rRNA genes from the lower chordate Herdmania momus: structural similarity with higher eukaryotes

Relationships among problematic North American stagnicoline snails (Pulmonata: Lymnaeidae) reinvestigated using nuclear ribosomal DNA internal transcribed spacer sequences

The taxonomic relationships among four stagnicoline snail species from North America were reassessed by analysing nucleotide sequences from their nuclear ribosomal internal transcribed spacer (ITS) region. Three of the species (Stagnicola catascopium, Stagnicola emarginata, and Stagnicola elodes) are representatives of the subgenus Stagnicola s.str. from the northern U.S.A. and the fourth is a closely related Canadian species (Stagnicola caperata) belonging to the subgenus Hinkleyia. Members of the two subgenera differed considerably in their ITS sequences, demonstrating the usefulness of these sequences for distinguishing species from closely related lymnaeid subgenera. In contrast, ITS sequences for the three members of the subgenus Stagnicola s.str. were very similar, which supports an earlier view that they may not be separate species.

Molecular phylogenetics of the four Schistosoma species groups determined with partial 28S ribosomal RNA gene sequences

Partial 28S ribosomal RNA (rRNA) gene sequences, including the variable domains D1, D2 and D3, were determined for representative species from the 4 Schistosoma species groups. On an alignment of 1345 bp from S. mansoni, S. haematobium, S. spindale and S. japonicum (with Heterobilharzia americana chosen as an outgroup), both maximum likelihood and maximum parsimony analyses provide a robust molecular phylogeny for the genus; ((((S. haematobium, S. spindale), S. mansoni), S. japonicum), H. americana). When analysed separately, both domain D1 and domain D2 yielded similarly informative data whereas D3 failed to resolve the phylogeny. These results confirm a phylogeny previously suggested by 18S rRNA gene sequences, corroborating the status of S. spindale as a sister taxon to S. haematobium, and demonstrate the utility of 28S rRNA gene sequence data for resolving phylogenies within the Schistosomatidae.

Multiple origins of anural development in ascidians inferred from rDNA sequences

Ascidians exhibit two different modes of development. A tadpole larva is formed during urodele development, whereas the larval phase is modified or absent during anural development. Anural development is restricted to a small number of species in one or possibly two ascidian families and is probably derived from ancestors with urodele development. Anural and urodele ascidians constitute a model system in which to study the evolution of development, but the phylogeny of anural development has not been resolved. Classification based on larval characters suggests that anural species are monophyletic, whereas classification according to adult morphology suggests they are polyphyletic. In the present study, we have inferred the origin of anural development using rDNA sequences. The central region of 18S rDNA and the hypervariable D2 loop of 28S rDNA were amplified from the genomic DNA of anural and urodele ascidian species by the polymerase chain reaction and sequenced. Phylogenetic trees inferred from 18S rDNA sequences of 21 species placed anural developers into two discrete groups corresponding to the Styelidae and Molgulidae, suggesting that anural development evolved independently in these families. Furthermore, the 18S rDNA trees inferred at least four independent origins of anural development in the family Molgulidae. Phylogenetic trees inferred from the D2 loop sequences of 13 molgulid species confirmed the 18S rDNA phylogeny. Anural development appears to have evolved rapidly because some anural species are placed as closely related sister groups to urodele species. The phylogeny inferred from rDNA sequences is consistent with molgulid systematics according to adult morphology and supports the polyphyletic origin of anural development in ascidians.

The sequence of 28S ribosomal RNA varies within and between human cell lines

The primary structure of 28S ribosomal RNA constitutes a conserved core which is similar among most 23S-like rRNAs and expansion segments which occur at specific positions in the sequence. The expansion segments account for most of the size difference between prokaryotic (archaeal and eubacterial) and eukaryotic rRNAs and they exhibit a sequence variation which is unique among rRNAs. We have investigated the sequence variation of one of the expansion segments, V8, by sequencing a total of 111 V8 segments from 9 different human cell lines and tissues and have found 35 different variants. The variation occur mainly at two 'hot spots' which are separated by 170 nucleotides in the primary sequence but are neighbours in the secondary structure. The sequence of V8 segments varies both within and between human cell lines and tissues. The implications for the evolution of the eukaryotic 28S rRNA are discussed together with possible functions of the expansion segments. We also present a secondary structure model for the V8 segment based on comparative sequence analysis and chemical and enzymatic foot printing.

Extrachromosomal ribosomal DNA of Didymium iridis: sequence analysis of the large subunit ribosomal RNA gene and sub-telomeric region

The ribosomal DNA of the myxomycete Didymium iridis is organized as extrachromosomal linear molecules of about 20 kb, containing only one transcription unit of the ribosomal RNA genes. We have determined the sequence of the large subunit ribosomal RNA (LSU rRNA) gene as well as the sub-telomeric and telomeric regions. The LSU rRNA gene was found to encode a 3857 nucleotide-long LSU rRNA, interrupted by a transcribed spacer and two group I introns. A complete secondary structure model of D. iridis LSU rRNA has been constructed. The compact sub-telomeric region of D. iridis rDNA was found to contain several directly repeated sequence elements that include the simple telomere motif TTAGGG. Based on pairwise comparisons of LSU rRNA sequences, the time of divergence between the two myxomycete genera Didymium and Physarum was estimated.

Identification of cis-regulatory sequences in ascidian ribosomal DNA using a rapid filter-binding assay

Using 32P-labelled random primed ribosomal DNA (rDNA) from the ascidian, Herdmania momus, multiple and large-scale filter-binding assays were performed to identify cis-regulatory sequences interacting with H. momus oocyte germinal vesicle protein. A vacublot apparatus was used to isolate DNA-protein complexes, providing a means of filtering multiple binding reactions simultaneously and for isolating sufficient amounts of bound DNA for further investigations. DNA bound to the filter was used to identify unknown cis-elements in the rDNA by Southern-blot analysis. The trapped rDNA hybridized specifically to the intergenic spacer, a region which contains cis-regulatory sequences that interact with rDNA transcription factors in several other species. Gel shift analysis of intergenic spacer fragments and native Southwestern blots confirmed that cis-elements were localized in the rDNA intergenic spacer. In principle, this method allows for the rapid identification of cis-regulatory sequences within any large, cloned DNA fragment which interact with nuclear extract.