Polymorphic DNA markers in the genome of parasitic nematodes

Genetic Diversity and Population Structure of Haemonchus contortus

Haemonchus contortus is one of the most successful and problematic livestock parasites worldwide. From its apparent evolutionary origins in sub-Saharan Africa, it is now found in small ruminants in almost all regions of the globe, and can infect a range of different domestic and wildlife artiodactyl hosts. It has a remarkably high propensity to develop resistance to anthelmintic drugs, making control increasingly difficult. The success of this parasite is, at least in part, due to its extremely high levels of genetic diversity that, in turn, provide a high adaptive capacity. Understanding this genetic diversity is important for many areas of research including anthelmintic resistance, epidemiology, control, drug/vaccine development and molecular diagnostics. In this article, we review the current knowledge of H. contortus genetic diversity and population structure for both field isolates and laboratory strains. We highlight the practical relevance of this knowledge with a particular emphasis on anthelmintic resistance research.

Characterisation ofLymnaea cubensis,L. viatrixandL. neotropican. sp., the main vectors ofFasciola hepaticain Latin America, by analysis of their ribosomal and mitochondrial DNA

Although, in the endemic areas throughout the world, human fascioliasis presents varying patterns in its epidemiology, the species of lymnaeid snail that act as intermediate hosts and vectors are always crucial in the transmission of the causative parasites. Species in the Galba/Fossaria group of snails, such as Lymnaea cubensis, L. viatrix var. A ventricosa, L. viatrix var. B elongata and Galba truncatula, appear to be frequently involved in the transmission of Fasciola hepatica in Central and South America, although specific classification within this morphologically and anatomically confusing group is often very difficult. To explore the potential use of molecular analyses in the identification of vector snails, regions of the ribosomal DNA - the small subunit (18S) gene and internal transcribed spacers (ITS-2 and ITS-1) - and of the mitochondrial DNA - the cytochrome c oxidase subunit I (COI) - of wild-caught lymnaeid snails of L. cubensis, L. viatrix var. A ventricosa, L. viatrix var. B elongata and G. truncatula have been sequenced. The samples of the Latin American species included specimens from the respective type localities. The genetic distances observed and the results of phylogenetic analyses demonstrate that two different species exist within L. viatrix. Lymnaea neotropica n. sp. (=L. viatrix var. B elongata) is here proposed for specimens from Lima, Peru, and is differentiated from L. viatrix (=L. viatrix var. A ventricosa), L. cubensis and G. truncatula. The data collected on the 18S ribosomal-RNA gene indicate that the snails investigated may cover more than one supraspecific taxon. The ITS-2, ITS-1 and COI nucleotide sequences are clearly useful markers for the differentiation of these morpho-anatomically similar lymnaeid species. The numerous microsatellite repeats found within ITS-2 are potential tools for differentiation at population level.

Populations, hybrids and the systematic concepts of species and subspecies in Chagas disease triatomine vectors inferred from nuclear ribosomal and mitochondrial DNA

In Chagas disease, triatomine vectors are the main target for control measures because of the absence of effective drugs. The broad usefulness of nuclear rDNA and mtDNA sequences explains why triatomine studies using these markers have increased so pronouncedly in recent years. This indicates the appropriateness of an updated review about these molecular markers, concentrating on aspects useful for research on Chagas disease vectors. A comparative analysis is presented on the efficiency, weight of their different characteristics, limitations and problems of each of the different DNA markers in the light of the results obtained in studies on populations, hybrids, subspecies and species of the subfamily Triatominae. The use of a standardized composite haplotype code nomenclature for both nuclear rDNA and mtDNA markers is strongly encouraged to avoid difficulties in comparative studies. Triatomine aspects related to concerted evolution, microsatellites, minisatellites and insertions/deletions in nuclear rDNA and silent/non-silent mutations, pseudogenes and weaknesses of partial sequences in mtDNA are analysed. Introgression and hybrids, nuclear and mitochondrial DNA strengths, and compared evolutionary rates of nuclear rDNA and mtDNA in triatomines are discussed. Many conclusions are obtained thanks to the availability, for the first time in triatomines, of a complete sequence of a protein-coding mtDNA gene as ND1 from very numerous triatomine species covering from different populations of a species up to members belonging to different tribes. The evolutionary rates of each nuclear rDNA marker and mtDNA marker are analysed by comparison at subspecies level (intrapopulational, interpopulational, between morphs, and between subspecies) and species level (close and distant species of the same genus, species of different genera, and species of different tribes). Weaknesses of mtDNA for systematic-taxonomic purposes detected recently and newly in insects and triatomines, respectively, are discussed in detail. Emphasis is given to taxonomic units and biological entities presenting well-known problematics, both from the systematic-taxonomic and/or epidemiological-control points of view, as well as to molecular situations which can give rise to erroneous conclusions. All these aspects constitute the background on which the key question about the systematic concepts of species and subspecies in triatomines is focused. The global purpose is to facilitate future work on triatomines by highlighting present gaps, how better choice the appropriate markers, and marker aspects which should be taken into account. Key characteristics as alpha, CI and transformation rate matrices ought to be obtained and noted to get appropriate results and allow correct interpretations. The main aim is to offer a baseline for future fundamental research on triatomines and applied research on transmission, epidemiology and control measures related to Chagas disease vectors.

Genomic variability within laboratory and wild isolates of the trichostrongyle mouse nematodeHeligmosomoides polygyrus

PCR-RFLP techniques have been used to characterize wild and laboratory isolates of the trichostrongyle nematodeHeligmosomoides polygyrusfrom the wood mouseApodemus sylvaticusand the laboratory mouseMus musculusrespectively. Both isolates can be distinguished by eight endonuclease digestions of the ITS region of the rDNA repeat namely,AluI,DdeI,HpaII,HaeIII,HinfI,HhaI,PvuII andSalI. In two of the digests,HinfI andRsaI, a minor polymorphism was observed in the wild isolate ofH. polygyruswhich has been cultured in laboratory-bredA. sylvaticusfor several generations when compared withH. p. polygyrusfrom wildA. sylvaticus. A minor polymorphism was also identified in further wild isolates ofH. polygyruscollected fromA. sylvaticusin a field site in Egham, Surrey. However no evidence of polymorphism was observed in the laboratory isolate ofH. polygyrusfrom the CD1 strain ofM. musculusand the laboratory-bredA. sylvaticus. Reasons for this are discussed and further studies on the population genetics ofH. polygyrusare suggested.

Reviewing lymnaeid vectors of fascioliasis by ribosomal DNA sequence analyses

Snails of the family Lymnaeidae are of great parasitological importance due to the numerous helminth species they transmit, mainly trematodiases (such as fascioliasis) of considerable medical and veterinary impact. The present knowledge of the genetics and host-parasite relationships of this gastropod group is far from adequate. Fascioliasis is caused by two species, Fasciola hepatica and F. gigantica, which, as in the case of other trematodes, show a marked snail host specificity. Many lymnaeid species involved in fascioliasis transmission still show a confused systematic-taxonomic status. The need for tools to distinguish and characterize species and populations of lymnaeids is evident and the present review concerns new molecular tools developed in recent years using nuclear ribosomal DNA sequences. The small subunit or 18S gene and the internal transcribed spacers ITS-2 and ITS-1 are analysed and evaluated as markers for taxon differentiation and relationships within the Lymnaeidae from genus and species levels to subspecies and population levels. rDNA sequence differences and genetic distances, and their value for reconstructing phylogenetic trees using different methods are considered. Nuclear rDNA sequences are appropriate tools on which to base a review of the systematics and taxonomy of the family Lymnaeidae, without excluding other valuable snail characteristics already available. A reconstruction of the lymnaeid system towards a more natural classification will undoubtedly be helpful in understanding parasite transmission and epidemiological features as well the dispersion of an emerging-reemerging disease such as fascioliasis. Nomenclature for nuclear rDNA genotyping in lymnaeids includes the main rDNA sequence regions able to furnish important information on interspecific differentiation and grouping as well as intraspecific variability of lymnaeid species. The composite haplotype code includes the rDNA markers arranged in order according to their well-known usefulness, in its turn related to their respective, more or less rapid evolutionary ratios, to distinguish between different taxonomic levels, from supraspecific taxa to the species level and up to the population level.

Molecular tools--advances, opportunities and prospects

Modern molecular technologies are having a substantial impact in many fundamental and applied areas of parasitology. In particular, polymerase chain reaction (PCR)-coupled approaches have found broad applicability because their sensitivity permits the enzymatic amplification of gene fragments from minute quantities of nucleic acids from tiny amounts of parasite material. Also, high-resolution electrophoretic and genomic methods are finding increased utility. This paper briefly discusses some developments and applications of DNA methods to parasites and highlights their usefulness or potential for those of veterinary importance. Selected examples of applications with implications in fundamental (systematics, population genetics, epidemiology and ecology) and applied (diagnosis, prevention and control) areas are presented. The focus is mainly on tools for the accurate identification of parasitic nematodes and protozoa of socio-economic importance, the diagnosis of infections and the detection of genetic variability using PCR-coupled mutation scanning technology.

Genetic analysis of inbreeding of two strains of the parasitic nematode Haemonchus contortus

Haemonchus contortus is a sheep parasitic nematode that causes severe economic losses. Previous studies have indicated a high degree of genetic heterogeneity, which is hardly affected by selection for drug resistance. As a tool for the analysis of the population dynamics of H. contortus and its response to drug resistance, we designed a strategy to study the inbreeding of a benzimidazole-sensitive and a benzimidazole-resistant strain. After 15 generations, a theoretical inbreeding coefficient of 0.87 was achieved. The different stages of inbreeding were analysed using restriction fragment polymorphism, microsatellite variability and amplified fragment length polymorphism. Model-based clustering of the amplified fragment length polymorphism genotypes showed that the allele frequencies of the benzimidazole-resistant strain were stable during the last eight generations. In the sensitive strain a gradual shift of allele frequencies was observed, which led to a temporary increase of the genetic diversity around the eight generations.

Genetic diversity assessed by amplified fragment length polymorphism analysis of the parasitic nematode Dictyocaulus viviparus the lungworm of cattle

We have examined the population genetic structure in a collection of nine isolates of the parasitic lungworm Dictyocaulus viviparus. Eight of the isolates were sampled from cattle in geographically separated farms throughout south-central Sweden, and one isolate was a laboratory strain that has been maintained in experimentally infected calves for almost four decades. A total of 72 worms were examined, with eight individual worms from the same individual host representing each isolate. The genetic variation as revealed by amplified fragment length polymorphism analysis using four selective primer combinations was high. Depending on the primer combination a total of 66-79 restriction fragments were amplified, with 26-44 peaks of similar complexity from each of the isolates. The heterozygosity within populations was relatively small, as were the population mutation and immigration rates, which seemed to be in neutral equilibrium. The genetic diversity was therefore reasonably well structured in the field; and the laboratory isolate was quite distinct from the field samples. There was no relationship between the patterns of genetic diversity and the geographical proximity of the farms. The estimates of heterozygosity were much larger and more consistent than those previously estimated for this nematode species using mitochondrial sequencing, and the genetic structuring was thus much less pronounced and the gene flow greater. We attribute these differences in estimation to the broader sampling of loci available using amplified fragment length polymorphism markers, which may therefore constitute a superior technique for the study of patterns of lungworm diversity. Furthermore, the data estimating gene flow for D. viviparus was less than previously reported for closely related species in North America. This might be related to different rates of movements of infected hosts. It seems likely that lungworm infections are rather persistent on different farms, and the sudden outbreaks of disease that can be observed with host movements are most likely to be related to the introduction of susceptible stock.

EST sequencing of the parasitic nematode Haemonchus contortus suggests a shift in gene expression during transition to the parasitic stages

Expressed sequence tags from the parasitic nematode Haemonchus contortus were generated in order to identify anchor loci for comparative mapping between nematode genomes and candidate targets for future control measures. In total, 370 SL1 trans-spliced cDNAs from different developmental stages representing 195 different genes were partially sequenced. From these expressed sequence tags 50% were similar to genes with a known or predicted function and 19% were similar to nematode sequences with no ascribed function. From the first, free-living L1 and L3 stages relatively many cDNAs matched to housekeeping genes, and 11% (L1) or 23% (L3) of the encoded proteins were predicted to contain signal peptides. In contrast, no function could be ascribed to most of the cDNAs from the early L5 and adult parasitic stages, but for 30% (L5) or 55% (adult) of the encoded proteins a signal sequence was predicted. This limited analysis suggests that during the transition from the free-living to parasitic stages gene expression shifts towards the synthesis of less conserved extracellular proteins. These proteins offer the best perspectives for vaccine development and the development of anthelmintic drugs. In contrast, cDNAs from the first larval stages may be most suitable for comparative mapping with the free-living nematode Caenorhabditis elegans.

Genes and genomes of Necator americanus and related hookworms

The human hookworms (Necator americanus and Ancylostoma duodenale) infect over one billion people. The phylogenetic relationships of the human hookworms suggest independent acquisition of the human host. The hookworms probably have a haploid chromosome number n = 6, and an XX-XO sex determination mechanism is likely to be used. Genetic and molecular research on hookworms is in its infancy, but several important genes and gene products have already been identified. Of note are cathepsin genes, a family of secreted proteins known as Ancylostoma activation-associated proteins and a family of anticoagulants. The inception of an expressed sequence tag program on the human hookworm, N. americanus, promises to yield many new genes with novel functions in the biology of these important parasites.

Genomic and genetic research on bursate nematodes: significance, implications and prospects

Molecular genetic research on parasitic nematodes (order Strongylida) is of major significance for many fundamental and applied areas of medical and veterinary parasitology. The advent of gene technology has led to some progress for this group of nematodes, particularly in studying parasite systematics, drug resistance and population genetics, and in the development of diagnostic assays and the characterisation of potential vaccine and drug targets. This paper gives an account of the molecular biology and genetics of strongylid nematodes, mainly of veterinary socio-economic importance, indicates the implications of such research and gives a perspective on genome research for this important parasite group, in light of recent technological advances and knowledge of the genomes of other metazoan organisms.

Characterisation of a polymorphic Tc1-like transposable element of the parasitic nematode Haemonchus contortus

Hctc1, a member of the Tc1-family of transposable elements was isolated from the parasitic nematode Haemonchus contortus. Hctc1 is 1590 bp long, is flanked by 55 bp inverted repeats and carries a single open reading frame of a 340 amino acid transposase-like protein. Hctc1 is similar to Tc1 of Caenorhabditis elegans and elements Tcb1 and Tcb2 of Caenorhabditis briggsae in the inverted terminal repeats, the open reading frame, as well as the target insertion sequence. Furthermore, the copy number of Hctc1 is comparable with the Tc1 copy number in low copy strains of C. elegans. The sequence of Hctc1 is highly variable in H. contortus due to deletions, insertions and point mutations, with at least five distinct length variants of Hctc1. Most of the Hctc1 variation was within rather than between H. contortus populations. The high level of sequence variation is probably due to variation generally found for members of the Tc1-family, as well as a high background level of genetic variation of H. contortus.