Fig. 4: Repeats and recombination in the Haplopteris ensiformis mitogenome.

Recombinations across repeats (in orange) R596 (A), repeats R203 and R 513 (B) and R180 (C) was investigated by tsa-PCR (”template-switch-avoiding”) strategies. a R596 is identically present in domains IV of group II introns nad5i1242g2 and rrnLi833g2. Average read coverage of the flanking single copy regions were ca. 150× for nad5 (arrangement A-C) and ca. 350× for rrnL (arrangement B-D), apparently adding up to ca. 500× for R596. PCR products are obtained for the expected gene continuities (AC, BD) with only minor evidence for reciprocal exchanges (AD, BC). b All combinations of flanking sequences (AC-BD) are identified for recombination across R203 whereas a clear bias is seen for recombination across R513 where a product for primer combination B-C remains undetected. c One copy of repeat R180 is located in intron nad2i709g2, another one downstream of the nad9 gene. The region between R180 and nad9 contains additional repeats R137 and R259 and all consecutive recombination products can be found whereas there is only very weak evidence for recombination across the R180 copy located in nad2i709g2. The marker lane of the electrophoresis gel covering R180 has been rearranged as indicated by the dotted line. The images of electrophoretic gels used in this figure are deposited as supplementary figures 5a and 5b.