Ribosomal DNA variability due to the presence of optional group I introns

Earlier, we assumed all SSU rDNA genes were highly conserved with little sequence variation between species of closely related genera. Yet from DNA isolated from a fungal culture, using different PCR primer pairs, amplified PCR fragments from the same region differed in size by up to 450 nt. These extra nucleotides resulted from discrete insertions in the SSU rDNA. P. T. DePriest discovered similar insertions in the SSU rDNA isolated from species of the pixie cup lichen Cladonia, and determined that these were group I introns. Some insertion locations appear to be ancient and conserved for example between fungi, green algae, and amoebae, although there is little homology of these introns' DNA sequences, other introns are of more recent origin. In our analyses of over one hundred SSU rDNA sequences from various ascolichens we found variation in intron occurrence within species, within populations, and possibly, within rDNA repeats in a single tandem array.
intron locations in SSU rDNA Insertions, most of which have been identified as group I introns, occur in at least 17 positions in highly conserved regions of the SSU rDNA in fungi, algae, and plastids. Introns of similar size were located at identical locations within the SSU rDNA genes we had sequenced. Paula T. DePriest and I published a list of all currently reported positions of insertions and group I introns in the SSU rDNA (Molecular Biology and Evolution 12: 208-218; download PDF). Lichen-forming fungi have a surprising large number of insertions in their SSU rDNA; a culture of Lecanora dispersa contains eight insertions within its SSU rDNA, doubling the typical size of 1,800 nt. DePriest and I found variation within species, within populations, and possibly, within rDNA repeats in a single tandem array. For a closer view of this secondary structure please see this descriptive page.

Research on SSU rDNA insertions and introns has continued in the DePriest laboratory. At present, at least 30 locations of insertions and group I introns have been determined.

Current research in the DePriest Laboratory.

Click here for a summary of currently known insertion locations, with reference to both the sequence of Eschericia coli (Genbank:) and Saccharomyces cerevisiae (Genbank:YSCRGEA).


Some insertion locations appear to be ancient and conserved for example between fungi, green algae, and amoebae, although there is little homology of this intron's DNA sequences, other introns are of more recent origin. The origin of these introns, or the reasons for their remarkable abundance in lichen-forming fungi, and also in green algae, remains a mystery. Ribosomal DNA can apparently undergo profound changes with insertions of large stretches of DNA. Refined phylogenies of fungi provide a better context for understanding the evolution of group I introns, and also how they may affect ribosomal DNA evolution.

Link to other information on Group I introns:

gargas lab | molecular systematics | PCR primers | rDNA introns | publications & resume
last update 13.nov 2006