TREMATODE AND MONOGENEAN RIBOSOMAL-RNA ITS2 SECONDARY STRUCTURES SUPPORT A 4-DOMAIN MODEL

The secondary structure of rRNA internal transcribed spacer 2 is impor tant in the process of ribosomal biogenesis. Trematode ITS sequences a re poorly conserved and difficult to align for phylogenetic comparison s above a family level. Lf a conserved secondary structure can be iden tified, it carl be used to guide primary sequence alignments. ITS2 seq uences from 39 species were compared, These species span four orders o f trematodes (Echinostomiformes, Plagiorchiformes, Strigeiformes, and Paramphistomiformes) and one monogenean (Gyrodactyliformes). The seque nces vary in length from 251 to 431 bases, with an average GC content of 48%. The monogenean sequence could not be aligned with confidence t o the trematodes, Above the family level trematode sequences were alig nable from the 5' end for 139 bases. Secondary structure foldings pred icted a four-domain model. Three folding patterns were required for th e apex of domain B. The folding pattern of domains C and D varies for each family-The structures display a high GC content within stems. Bas es A and U are favored in unpaired regions and variable sites cluster. This produces a mosaic of conserved and variable regions with a struc tural conformation resistant ra change. Two conserved strings were ide ntified,one in domain B and the other in domain C, The first site can be aligned to a processing site identified in yeast and rat. The secon d site has been found in plants, and structural location appears to be important. A phylogenetic tree of the trematode sequences, aligned wi th the aid of secondary structures, distinguishes the four recognized orders.