Genome assemblies can form the basis of comparative analyses fostering insight into the evolutionary genetics of a parasite's pathogenicity, host–pathogen interactions, environmental constraints and invasion biology; however, the length and complexity of many parasite genomes has hampered the development of well-resolved assemblies. In order to improve Trichinella genome assemblies, the genome of the sylvatic encapsulated species Trichinella murrelli was sequenced using third-generation, long-read technology and, using syntenic comparisons, scaffolded to a reference genome assembly of Trichinella spiralis, markedly improving both. A high-quality draft assembly for T. murrelli was achieved that totalled 63·2 Mbp, half of which was condensed into 26 contigs each longer than 571 000 bp. When compared with previous assemblies for parasites in the genus, ours required 10-fold fewer contigs, which were five times longer, on average. Better assembly across repetitive regions also enabled resolution of 8 Mbp of previously indeterminate sequence. Furthermore, syntenic comparisons identified widespread scaffold misassemblies in the T. spiralis reference genome. The two new assemblies, organized for the first time into three chromosomal scaffolds, will be valuable resources for future studies linking phenotypic traits within each species to their underlying genetic bases.

An oligonucleotide mixture based on the 21 base pair repeat sequence of Plasmodium falciparum was covalently coupled to biotin and used as a probe to detect P. falciparum DNA. The limit of detection was 10 ng. This method was further developed as a fingerprint assay for parasite strain typing. After restrictian enzyme digestion, blotting and hybridization, distinct banding patterns were obtained for the strains tested and these were reproducible. In addition, discrete differences were found between PLF-3 S + /S-strains which may implicate genetic reorganization in the switching mechanism which occurs when parasites are passed from an intact to a splenectomized animal.

A genomic library of Entamoeba histolytica (pathogenic strain HM-1: IMSS) was screened to detect repetitive DNA clones other than those from the highly abundant ribosomal DNA (rDNA). One such clone (HMc) had a 2·3 kb insert which hybridized with the main genome and not the rDNA circle. Southern hybridization of E. histolytica genomic DNA, digested with EcoR I and probed with HMc, showed multiple bands. The banding pattern was identical in all axenic pathogenic strains tested. Differences, however, existed when the banding pattern of a pathogenic strain was compared with that of a non-pathogenic strain. HMc was present in about 25–30 copies per genome in strain HM-1: IMSS. Nucleotide sequence analysis of HMc revealed a partial open reading frame which hybridized with a 1·35 kb poly A+ transcript in Northern blots. The deduced amino acid sequence did not, however, show significant homology with known proteins. The HMc sequence was found only in E. histolytica as it hybridized with 5 different axenic strains of E. histolytica but did not recognize other closely related species of Entamoeba. It has thus the potential to be used as a species-specific DNA probe.

Two repetitive DNA sequences have been characterized from Schistosoma mansoni which were transcribed into mRNAs and translated to give two families of cross-reactive proteins. One DNA element, which was present as a 230 bp Pst I fragment was arranged in tandem arrays of at least 17 copies in the genome. The second element, which could be localized to a 1800 bp Pst I fragment, was dispersed in the genome. The 1800 bp repeat was found on the mRNA encoding the 45 kDa polypeptide precursor of a potential surface antigen. This precursor was post-translationally modified to give a 50 kDa antigen (Sm50) which was expressed from the cercaria to the adult worm and in the egg. However, a proportion of this antigen was differentially modified in females and eggs to give a 60 kDa form. Two copies of the 230 bp repeat and one copy of the 1800 bp repeat were found on a second cDNA clone. The antiserum raised against the fusion protein of this clone recognized a family of cross-reactive proteins ranging from 14 to 70 kDa in size. The members of this family were also differentially expressed between the sexes. Consequently, two families of antigens have been identified which were both encoded by repetitive DNA elements and whose members were both differentially expressed in adult male and female worms.

There is no logical or theoretical barrier to the proposition that organismal and cell signaling could transduce environmental signals into specific, beneficial changes in primary structure of noncoding DNA via repetitive element movement or mutation. Repetitive DNA elements, including transposons and microsatellites, are known to influence the structure and expression of protein-coding genes, and to be responsive to environmental signals in some cases. These effects may create fodder for adaptive evolution, at rates exceeding those observed for point mutations. In many cases, the changes are no doubt random, and fitness is increased through simple natural selection. However, some transposons insert at specific sites, and certain regions of the genome exhibit selectively and beneficially high mutation rates in a range of organisms. In multicellular organisms, this could benefit individuals in situations with significant potential for clonal expansion: early life stages or regenerative tissues in animals, and most plant tissues. Transmission of the change to the next generation could occur in plants and, under some circumstances, in animals.

As shown by RFLP analysis, there is a high variability in the β-tubulin gene region of Leishmania sp. Such variability has been used in the identification of these parasites, establishing differences between subgenera of New World Leishmania. We have found a region of 500 bp (β500) upstream of the coding region of the β-tubulin gene that is present in all strains tested belonging to the L. (Viannia) subgenus. This region apparently is a repetitive sequence and we have shown that it is specific to the Leishmania (Viannia) subgenus. This sequence has no homology with the genomic DNA isolated from either the species belonging to the L. (Leishmania) subgenus or other Kinetoplastida, such as Trypanosoma cruzi, T. brucei, Leptomonas samueli, or Crithidia fasciculata. The β500 sequence showed sufficient variation to be used as a molecular marker in the identification of parasites. We established inter- and intrasubgenus differentiation and were able to discriminate at the species level in the Vianna subgenus. A PCR assay confirmed the specificity of the β500 sequence.

The intergenic spacer of the ribosomal RNA gene array from the monogenean Gyrodactylus salaris was isolated using PCR amplification. PCR products were cloned and sequenced. Three different fragments of 0·63, 1·0 and 2·62 kb, were consistently obtained. These showed homology at the 5′ and 3′ termini but differed in their overall size and intervening sequence. The 5′ end showed homology to various 28S ribosomal RNA gene sequences, suggesting that this represented the 3′ terminus of the G. salaris 28S ribosomal RNA gene. A number of features common to other eukaryotic intergenic spacers were found in the longest sequence, including A + T rich sequences, palindromic sequences and tandemly repeated elements. Two regions of 23 bp sequences arranged in non-identical tandem repeats were identified. There were 9 repeats in both regions, separated by 81 bp of non-repetitive sequence. The repeat units from the two regions shared some similarity at their 3′ ends. The G. salaris intergenic spacer sequence was examined for sequence motifs involved in the transcription of the ribosomal RNA genes in other species. Several regions with homology to transcription start sites were identified.