Characterization of a flatworm ribosomal RNA-encoding gene: promoter sequence and small subunit rRNA secondary structure

The ribosomal intergenic spacer (IGS) region in Schistosoma japonicum: structure and comparisons with related species

The intergenic spacer (IGS) between the 28S and 18S ribosomal RNA genes was PCR-amplified, sequenced and characterized for Schistosoma japonicum from mainland China, and compared with those of other Schistosoma species. Excluding flanking portions of the 28S and 18S genes, the IGS in the longest sequenced amplicon from S. japonicum IGS was 1457bp in length. However, intra-specific and intra-individual variation was noted. The IGS region of S. japonicum is strikingly different in structure from those of African Schistosoma species for which data are available. S. japonicum has a shorter IGS and largely lacks a long region of complex repeats seen in the African species. However, careful comparisons with African species highlighted the presence of a few shared repeat motifs that were not apparent from study of African species only. Such motifs presumably have functional significance. Discovery of such motifs may in general be aided by comparisons of relatively distant taxa rather than of sibling taxa.

Large expansion segments in 18S rDNA support a new sponge clade (Class Demospongiae, Order Haplosclerida)

Newly emerging molecular phylogenetic hypotheses involving the sponge Order Haplosclerida (Class Demospongiae) are far removed from traditional views on their classification using morphology. In the new grouping of marine haplosclerid taxa by molecular data all members of one highly supported clade were found to have three large indels in the 18S rRNA gene. These indels were not found in this gene in other marine haplosclerids or in any other demosponges analysed. These indels were found in the variable V4 and V7 region of the gene, had high GC contents and formed stable double stranded helices in the 18S rRNA secondary structure. These indels are very important synapomorphies, provide high support for an alternative taxonomic scheme and could help resolve the phylogeny of this order in conjunction with other phylogenetically informative characters.

Regulatory motifs are present in the ITS1 of some flatworm species

Particular sequence motifs can act as transcription regulators. Because the total regulatory effects of such motifs can be related to their abundance, their presence might be expected at locations within the genome where sequences are repeated. Multiple repeats that vary in number among individuals occur within the ribosomal first internal transcribed spacer (ITS1) in some species in three trematode genera: Paragonimus, Schistosoma and Dolichosaccus. In all of these genera we found in ITS1, sequences identical to known enhancer motifs. We also searched for, and identified, known regulatory motifs in published ITS1 sequences of other parasitic flatworms including Echinostoma spp. (Trematoda) and Echinococcus spp. (Cestoda) which lack multiple repeats in ITS1. We present three lines of evidence that this widespread occurrence of such motifs within the ITS1 of parasitic flatworms may indicate a functional role in regulating tissue- or stage-specific transcription of ribosomal genes. First, these motifs are identical to ones whose functional roles have been established using in vitro assays of transcriptional rates. Second, in all 18 species investigated here, between one and three different regulatory motifs were identified. In 14 of these 18 species, the probability that at least one of these motifs occurred because of the random assortment of bases within the regions investigated was 10% or less. In 12 of these 14 species, the probability was 5% or less. Third, the evolutionary divergence of flatworm species investigated is quite ancient. Therefore, the interspecific distribution of motifs observed here, in a rapidly evolving region such as ITS1, is unlikely to be attributable solely to shared evolutionary histories. These results, therefore, suggest a broader functional role for the ITS1 than previously thought.

Molecular evolution of the small subunit ribosomal DNA in woodlice (Crustacea, Isopoda, Oniscidea) and implications for Oniscidean phylogeny

The small subunit ribosomal DNA (ssu rDNA) of 13 isopods was sequenced. The entire length of the ribosomal gene is unusually long, resulting from the presence of five expansion elements accounting for more than 40% of the gene. We found that in terrestrial isopods the length of the ssu rDNA ranges from 2414 bp (Ligidium hypnorum) to 3537 bp (Cubaris murina). This is the longest metazoan ssu rDNA reported to date. The conserved regions are highly informative for analysis of the early nodes of the tree, whereas the variable expansion elements are better suited to reconstruction of the branching pattern between closely related taxa. The suggested relationship among Synochaeta, Crinochaeta, and Diplochaeta based on the conserved regions confirms that based on previous morphological analyses. In contrast, the phylogeny within the Crinochaeta based on the entire ssu rDNA including the variable domains is in conflict with that based on most of the morphological analyses. The phylogenetic analyses of the ssu rDNA support a repeated independent evolution of the three different types of pleopodal lungs in the Crinochaeta.