Figure 1

The structure of rDNA and its transposons in the Daphnia genome sequence. (A) The rDNA is an array of transcription units repeated in tandem and separated by the intergenic spacer (IGS), which contains a repeated sequence (purple boxes), as well as non-repeated regions. Pink boxes in the IGS and internal transcribed spacer (ITS)2 indicate the position of sequences found in the 5′ noncoding region (NCR) of Pokey elements. (B) The structure of Pokey and Pokey-derived miniature inverted repeat transposable elements (mPok), which insert in a specific TTAA site in 28S rRNA genes. The approximate length of each region of a canonical autonomous Pokey element is given below the diagram. The black triangles at each end represent the inverted terminal repeats (ITRs). The dashed line in Pokey represents the highly length-variable region composed of both repetitive and unique sequences (more detail is provided in Figure 5). The green and orange regions correspond to regions that are similar in Pokey and mPok, the sequences of which are shown in Figure 2. (C) Sequence of the two types of ITRs. Complementary regions between the imperfect 5′ and 3′ ITRs are underlined. The TTAA target site duplication is shown in lower case.