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. 2008 Sep;18(9):1484–1499. doi: 10.1101/gr.074336.107

Figure 4.

Figure 4.

Nested SDR elements. (A) A nested structure consisting of multiple SDR4 elements using color conventions described in Figure 1. The nested element (line 4), located in the chromosome of N. punctiforme from 671,496 to 671,583 (inverted), may have arisen, as shown, by the insertion of SDR4.5 (lines 1 and 2), followed by the insertion of an unnamed SDR4 element in the opposite orientation (lines 2 and 3), and finally by the insertion of SDR4.3 (lines 3 and 4). The sequence of the proposed intermediate shown in line 3 actually exists elsewhere in the chromosome, between coordinates 3,226,461 and 3,226,527 (inverted). Proposed intermediates 1 and 2 are hypothetical. (B) Nested structures derived from multiple apparent insertions of SDR1 elements, highlighted in yellow. SDR1 elements in the forward orientation are given in black or green characters. Those in the reverse orientation are given in red characters. Sequences in red characters flanking the nested elements are the inverted terminal repeats of a putative minitransposon into which the nested elements are embedded. Sequences highlighted in gray are conserved but otherwise uncharacterized. The low-order coordinates of the sequences shown are (B1) 3368609F, (B2) 2564863B, (B3) 1746187F, (B4) 8086669B, (B5) 633195F, (B6) 50757F, (B7) 8020729F, (B8) 6448446F, (B9) 1811789b, (B10) 7091736B, and (B11) 2217329F, where F and B indicate the forward and backward (inverse) strand, respectively. The inset at top presents a series of plausible events that might have given rise to the observed sequences. Numbers in circles refer to the lines in the alignment. Gray circles are hypothetical intermediates. (C) Seemingly related compound elements composed of SDR1, SDR4, and SDR6. The sequences are organized first by the outermost elements, two unnamed subfamilies of SDR1. Each grouping is then divided according to whether SDR4.11 or SDR4.12 has inserted into the SDR1 element. The low-order coordinates of the sequences shown are (D1) 3134527B, (D2) 2144806F, (D3) 4962007F, (D4) 3363464F, (D5) 5179224F, (D6) 8021963F, (D7) 6220474F, (D8) 733274B, (D9) 187174B, (D10) 676346B, (D11) 5070575B, (D12) 7201684F, (D13) 6371472B, (D14) 5596457F, and (D15) 3424319B.