The complete mitochondrial sequence of 17,030 bp was obtained from Echinostoma revolutum and characterized with those of previously reported members of the superfamily Echinostomatoidea, i.e. six echinostomatids, one echinochasmid, five fasciolids, one himasthlid, and two cyclocoelids. Relationship within suborders and between superfamilies, such as Echinostomata, Pronocephalata, Troglotremata, Opisthorchiata, and Xiphiditata, are also considered. It contained 12 protein-coding, two ribosomal RNA, 22 transfer RNA genes and a tandem repetitive consisting non-coding region (NCR). The gene order, one way-positive transcription, the absence of atp8 and the overlapped region by 40 bp between nad4L and nad4 genes were similar as in common trematodes. The NCR located between tRNAGlu (trnE) and cox3 contained 11 long (LRUs) and short repeat units (SRUs) (seven LRUs of 317 bp, four SRUs of 207 bp each), and an internal spacer sequence between LRU7 and SRU4 specifying high-level polymorphism. Special DHU-arm missing tRNAs for Serine were found for both tRNAS1(AGN) and tRNAS2(UCN). Echinostoma revolutum indicated the lowest divergence rate to E. miyagawai and the highest to Tracheophilus cymbius and Echinochasmus japonicus. The usage of ATG/GTG start and TAG/TAA stop codons, the AT composition bias, the negative AT-skewness, and the most for Phe/Leu/Val and the least for Arg/Asn/Asp codons were noted. Topology indicated the monophyletic position of E. revolutum to E. miyagawai. Monophyly of Echinostomatidae and Fasciolidae was clearly solved with respect to Echinochasmidae, Himasthlidae, and Cyclocoelidae which were rendered paraphyletic in the suborder Echinostomata.

Computer analysis of biological sequences often detects deviations from a random model. In the usual model, sequence letters are chosen independently, according to some fixed distribution over the relevant alphabet. Real biological sequences often contain simple repeats, however, which can be broadly characterized as multiple contiguous copies (usually inexact) of a specific word. This paper quantifies inexact simple repeats as local sums in a Markov additive process (MAP). The maximum of the local sums has an asymptotic distribution with two parameters (λ and k), which are given by general MAP formulas. The general MAP formulas are usually computationally intractable, but an essential simplification in the case of repeats permits λ and k to be computed from matrices whose dimension equals the size of the relevant alphabet. The simplification applies to some MAPs where the summand distributions do not depend on consecutive pairs of Markov states as usual, but on pairs with a fixed time-lag larger than one.

Schistosomes are parasites of considerable medical and veterinary importance and, therefore, all aspects of their biology have been intensively studied. In contrast, our knowledge of species of the largest genus, Trichobilharzia, is insufficient. Because morphological characterization of Trichobilharzia species provides a limited number of criteria for species determination, molecular data are required. In the present paper, we sequenced internal transcribed spacers ITS1 and ITS2, and 5·8S ribosomal RNA (rRNA) genes of 3 European Trichobilharzia species (T. regenti, T. szidati and T. franki). We showed that ITS1 and ITS2 sequences can be used in species identification. Repetitive elements were found in ITS1 of all 3 Trichobilharzia species; their number and length varied depending on the species. Phylogenetic analysis showed that the visceral T. franki is more related to the nasal T. regenti, than to the visceral T. szidati. The newly designed primer, which is specific for T. regenti, might be used as a tool for diagnosis of this potential pathogen.

In order to provide a better understanding of the interaction between the liver fluke (Fasciola hepatica) and the immune system of its mammalian host immunoreactive λ bacteriophage clones containing F. hepatica cDNA have been isolated. Plasmids from these clones were sequenced and found to encode a family of proteins containing certain common elementsThe nucleotide sequence data reported in this paper are available in the GenBank database with the accession number AF153056.. All the clones contained a coding repeating sequence (RRRXCA) which is conserved at the nucleic acid level followed by a non-repeating element coding for the C terminal used by the proteins which shows conservation of amino acids at certain positions. Antisera raised against a β-galactosidase fusion protein with one of these sequences as a terminal extension was used to localize the immunoreactive antigens. Binding was predominantly in the tegument of the juvenile fluke but was reduced in the adult tegument. The wall of the uterus showed strong reactivity in the adult. Rats immunized with the β- galactosidase fusion protein showed enhanced resistance to challenge infections. The role of these antigens in the host response to infection by F. hepatica is discussed.

All proteins of Saccharomyces cerevisiae have been compared to determine how frequently segments from one protein are present in other proteins. Proteins that are recently evolutionarily related were excluded. The most frequently present protein segments are long, tandem repetitions of a single amino acid. For some of these segments, up to 14% of all proteins in the genome were found to have similar peptides within them. These peptide segments may not be functional protein domains. Although they are the most common shared feature of yeast proteins, their ubiquity and simplicity argue that their probable function may be to simply serve as spacers between other protein motifs.

The sequences for the entire intergenic spacer (IGS) and 3′ end region of the large subunit (28S) ribosomal RNA gene are presented for Schistosoma intercalatum, S. haematobium and S. mansoni. The IGS was found to have at least 2 size formats for S. intercalatum and S. haematobium and the region for all 3 species contains numerous repeats and evidence of recombination. An A+T rich sequence found in S. intercalatum and S. haematobium is described and its possible function and origins are discussed. The amplification of this region by means of the polymerase chain reaction can be used to discriminate clearly between the 3 species involved in this study. The putative end of the 28S gene is identified.

The first internal transcribed spacer (ITS1) of the nuclear ribosomal DNA repeat was sequenced for members of the Schistosoma japonicum species complex (S. malayensis, S. mekongi and 2 geographical isolates of S. japonicum). The ITS1 is composed of 3 distinct regions: the 5′ end (23 nucleotides); a tract of approximately 90–140 nucleotides, which occurs up to 7 times in tandem, the number varying even within an individual in all species investigated in this study; the 3′ region (378 nucleotides), which lacks repeats. There is size and sequence variation among copies of the ITS1 repeat within a single individual. The relative abundances of size variants of ITS1 in S. japonicum have been ascertained by hybridizing genomic digests with an ITS1 probe. Multiple repeats and intra-individual variation in numbers and abundance of these is a feature of the Asian schistosomes, but not generally of African schistosomes. Possible reasons for this difference in ITS1 between African and Asian schistosomes are discussed. The ITS1 repeat sequences described for African schistosomes are different to, and cannot be aligned with, those from the Asian species described here, whereas the remainder of the ITS1 can be aligned quite easily.