Figure 1.
Common instances of SDR elements. Families: The most representative examples are shown of members of different families of SDR elements and their subfamilies. All families with at least four occurrences in the genome of Nostoc punctiforme are given, along with examples from every cyanobacterial genome considered (listed in Fig. 5) in which an instance of the SDR element was observed (see Supplemental Files 1–8 for more complete listings). The name of each organism is followed by a fraction consisting of the number of instances of the SDR element in the chromosome divided by the total number of instances. Only the total is given for organisms whose genome sequences have not been completely determined. SDR elements identified in the survey of the tRNALeu (UAA) intron of different Nostoc strains (Costa et al. 2002) are also shown. Color conventions: Each SDR element is highlighted with a characteristic color, used in other figures as well. Deviations from the reference sequence of the group are shown by gray highlighting. Nearby SDR elements are also highlighted in their characteristic color. For these elements, a green or black font is used if the orientation of the element is the same as the central element, otherwise a red font or italics are used. Sequences that are italicized and in red font are parts of putative minitransposons. Blocks outside of the central element highlighted in gray are unnamed sequences found multiple times in the genome. Nearby tandemly repeated sequences are colored and in bold, and the repeating units are separated by vertical bars. Vertical bars also mark the end of SDR elements. Tandem repeats with lines running through them are the inversion of repeats represented by the same color. Inverted repeats: Underscores indicate regions potentially involved in self-base pairing, and extended arrows at the top of the grouping indicate whether the pairing is strongly supported by compensatory mutation (solid arrows) or not (broken arrows).