Figure 1 .

Structure and organization of Class I and II elements identified in the genome of Verticillium dahliae (strain VdLs.17).A) Class I LTR retrotransposons. Schematic representations of the structure of the Ty1/Copia-like and Ty3/Gypsy-like LTR elements, as well as a LINE-like non-LTR retrotransposon . The conserved domains identified in the putative protein sequences encoded by the GAG and POL genes are indicated below the open reading frames (ORFs). VdLTRE1 (upper schematic) contains direct long terminal repeats (LTR), and a fused GAG and POL ORF, while VdLTRE5 GAG and POL ORFs are separated by a UGA stop codon. The highly similar sequences of VdLTRE2, VdLTRE3, and VdLTRE4 (VdLTRE2/3/4) have overlapping GAG and POL ORFs. VdLINE sequence contains linked, but separate, GAG and POL ORFs. Domain abbreviations: INT, integrase (pfam00665); RVT2, reverse transcriptase 2 (pfam07727); RnaseH (pfam0075.16), GAG, group specific antigen; ZK, zinc knuckle (pfam00098); PR, Retropepsin protease (CD00303); RVT_1, reverse transcriptase 1; CR, chromatin organization modifier (CD00024); EEP, endonuclease-exonuclease-phosphatase; B) Class II transposable elements of the superfamilies Tc1/mariner, Activator and Mutator. Each TE type possesses terminal inverted repeats (TIRs) of different length flanking a transposase gene (shown is the corresponding ORF). The Tc1/mariner transposases are characterized by the endonuclease superfamily motif DDE_1 (pfam03184) and the presence of the additional N-terminal DNA-binding domains helix-turn-helix_pipsqueak (here indicated as psq, pfam05225), and helix-turn-helix_Tnp_Tc5 (here indicated as Tc5, pfam3221). The relative position of the hAT dimerization (pfam05699) and the MULE (pfam10551) domains characterizing the Activator and Mutator transposases are also shown. Flanking the TIRs are the nucleotide sequences of the direct target site duplications (TSDs) generated in the fungal genome by the TE insertion.

Amyotte et al. BMC Genomics 2012 13:314   doi:10.1186/1471-2164-13-314
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