Additional file 4.

Complex repeat structure in SIX8, SIX8b and SIX14 upstream regions. The most upstream sequence shared between the SIX8 and SIX8b loci (dark grey, blue and green highlighted) is more similar between SIX8 and SIX8b loci than the coding sequences and the immediate upstream sequences (light grey). The SIX8b upstream region is the most complex. Compared to that of SIX8, there are: (a) a mimp4 insertion, (b) a Han insertion, (c) an inversion and duplication (indicated with < signs), (d) a mimp1 insertion, (e) a partial mimp3 and (f) an extra sequence that includes an mFot5. A total of 9 mimp-related inverted repeats are present, of which two are interrupted by a TE. Part of the SIX14 upstream region is almost identical to a part of the SIX8b upstream region (green/blue highlighted including the mimp4) – except that the Han insertion is missing in the SIX14 locus. In both cases, a mimp1 is present immediately downstream of this region but, though similar in sequence, these mimp1 insertions appear to be independent. Blue capital letters: effector ORF (introns in lower case); Green capital letters: mimp; Dark red capital letters: mFot5; Orange capital letters: Han; Gray highlight: shared between SIX8 and SIX8b loci only; Light gray highlight: similarity between SIX8 and SIX8b upstream (leader/promoter) sequences; Blue highlight: mimp-like inverted repeat sequence, present one or more times in SIX8, SIX8b and SIX14 loci (numbers of likely orthologous sequences correspond between the three loci – note that mimp-IR1 does not conform to the consensus sequence for mimp inverted repeats); Green and dark green highlight: sequences present one or more times in SIX8, SIX8b and SIX14 loci; Yellow highlight: TGCCGA motif; Bold: target site duplications associated with TE insertions.

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Schmidt et al. BMC Genomics 2013 14:119   doi:10.1186/1471-2164-14-119