80 short, Conserved Sequence Elements in Allomyces macrogynus mtDNA

The mitochondrial DNA (mtDNA) of the chytridiomycete fungus Allomyces macrogynus is unusually G+C rich, in intergenic (49%) versus protein coding regions (32%). These intergenic regions comprise 26-79 bases long G+C-rich sequence elements that can be folded into distinctive structures, consisting of two stem-loops. We found a total of 65 similar structural elements in the A. macrogynus mtDNA, of which 39 are inserted in intergenic regions, 20 in introns and 6 in variable regions of the rRNA genes. Some of these hairpin structures are embedded in others, as twins or even multiples. When comparing the most similar elements, more sequence variation is found in loops than in helical regions, and the latter contain compensatory base changes in base-paired regions, suggesting that the particular secondary structure of the element has a yet unidentified, important function. We have sequenced a region comprising the carboxy-terminal of nad5, atp6 and the amino-terminal portion of cox1 from another Allomyces species, A arbusculus, comprising 7 of these double hairpin structural elements (DHE). Five DHE are inserted at the same position as in A. macrogynus, while two others appear in new locations and are identical in primary sequence to elements in A. macrogynus. The distribution pattern of DHE in A. macrogynus and between the two related species of Allomyces suggests that deletion and transposition of these elements occur at a high frequency. We propose that the conserved structure of DHE play a role in their mobility.