Widespread Occurrence of Spliceosomal Introns in the rDNA Genes of Ascomycetes

Abstract

Spliceosomal (pre-mRNA) introns have previously been found in eukaryotic protein-coding genes, in the small nuclear RNAs of some fungi, and in the small- and large-subunit ribosomal DNA genes of a limited number of ascomycetes. How the majority of these introns originate remains an open question because few proven cases of recent and pervasive intron origin have been documented. We report here the widespread occurrence of spliceosomal introns (69 introns at 27 different sites) in the small- and large-subunit nuclear-encoded rDNA of lichen-forming and free-living members of the Ascomycota. Our analyses suggest that these spliceosomal introns are of relatively recent origin, i.e., within the Euascomycetes, and have arisen through aberrant reverse-splicing (in trans) of free pre-mRNA introns into rRNAs. The spliceosome itself, and not an external agent (e.g., transposable elements, group II introns), may have given rise to these introns. A nonrandom sequence pattern was found at sites flanking the rRNA spliceosomal introns. This pattern (AG-intron-G) closely resembles the proto-splice site (MAG-intron-R) postulated for intron insertions in pre-mRNA genes. The clustered positions of spliceosomal introns on secondary structures suggest that particular rRNA regions are preferred sites for insertion through reverse-splicing.

Cardinal characters on a slippery slope – A re-evaluation of phylogeny, character evolution, and evolutionary rates in the jelly lichens (Collemataceae s. str)

“…These results indicate that the ribosomal RNA genes have higher rates of heterogeneity among lineages than protein coding genes. This may not be unexpected as these genes include more insertions (DNA regions highly affected by mutations) compared with other genes, in fungi (Bhattacharya et al, 2000; DePriest, 2004;Simon et al, 2005;Hofstetter et al, 2007), and some of such insertions may have remained in our final dataset.…”

“…These results indicate that the ribosomal RNA genes have higher rates of heterogeneity among lineages than protein coding genes. This may not be unexpected as these genes include more insertions (DNA regions highly affected by mutations) compared with other genes, in fungi (Bhattacharya et al, 2000; DePriest, 2004;Simon et al, 2005;Hofstetter et al, 2007), and some of such insertions may have remained in our final dataset.Heterogeneity in substitution rates among lineages is a common observation in molecular phylogenetic studies (Lutzoni and Pagel, 1997;Allen et al, 2006;Lumbsch et al, 2008;Smith and Donoghue, 2008). In the present study, we found significant rate heterogeneity between the wet-tropical/moist-temperate clade ABC and the rest of the lineages (Table 4), which together with the comparatively longer branches in clade ABC, suggests that this clade evolves faster than the other lineages.…”

A new Drosophila spliceosomal intron position is common in plants

“…Convergent intron insertion has been invoked to account for some patchy intron phylogenetic distributions (33)(34)(35)(36). Perhaps the strongest case is that reported in several species of Chironomus by Hankeln …”

Molecular phylogeny reveals the true colours of Myeloconidaceae (Ascomycota: Ostropales)

“…The first available molecular data, provided by Bhattacharya et al (2000), suggested that Porina formed part of Lecanoromycetes, specifically being sister to Stereocaulon in the Lecanorales; this, however, stemmed from the sequences of the species used (P. guentheri) apparently being incorrectly labelled or from contaminants (the nuSSU appears to be part of Dothideomycetes, whereas the nuLSU is suggested to belong to Parmeliaceae and includes a rare intron). Nevertheless, the placement of Porinaceae in Lecanoromycetes was subsequently shown by Grube et al (2004), who demonstrated that it belonged in Ostropomycetidae, not Lecanoromycetidae, close to taxa in Ostropales.…”