by the neighbor-Joining distance algorithm of Saitou and Nei (1987) using Phylip (Felsenstein, 1993) and is based on the amino acid sequence of their reverse transcriptase domains. For details of the sequence alignments and analysis see Xiong and Eickbush, 1990. The tree was rooted using sequences of members of the family Metaviridae. Numbers above branch nodes are bootstrap values and are shown as percentages. Branch nodes without numbers have bootstrap values below 50% and thus have little reliability.
Figure 4 Unrooted phylogenetic tree of all class of reverse transcriptase containing elements. While over 100 reverse transcriptase sequences were used to generate this phylogeny, to simplify visual comparison of the major topologies of the tree, elements from the same class that are located on the same branch of the tree are indicated by a box. The length of the boxes correspond to the most divergent element within that box. The arrow indicates a possible root of the tree using RNA polymerase sequences.
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