Widespread occurrence of spliceosomal introns in the rDNA genes of ascomycetes

Spliceosomal (pre-mRNA) introns have previously been found in eukaryotic pr otein-coding genes, in the small nuclear RNAs of some fungi, and in the sma ll- and large-subunit ribosomal DNA genes of a limited number of ascomycete s. How the majority of these introns originate remains an open question bec ause few proven cases of recent and pervasive intron origin have been docum ented. We report here the widespread occurrence of spliceosomal introns (69 introns at 27 different sites) in the small- and large-subunit nuclear-enc oded rDNA of lichen-forming and free-living members of the Ascomycota. Our analyses suggest that these spliceosomal introns are of relatively recent o rigin, i.e., within the Euascomycetes, and have arisen through aberrant rev erse-splicing tin trans) of free pre-mRNA introns into rRNAs. The spliceoso me itself, and not an external agent (e.g., transposable elements, group II introns), may have given rise to these introns. A nonrandom sequence patte rn was found at sites flanking the rRNA spliceosomal introns. This pattern (AG-intron-G) closely resembles the proto-splice site (MAG-intron-R) postul ated for intron insertions in pre-mRNA genes. The clustered positions of sp liceosomal introns on secondary structures suggest that particular rRNA reg ions are preferred sites for insertion through reverse-splicing.