Mitochondrial DNA diversity in nematodes

Distribution of large lungworms (Nematoda: Dictyocaulidae) in free-roaming populations of red deer Cervus elaphus (L.) with the description of Dictyocaulus skrjabini n. sp

Lungworms of the genus Dictyocaulus are causative agents of parasitic bronchitis in domestic and wild ungulates. This study investigates the distribution, morphology and genetic diversity of D. cervi and a new lungworm species, Dictyocaulus skrjabini n. sp. infecting red deer Cervus elaphus, fallow deer Dama dama and moose Alces alces in Poland and Sweden. The study was conducted on 167 red deer from Poland and on the DNA of lungworms derived from 7 fallow deer, 4 red deer and 2 moose collected in Sweden. The prevalence of D. cervi and D. skrjabini n. sp. in dissected red deer in Poland was 31.1% and 7.2%, respectively. Moreover, D. skrjabini n. sp. was confirmed molecularly in 7 isolates of fallow deer lungworms and 1 isolate of red deer lungworms from Sweden. Dictyocaulus skrjabini n. sp. was established based on combination of their distinct molecular and morphological features; these included the length of cephalic vesicle, buccal capsule (BC), buccal capsule wall (BCW), distance from anterior extremity to the nerve ring, the width of head, oesophagus, cephalic vesicle, BC and BCW, as well as the dimensions of reproductive organs of male and female. Additionally, molecular analyses revealed 0.9% nucleotide sequence divergence for 1,605 bp SSU rDNA, and 16.5–17.3% nucleotide sequence divergence for 642 bp mitochondrial cytB between D. skrjabini n. sp. and D. cervi, respectively, and 18.7–19% between D. skrjabini n. sp. and D. eckerti, which translates into 18.2–18.7% amino acid sequence divergence between D. skrjabini n. sp. and both lungworms.

Molecular typing of Strongyloides stercoralis in Latin America, the clinical connection

This study analysed Strongyloides stercoralis genetic variability based on a 404 bp region of the cox1 gene from Latin-American samples in a clinical context including epidemiological, diagnosis and follow-up variables. A prospective, descriptive, observational study was conducted to evaluate clinical and parasitological evolution after ivermectin treatment of 41 patients infected with S. stercoralis. Reactivation of the disease was defined both by clinical symptoms appearance and/or direct larvae detection 30 days after treatment or later. We described 10 haplotypes organized in two clusters. Most frequent variants were also described in the Asian continent in human (HP24 and HP93) and canine (HP24) samples. Clinical presentation (intestinal, severe, cutaneous and asymptomatic), immunological status and eosinophil count were not associated with specific haplotypes or clusters. Nevertheless, presence of cluster 1 haplotypes during diagnosis increased the risk of reactivation with an odds ratio (OR) of 7.51 [confidence interval (CI) 95% 1.38–44.29, P = 0.026]. In contrast, reactivation probability was 83 times lower if cluster 2 (I152V mutation) was detected (OR = 0.17, CI 95% 0.02–0.80, P = 0.02). This is the first analysis of S. stercoralis cox1 diversity in the clinical context. Determination of clusters during the diagnosis could facilitate and improve the design of follow-up strategies to prevent severe reactivations of this chronic disease.

Large lungworms (Nematoda: Dictyocaulidae) recovered from the European bison may represent a new nematode subspecies

Although the Dictyocaulus lungworm, the agent of dictyocaulosis, is one of parasitological threats to European bison, its systematic position remains unclear. The aim of the present study was to evaluate the morphological features of the lungworm and the pathological lesions it induces, and to analyse mitochondrial (mt) genetic markers for systematic and molecular epidemiological studies. The morphological findings indicate that Dictyocaulus lungworms of European bison can be distinguished from those of cattle on the basis of differences in buccal capsule wall length, total body length, and spicules length in males, all of which were significantly longer in those of European bison. Nucleotide diversity calculated from pairwise sequence alignments of partial cytochrome c oxidase subunit 1 (cox1), cytochrome B (cytB) and NADH dehydrogenase subunit 5 (nad5) of specimens from cattle and European bison varied from 1.7% for nad5, 2.1% for cytB, to 3.7% for cox1 gene. Thus, among the lungworms of European bison and cattle, nad5 and cytB were the most conserved proteins, whereas cox1 was the most diverse. The mt cytB marker gene may be a suitable candidate for distinguishing between the two genotypes, as nad5 demonstrated the greatest within-genus sequence variation. The lung tissue of infected European bison manifests signs of verminous pneumonia characterized by interstitial pneumonia, bronchitis and bronchiolitis. Therefore, it appears that European bison and cattle are infected with slightly diverged, morphologically-different, genotypes of D. viviparus, indicating they belong to two separate worm populations. We propose, therefore, that the lungworm of European bison should be classified as D. viviparus subsp. bisontis.

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European bison harbour a unique morphotype and genotype of Dictyocaulus viviparus.

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Mt cytB is an efficient genetic marker for studying large lungworms in bovids.

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European bison lungworm can be classified as D. viviparus subsp. bisontis.

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Pathologies induced by a newly described nematode subspecies mirrored those of lungworm in cattle.

Pinworms of the red howler monkey (Alouatta seniculus) in Colombia: Gathering the pieces of the pinworm-primate puzzle

Pinworms of primates are believed to be highly host specific parasites, forming co-evolutionary associations with their hosts. In order to assess the strength and reach of such evolutionary links, we need to have a broad understanding of the pinworm diversity associated with primates. Here, we employed an integrative taxonomic approach to assess pinworm diversity in red howler monkeys in Colombia. Molecular and morphological evidence validate the presence of at least four different species of Trypanoxyuris occurring in red howler monkeys: T. minutus, a widely distributed species, and three new species, T. seunimiii n. sp., T. kemuimae n. sp. and T. kotudoi n. sp. The mitochondrial COI gene and the 28S ribosomal gene were used for phylogenetic assessments through Bayesian inference. The three new species were morphologically distinct and formed reciprocally monophyletic lineages. Further molecular lineage subdivision in T. minutus and T. kotudoi n. sp. without morphological correspondence, suggests the potential scenario for the existence of cryptic species. Phylogenetic relationships imply that the different species of Trypanoxyuris occurring in each howler monkey species were acquired through independent colonization events. On-going efforts to uncover pinworm diversity will allow us to test the degree of host specificity and the co-phylogenetic hypothesis, as well as to further unravel the primate-pinworm evolutionary history puzzle.

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Three new species of pinworms from red howler monkeys are described.

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Phylogenetic analysis suggests the potential existence of cryptic species.

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Our results agree with pinworms of primates as highly host specific parasites.

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Trypanoxyuris species occurring in each howler species are not closely related.

Taxonomic status of Rhabdochona ictaluri (Nematoda: Rhabdochonidae) based on molecular and morphological evidence

The genus Rhabdochona includes more than 100 species infecting freshwater fishes in all zoogeographical regions of the world. In Mexico, 12 nominal species of Rhabdochona have been recorded. Of these, Rhabdochona ictaluri was originally described as a parasite of endemic catfishes of the family Ictaluridae; however, the species was later considered on morphological grounds as a junior synonym of Rhabdochona kidderi. In this study, newly sampled specimens of R. ictaluri were obtained from the type host and type locality and were used to perform a detailed morphological analysis and molecular phylogenetic inferences through one mitochondrial and two nuclear genes; data were used in an integrative taxonomy context to test the taxonomic status of R. ictaluri. This approach proved to be very useful to confirm the validity of this species, and robust species limits were established between these two putative species considering morphology, molecular data, host association, and biogeography.

Unveiling patterns of genetic variation in parasite–host associations: an example with pinworms and Neotropical primates

Patterns of genetic variation among populations can reveal the evolutionary history of species. Pinworm parasites are highly host specific and form strong co-evolutionary associations with their primate hosts. Here, we describe the genetic variation observed in four Trypanoxyuris species infecting different howler and spider monkey subspecies in Central America to determine if historical dispersal processes and speciation in the host could explain the genetic patterns observed in the parasites. Mitochondrial (cox1) and ribosomal (28S) DNA were analysed to assess genetic divergence and phylogenetic history of these parasites. Sequences of the 28S gene were identical within pinworms species regardless of host subspecies. However, phylogenetic analyses, haplotype relationships and genetic divergence with cox1 showed differentiation between pinworm populations according to host subspecies in three of the four Trypanoxyuris species analysed. Haplotype separation between host subspecies was not observed in Trypanoxyuris minutus, nor in Trypanoxyuris atelis from Ateles geoffoyi vellerosus and Ateles geoffoyi yucatanensis. Levels of genetic diversity and divergence in these parasites relate with such estimates reported for their hosts. This study shows how genetic patterns uncovered in parasitic organisms can reflect the host phylogenetic and biogeographic histories.

An assessment of the use of cox1 and cox3 mitochondrial genetic markers for the identification of Dictyocaulus spp. (Nematoda: Trichostrongyloidea) in wild ruminants

Lungworms of the genus Dictyocaulus Railliet and Henry, 1907 (Nematoda: Trichostrongyloidea) are the causative agents of parasitic bronchitis (dictyocaulosis, husk) of various ungulate hosts, including domestic and wild ruminants. Correct diagnosis of lungworm species and a better understanding of the transmission patterns of Dictyocaulus spp. are crucial in minimising the risk of its cross transmission between wildlife and livestock, and for the control of dictyocaulosis. The study was conducted on large lungworms collected from European bison, roe deer and red deer. The study resulted in 14 sequences of the partial cox1 region of Dictyocaulus spp. and 10 novel DNA sequences of partial cox3 region, including the first available mt cox3 sequence, of the roe deer lungworm (D. capreolus). The European bison was infected with bison genotype of D. viviparus, whereas red deer and roe deer were infected with D. cervi and D. capreolus respectively. The current study revealed that the cox3 nucleotide sequences of D. capreolus and D. viviparus were 100% homologous to each other. Our findings indicate that the mt cox3 gene does not serve as an efficient mt marker for systematic, population genetic or molecular epidemiological studies of Dictyocaulus lungworms.

Phylogenetic patterns of Haemonchus contortus and related trichostrongylid nematodes isolated from Egyptian sheep

Haemonchus contortus is a major parasite of small ruminants and its blood-feeding behaviour causes effects ranging from mild anaemia to death. Knowledge of the genetic variation within and among H. contortus populations can provide the foundation for understanding transmission patterns and aid in the control of haemonchosis. Adult male H. contortus were collected from three geographical regions in Egypt. The second internal transcribed spacer (ITS2) of nuclear ribosomal DNA was amplified using the polymerase chain reaction (PCR) and sequenced directly. The population genetic diversity and sequence variations were determined. Nucleotide sequence analyses revealed one genotype (ITS2) in all worms, without genetic differentiation. The similarity in population genetic diversity and genetic patterns observed among the three geographical regions could be attributed to possible movement between the sites. This is the first study of genetic variation in H. contortus in Egypt. The present results could have implications for the rapid characterization of H. contortus and other trichostrongyloid nematodes, and evaluation of the epidemiology of H. contortus in Egypt.

Genetic diversity and population genetics of large lungworms (Dictyocaulus, Nematoda) in wild deer in Hungary

Dictyocaulus nematode worms live as parasites in the lower airways of ungulates and can cause significant disease in both wild and farmed hosts. This study represents the first population genetic analysis of large lungworms in wildlife. Specifically, we quantify genetic variation in Dictyocaulus lungworms from wild deer (red deer, fallow deer and roe deer) in Hungary, based on mitochondrial cytochrome c oxidase subunit 1 (cox1) sequence data, using population genetic and phylogenetic analyses. The studied Dictyocaulus taxa display considerable genetic diversity. At least one cryptic species and a new parasite–host relationship are revealed by our molecular study. Population genetic analyses for Dictyocaulus eckerti revealed high gene flow amongst weakly structured spatial populations that utilise the three host deer species considered here. Our results suggest that D. eckerti is a widespread generalist parasite in ungulates, with a diverse genetic backround and high evolutionary potential. In contrast, evidence of cryptic genetic structure at regional geographic scales was observed for Dictyocaulus capreolus, which infects just one host species, suggesting it is a specialist within the studied area. D. capreolus displayed lower genetic diversity overall, with only moderate gene flow compared to the closely related D. eckerti. We suggest that the differing vagility and dispersal behaviour of hosts are important contributing factors to the population structure of lungworms, and possibly other nematode parasites with single-host life cycles. Our findings are of relevance for the management of lungworms in deer farms and wild deer populations.

Trypanoxyuris atelis and T. atelophora (Nematoda: Oxyuridae) in wild spider monkeys (Ateles geoffroyi) in tropical rain forest in Mexico: Morphological and molecular evidence

Two species of pinworms, Trypanoxyuris atelis and Trypanoxyuris atelophora were collected from the black-handed spider monkey (Ateles geoffroyi) in several localities across southeastern Mexico, representing the first record for both species in Mexican primates. Identification of pinworm species was based on morphological and molecular data. These pinworms are distinguished from other congeners, and from each other, by the buccal structure, the lateral alae, and the morphology of the oesophagus. Phylogenetic analyses based on sequences of the mitochondrial cytochrome c oxidase subunit 1 gene placed T. atelis as the sister species of Trypanoxyuris minutus, a parasite of the howler monkey Alouatta palliata, and T. atelophora as the sister species of T. microon, a parasite of the night monkey, Aotus azarae. These relationships were supported with high posterior probability values by Bayesian inference. Comparisons of additional pinworm taxa from Neotropical primates are needed to assess oxyurid diversity, and to better understand the evolutionary relationships among these nematodes and their primate hosts.

Absence of genetic structure in Baylisascaris schroederi populations, a giant panda parasite, determined by mitochondrial sequencing

Background

Infection with the parasitic nematode, Baylisascaris schroederi (Ascaridida: Nematoda), is one of the most important causes of death in giant pandas, and was responsible for half of deaths between 2001 and 2005. Mitochondrial (mt) DNA sequences of parasites can unveil their genetic diversity and depict their likely dynamic evolution and therefore may provide insights into parasite survival and responses to host changes, as well as parasite control.

Methods

Based on previous studies, the present study further annotated the genetic variability and structure of B. schroederi populations by combining two different mtDNA markers, ATPase subunit 6 (atp6) and cytochrome c oxidase subunit I (cox1). Both sequences were completely amplified and genetically analyzed among 57 B. schroederi isolates, which were individually collected from ten geographical regions located in three important giant panda habitats in China (Minshan, Qionglai and Qinling mountain ranges).

Results

For the DNA dataset, we identified 20 haplotypes of atp6, 24 haplotypes of cox1, and 39 haplotypes of atp6 + cox1. Further haplotype network and phylogenetic analyses demonstrated that B. schroederi populations were predominantly driven by three common haplotypes, atp6 A1, cox1 C10, and atp6 + cox1 H11. However, due to low rates of gene differentiation between the three populations, both the atp6 and cox1 genes appeared not to be significantly associated with geographical divisions. In addition, high gene flow was detected among the B. schroederi populations, consistent with previous studies, suggesting that this parasite may be essentially homogenous across endemic areas. Finally, neutrality tests and mismatch analysis indicated that B. schroederi had undergone earlier demographic expansion.

Conclusions

These results confirmed that B. schroederi populations do not follow a pattern of isolation by distance, further revealing the possible existence of physical connections before geographic separation. This study should also contribute to an improved understanding of the population genetics and evolutionary biology of B. schroederi and assist in the control of baylisascariasis in giant pandas.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-014-0606-3) contains supplementary material, which is available to authorized users.

Mitochondrial genomes of Anisakis simplex and Contracaecum osculatum (sensu stricto)--comparisons with selected nematodes

Anisakid nematodes parasitize mainly fish, marine mammals and/or fish-eating birds, and can be transmitted to a range of fish-eating mammals, including humans, where they can cause gastrointestinal disease linked to larval infection or allergic responses. In spite of the animal and human health significance of these parasites, there are still gaps in our understanding of the systematics, biology, epidemiology and ecology of anisakids. Mitochondrial (mt) DNA provides useful genetic markers for investigations in these areas, but complete mt genomic data have been lacking for most anisakids. In the present study, the mt genomes of Anisakis simplex sensu stricto and Contracaecum osculatum sensu stricto were amplified from genomic DNA by long-range polymerase chain reaction and sequenced using 454 technology. The circular mt genomes of these species were 13,926 and 13,823 bp, respectively, and each of them contained 12 protein-coding, 22 transfer RNA, and 2 ribosomal RNA genes consistent for members of the Ascaridida, Oxyurida, Spirurida, Rhabditida and Strongylida. These mt genomes provide a stepping-stone for future comparative analyses of a range of anisakids and a basis for reinvestigating their genetic relationships. In addition, these markers might be used in prospecting for cryptic species and exploring host affiliations.

An assessment of genetic variability in the mitochondrial cytochrome c oxidase subunit 1 gene of Cercopithifilaria sp. (Spirurida, Onchocercidae) from dog and Rhipicephalus sanguineus populations

This study investigates sequence variation in mitochondrial cytochrome c oxidase subunit 1 gene within Cercopithifilaria sp. recorded recently in Italy. Fourteen sequence types (haplotypes) were characterized for 163 (7.7%) amplicons from 2111 Genomic DNA samples prepared from skin samples from dogs and from Rhipicephalus sanguineus (ticks) from different geographical areas of the Mediterranean basin (i.e., Italy, Spain and Greece). The most prevalent sequence types represented haplotypes I (70.5%) and X (16.0%), followed by haplotype VIII (4.9%) and other 11 haplotypes (8.6%). Three haplotypes (II, V and VI) were found exclusively in ticks. The overall intraspecific nucleotide variation among pcox1 haplotypes ranged from 0.4 to 3.5% (mean = 1.6%), whereas a mean interspecific difference of 9.5% was detected as compared with other onchocercids. Phylogenetic analysis of the nucleotide sequence data showed a clustering of Cercopithifilaria sp. with the other Cercopithifilaria species (with strong statistical support) to the exclusion of other onchocercids. The number of haplotypes identified here might be explained by complex ecology and transmission patterns as well as the high mutation rate of mitochondrial DNA and/or inbreeding associated with hosts and their vectors.

The mitochondrial genome of Baylisascaris procyonis

Background

Baylisascaris procyonis (Nematoda: Ascaridida), an intestinal nematode of raccoons, is emerging as an important helminthic zoonosis due to serious or fatal larval migrans in animals and humans. Despite its significant veterinary and public health impact, the epidemiology, molecular ecology and population genetics of this parasite remain largely unexplored. Mitochondrial (mt) genomes can provide a foundation for investigations in these areas and assist in the diagnosis and control of B. procyonis. In this study, the first complete mt genome sequence of B. procyonis was determined using a polymerase chain reaction (PCR)-based primer-walking strategy.

Methodology/Principal Findings

The circular mt genome (14781 bp) of B. procyonis contained 12 protein-coding, 22 transfer RNA and 2 ribosomal RNA genes congruent with other chromadorean nematodes. Interestingly, the B. procyonis mtDNA featured an extremely long AT-rich region (1375 bp) and a high number of intergenic spacers (17), making it unique compared with other secernentean nematodes characterized to date. Additionally, the entire genome displayed notable levels of AT skew and GC skew. Based on pairwise comparisons and sliding window analysis of mt genes among the available 11 Ascaridida mtDNAs, new primer pairs were designed to amplify specific short fragments of the genes cytb (548 bp fragment) and rrnL (200 bp fragment) in the B. procyonis mtDNA, and tested as possible alternatives to existing mt molecular beacons for Ascaridida. Finally, phylogenetic analysis of mtDNAs provided novel estimates of the interrelationships of Baylisasaris and Ascaridida.

Conclusions/Significance

The complete mt genome sequence of B. procyonis sequenced here should contribute to molecular diagnostic methods, epidemiological investigations and ecological studies of B. procyonis and other related ascaridoids. The information will be important in refining the phylogenetic relationships within the order Ascaridida and enriching the resource of markers for systematic, population genetic and evolutionary biological studies of parasitic nematodes of socio-economic importance.

Complete mitochondrial genomes of Baylisascaris schroederi, Baylisascaris ailuri and Baylisascaris transfuga from giant panda, red panda and polar bear

Roundworms of the genus Baylisascaris are the most common parasitic nematodes of the intestinal tracts of wild mammals, and most of them have significant impacts in veterinary and public health. Mitochondrial (mt) genomes provide a foundation for studying epidemiology and ecology of these parasites and therefore may be used to assist in the control of Baylisascariasis. Here, we determined the complete sequences of mtDNAs for Baylisascaris schroederi, Baylisascaris ailuri and Baylisascaris transfuga, with 14,778 bp, 14,657 bp and 14,898 bp in size, respectively. Each mtDNA encodes 12 protein-coding genes, 22 transfer RNAs and 2 ribosomal RNAs, typical for other chromadorean nematodes. The gene arrangements for the three Baylisascaris species are the same as those of the Ascaridata species, but radically different from those of the Spirurida species. Phylogenetic analysis based on concatenated amino acid sequences of 12 protein-coding genes from nine nematode species indicated that the three Baylisascaris species are more closely related to Ascaris suum than to the three Toxocara species (Toxocara canis, Toxocara cati and Toxocara malaysiensis) and Anisakis simplex, and that B. ailuri is more closely related to B. transfuga than to B. schroeder. The determination of the complete mt genome sequences for these three Baylisascaris species (the first members of the genus Baylisascaris ever sequenced) is of importance in refining the phylogenetic relationships within the order Ascaridida, and provides new molecular data for population genetic, systematic, epidemiological and ecological studies of parasitic nematodes of socio-economic importance in wildlife.

An integrated pipeline for next-generation sequencing and annotation of mitochondrial genomes

Mitochondrial (mt) genomics represents an understudied but important field of molecular biology. Increasingly, mt dysfunction is being linked to a range of human diseases, including neurodegenerative disorders, diabetes and impairment of childhood development. In addition, mt genomes provide important markers for systematic, evolutionary and population genetic studies. Some technological limitations have prevented the expanded generation and utilization of mt genomic data for some groups of organisms. These obstacles most acutely impede, but are not limited to, studies requiring the determination of complete mt genomic data from minute amounts of material (e.g. biopsy samples or microscopic organisms). Furthermore, post-sequencing bioinformatic annotation and analyses of mt genomes are time consuming and inefficient. Herein, we describe a high-throughput sequencing and bioinformatic pipeline for mt genomics, which will have implications for the annotation and analysis of other organellar (e.g. plastid or apicoplast genomes) and virus genomes as well as long, contiguous regions in nuclear genomes. We utilize this pipeline to sequence and annotate the complete mt genomes of 12 species of parasitic nematode (order Strongylida) simultaneously, each from an individual organism. These mt genomic data provide a rich source of markers for studies of the systematics and population genetics of a group of socioeconomically important pathogens of humans and other animals.

The mitochondrial genomes of Ancylostoma caninum and Bunostomum phlebotomum--two hookworms of animal health and zoonotic importance

Background

Hookworms are blood-feeding nematodes that parasitize the small intestines of many mammals, including humans and cattle. These nematodes are of major socioeconomic importance and cause disease, mainly as a consequence of anaemia (particularly in children or young animals), resulting in impaired development and sometimes deaths. Studying genetic variability within and among hookworm populations is central to addressing epidemiological and ecological questions, thus assisting in the control of hookworm disease. Mitochondrial (mt) genes are known to provide useful population markers for hookworms, but mt genome sequence data are scant.

Results

The present study characterizes the complete mt genomes of two species of hookworm, Ancylostoma caninum (from dogs) and Bunostomum phlebotomum (from cattle), each sequenced (by 454 technology or primer-walking), following long-PCR amplification from genomic DNA (~20–40 ng) isolated from individual adult worms. These mt genomes were 13717 bp and 13790 bp in size, respectively, and each contained 12 protein coding, 22 transfer RNA and 2 ribosomal RNA genes, typical for other secernentean nematodes. In addition, phylogenetic analysis (by Bayesian inference and maximum likelihood) of concatenated mt protein sequence data sets for 12 nematodes (including Ancylostoma caninum and Bunostomum phlebotomum), representing the Ascaridida, Spirurida and Strongylida, was conducted. The analysis yielded maximum statistical support for the formation of monophyletic clades for each recognized nematode order assessed, except for the Rhabditida.

Conclusion

The mt genomes characterized herein represent a rich source of population genetic markers for epidemiological and ecological studies. The strong statistical support for the construction of phylogenetic clades and consistency between the two different tree-building methods employed indicate the value of using whole mt genome data sets for systematic studies of nematodes. The grouping of the Spirurida and Ascaridida to the exclusion of the Strongylida was not supported in the present analysis, a finding which conflicts with the current evolutionary hypothesis for the Nematoda based on nuclear ribosomal gene data.

The mitochondrial genome of Toxocara canis

Toxocara canis (Ascaridida: Nematoda), which parasitizes (at the adult stage) the small intestine of canids, can be transmitted to a range of other mammals, including humans, and can cause the disease toxocariasis. Despite its significance as a pathogen, the genetics, epidemiology and biology of this parasite remain poorly understood. In addition, the zoonotic potential of related species of Toxocara, such as T. cati and T. malaysiensis, is not well known. Mitochondrial DNA is known to provide genetic markers for investigations in these areas, but complete mitochondrial genomic data have been lacking for T. canis and its congeners. In the present study, the mitochondrial genome of T. canis was amplified by long-range polymerase chain reaction (long PCR) and sequenced using a primer-walking strategy. This circular mitochondrial genome was 14162 bp and contained 12 protein-coding, 22 transfer RNA, and 2 ribosomal RNA genes consistent for secementean nematodes, including Ascaris suum and Anisakis simplex (Ascaridida). The mitochondrial genome of T. canis provides genetic markers for studies into the systematics, population genetics and epidemiology of this zoonotic parasite and its congeners. Such markers can now be used in prospecting for cryptic species and for exploring host specificity and zoonotic potential, thus underpinning the prevention and control of toxocariasis in humans and other hosts.

Long PCR amplification of the entire mitochondrial genome from individual helminths for direct sequencing

Exploring mitochondrial (mt) genomes has significant implications for various fundamental research areas, including mt biochemistry and physiology, and, importantly, such genomes provide a rich source of markers for population genetics and systematic studies. Although some progress has been made, there is a paucity of information on mt genomes for many metazoan organisms, particularly invertebrates such as parasitic helminths, which relates mainly to the technical limitations associated with sequencing from tiny amounts of material. In this article, we describe a practical long PCR approach for the amplification and subsequent sequencing of the entire mt genome from individual helminths, which overcomes these limitations. The protocol includes the isolation of genomic DNA, long PCR amplification, electrophoresis and sequencing, and takes approximately 1-3 weeks to carry out. The present user-friendly, cost-effective approach has demonstrated utility to the study of a range of parasites, and has the potential to be applied to a wide range of organisms.

Microsatellite analysis reveals marked genetic differentiation between Haemonchus contortus laboratory isolates and provides a rapid system of genetic fingerprinting

Many of the Haemonchus contortus isolates currently used for experimental work were originally derived from different regions of the world and are commonly exchanged between laboratories. In most cases, these are largely genetically uncharacterised other than the analyses conducted on specific genes of interest. We have used a panel of eight microsatellite markers to genetically characterise five different commonly used H. contortus isolates including MHco3 (ISE), the isolate chosen for full genome sequencing as part of the H. contortus genome project. There is an extremely high level of genetic differentiation between each of the isolates except the two which have a common origin, MHco1 (MOSI) and MHco3 (ISE). We have investigated the amplification of microsatellite markers from pooled DNA as a potential method for fingerprinting different isolates. Good estimates of the true allele frequencies can be made by amplification from either pooled adult DNA or bulk L3 DNA for seven out of the eight markers tested. Both single worm genotyping and bulk DNA fingerprinting revealed no genetic differentiation between adult worms in the host and larvae derived from faecal culture. Furthermore, none of the eight markers showed genetic changes when isolates were passaged through different individual hosts. Hence the microsatellite genotyping of bulk larval DNA samples provides a simple and rapid method to genetically define and monitor laboratory isolates, and to determine their relationship with particular field populations.

Population genetics of anthelmintic resistance in parasitic nematodes

A key aim of anthelmintic resistance research is to identify molecular markers that could form the basis of sensitive and accurate diagnostic tests. These would provide powerful tools to study the origin and spread of anthelmintic resistance in the field and to monitor strategies aimed at preventing and managing resistance. Molecular markers could also form the basis of routine diagnostic tests for use in surveillance and clinical veterinary practice. Much of the research conducted to date has focused on the investigation of possible associations of particular candidate genes with the resistance phenotype. In the future, as full parasite genome sequences become available, there will be an opportunity to apply genome-wide approaches to identify the genetic loci that underlie anthelmintic resistance. Both the interpretation of candidate gene studies and the application of genome-wide approaches require a good understanding of the genetics and population biology of the relevant parasites as well as knowledge of how resistance mutations arise and are selected in populations. Unfortunately, much of this information is lacking for parasitic nematodes. This review deals with a number of aspects of genetics and population biology that are pertinent to these issues. We discuss the possible origins of resistance mutations and the likely effects of subsequent selection on the genetic variation at the resistance-conferring locus. We also review some of the experimental approaches that have been used to test associations between candidate genes and anthelmintic resistance phenotypes and highlight implications for future genome-wide studies.

Macrogeographic population structure in a parasitic nematode with avian hosts

Much remains to be discovered about the population genetic structure of parasites, despite the importance of such knowledge to understanding the processes involved in the spread of drug resistance through populations. Here we present a study of population genetic diversity in Trichostrongylus tenuis, an avian parasitic nematode infecting both poultry and game birds, where anthelmintic use is common. We examined diversity of nicotinamide dehydrogenase subunit 4 (nad4) mtDNA sequences within and between seven locations: five in the UK (red grouse hosts), one in Iceland (domestic goose) and one in Norway (willow grouse). Within-UK comparisons showed high nucleotide diversity (pi=0.015, n=23) but no structure between locations (Phi(ST)=0.022, P=0.27), with over 97% of variation distributed within-hosts. The highest diversity was found in Iceland (pi=0.043, n=4), and the lowest in Norway (pi=0.003, n=4). Differentiation between countries was considerable (Phi(CT)=0.44, P<0.05), in spite of the potential mixing effects of gene flow via migrating wild hosts and the poultry trade. However, significant pairwise F(ST) values were found only between Norway and the other locations. Phylogenetic analysis provided statistical support for a separate clade for Norwegian samples only, with unresolved diversity leading to a star-shaped relationship between Icelandic and UK haplotypes. These results suggest that Norwegian T. tenuis are isolated, but that there is some connectivity between UK and Icelandic populations. Although anthelmintic resistance has not yet been reported for T. tenuis, the population structure is such that emerging resistance has the potential to spread by gene flow over a large geographic scale.

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.

Population genetics of the bovine/cattle lungworm (Dictyocaulus viviparus) based on mtDNA and AFLP marker techniques

Mitochondrial DNA (mtDNA) sequence data and amplified fragment length polymorphism (AFLP) patterns were compared for the lungworm Dictyocaulus viviparus, a nematode parasite of cattle. Eight individual D. viviparus samples from each of 8 herds in Sweden and 1 laboratory isolate were analysed, with the aim of describing the diversity and genetic structure in populations using different genetic markers on exactly the same DNA samples. There was qualitative agreement between the whole-genome AFLP data and the mtDNA sequence data, both indicating relatively strong genetic differentiation among the Swedish farms. However, the AFLP data detected much more genetic variation than did the mtDNA data, even after allowing for the different inheritance patterns of the markers, and indicated that there was much less differentiation among the populations. The mtDNA data therefore seemed to be more informative about the most recent history of the parasite populations, as the general patterns were less obscured by detailed inter-relationships among individual worms. The 4 mtDNA genes sequenced (1542 bp) showed consistent patterns, although there was more genetic variation in the protein-coding genes than in the structural RNA genes. Furthermore, there appeared to be at least 3 distinct genetic groups of D. viviparus infecting Swedish cattle, 1 of which was predominant and showed considerable differentiation between farms, but not necessarily within farms. Second, the 2 smaller genetic groups occurred on farms where the predominant group also occurred, suggesting that these farms have had multiple introductions of D. viviparus.

Mitochondrial genomes of parasitic nematodes – progress and perspectives

Mitochondria are subcellular organelles in which oxidative phosphorylation and other important biochemical functions take place within the cell. Within these organelles is a mitochondrial (mt) genome, which is distinct from, but cooperates with, the nuclear genome of the cell. Studying mt genomes has implications for various fundamental areas, including mt biochemistry, physiology and molecular biology. Importantly, the mt genome is a rich source of markers for population genetic and systematic studies. To date, more than 696 mt genomes have been sequenced for a range of metazoan organisms. However, few of these are from parasitic nematodes, despite their socioeconomic importance and the need for fundamental investigations into areas such as nematode genetics, systematics and ecology. In this article, we review knowledge and recent progress in mt genomics of parasitic nematodes, summarize applications of mt gene markers to the study of population genetics, systematics, epidemiology and evolution of key nematodes, and highlight some prospects and opportunities for future research.

Analysis of genetic variability within Thelazia callipaeda (Nematoda: Thelazioidea) from Europe and Asia by sequencing and mutation scanning of the mitochondrial cytochrome c oxidase subunit 1 gene

This study investigated genetic variability within the 'eyeworm'Thelazia callipaeda (Nematoda: Thelazioidea) from Europe and Asia by polymerase chain reaction (PCR)-coupled sequencing and mutation scanning of the mitochondrial cytochrome c oxidase subunit 1 gene (cox 1). Eight different sequence variants of cox 1 (haplotypes) were determined for the 50 individual adult specimens of T. callipaeda (from dogs, foxes or cats from Italy, Germany and the Netherlands and from dogs from China and Korea). Nucleotide variation (0.3--2%) was detected at 23 of 649 positions in the cox 1. Six of these positions were invariable among all 37 individuals from Europe and among the 13 individuals from Asia (irrespective of host origin) but differed (five G<-->A and one C<-->T changes) between Europe and Asia. PCR-based single-strand conformation polymorphism (SSCP) analysis of the most variable portion (v-cox 1) of the cox 1 was validated (for a subset of samples) as a tool to rapidly screen for genetic (haplotypic) variability. The results for the SSCP analysis and sequencing were concordant, indicating that the mutation scanning approach provides a useful tool for investigating the population genetics and molecular ecology of T. callipaeda.

Testing the hypothesis of recent population expansions in nematode parasites of human-associated hosts

It has been predicted that parasites of human-associated organisms (eg humans, domestic pets, farm animals, agricultural and silvicultural plants) are more likely to show rapid recent population expansions than are parasites of other hosts. Here, we directly test the generality of this demographic prediction for species of parasitic nematodes that currently have mitochondrial sequence data available in the literature or the public-access genetic databases. Of the 23 host/parasite combinations analysed, there are seven human-associated parasite species with expanding populations and three without, and there are three non-human-associated parasite species with expanding populations and 10 without. This statistically significant pattern confirms the prediction. However, it is likely that the situation is more complicated than the simple hypothesis test suggests, and those species that do not fit the predicted general pattern provide interesting insights into other evolutionary processes that influence the historical population genetics of host-parasite relationships. These processes include the effects of postglacial migrations, evolutionary relationships and possibly life-history characteristics. Furthermore, the analysis highlights the limitations of this form of bioinformatic data-mining, in comparison to controlled experimental hypothesis tests.

Molecular ecology of parasites: elucidating ecological and microevolutionary processes

We review studies that have used molecular markers to address ecological and microevolutionary processes in parasites. Our goal is to highlight areas of research that may be of particular interest in relation to the parasitic lifestyle, and to draw attention to areas that require additional study. Topics include species identification, phylogeography, host specificity and speciation, population genetic structure, modes of reproduction and transmission patterns, and searching for loci under selection.

Phylogeography of a nematode (Heligmosomoides polygyrus) in the western Palearctic region: persistence of northern cryptic populations during ice ages?

This study establishes the continental phylogeographical pattern of a European nematode, Heligmosomoides polygyrus (Dujardin, 1845; Heligmosomoidea). We sequenced 687 base pairs of the mitochondrial DNA (mtDNA) cyt b gene for 136 individuals collected in 22 localities. The results revealed that H. polygyrus populations are separated into five major units corresponding to the Italian, northern European (Denmark and Ireland), Iberian, western European, and Balkan populations. Different subclades were also observed within the first two groups. Based on the rate of molecular evolution of H. polygyrus cyt b gene-estimated to 3.5%-3.7% divergence per million years (Myr) in a previous study--the isolation time of the five clades was estimated between 2.5 +/- 0.24 and 1.5 +/- 0.23 million years ago. Moreover, H. polygyrus presents a higher genetic variability in the Mediterranean peninsulas as compared to northwestern Europe, highlighting the role of these regions as refuge areas. Like its specific host, the wood mouse Apodemus sylvaticus, H. polygyrus' pattern of postglacial recolonization of northwestern Europe was initiated from Iberian populations, while Italian and Balkan populations did not expand to the north. The results also suggest the existence of forested and temperate refuges in the southern British Isles during the Quaternary. Finally, the genetic diversity as well as the level of genetic divergence between the lineages of H. polygyrus are compared to those observed in other vertebrate and invertebrate phylogeographical studies: the existence of highly differentiated lineages in H. polygyrus (5%-10% of genetic divergence) highlights that the effects of Pleistocene climate changes on free-living organisms are also reflected in their obligate parasites.

A parasite reveals cryptic phylogeographic history of its host

This study compares the continental phylogeographic patterns of two wild European species linked by a host-parasite relationship: the field mouse Apodemus sylvaticus and one of its specific parasites, the nematode Heligmosomoides polygyrus. A total of 740 base pairs (bp) of the mitochondrial cytochrome b (cyt b) gene were sequenced in 122 specimens of H. polygyrus and compared with 94 cyt b gene sequences (974 bp) previously acquired for A. sylvaticus. The results reveal partial spatial and temporal congruences in the differentiation of both species' lineages: the parasite and its host present three similar genetic and geographical lineages, i.e. Western European, Italian and Sicilian, and both species recolonized northwestern Europe from the Iberian refuge at the end of the Pleistocene. However, H. polygyrus presents three particular differentiation events. The relative rate of molecular evolution of the cyt b gene was estimated to be 1.5-fold higher in the parasite than in its host. Therefore, the use of H. polygyrus as a biological magnifying glass is discussed as this parasite may highlight previously undetected historical events of its host. The results show how incorporating phylogeographic information of an obligate associate can help to better understand the phylogeographic pattern of its host.

Host isolation and patterns of genetic variability in three populations of Teladorsagia from sheep

We have used a mitochondrial marker to explore the population genetics of an economically important parasite of sheep, Teladorsagia. We examined diversity within and between parasites from three very different host populations, as well as within and between individual hosts. One of our study populations, the Soay sheep on Hirta, St Kilda, is unusually isolated with no sheep having been introduced to the island since 1932. Worm haplotypes from Hirta were compared with those from two other host populations. Remarkably, despite its historical isolation the Hirta population shows similar levels of within-population diversity to the other study populations. No divergence between the three Teladorsagia populations was found, consistent with gene flow between the populations. The high diversity within Teladorsagia populations provides compelling evidence that this variability is a general feature of parasitic nematode populations. Such diversity may be caused by high effective population size, coupled with an increased mutation rate for mtDNA, which has important implications for the spread of anthelmintic resistance in nematode populations.

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.

Cytochrome oxidase c subunit 1 polymorphisms show significant differences in distribution between a laboratory maintained population and a field isolate of Cooperia oncophora

A 474 bp fragment of the mitochondrial cytochrome oxidase c subunit 1 (cox1) of Cooperia oncophora was cloned and sequenced. The overall nucleotide diversity of the cox1 fragment varied from 0.5 to 2.0% between individuals. Two nucleotide substitutions were found within two RsaI endonuclease restriction sites and were used in a PCR-based restriction fragment length polymorphism (PCR-RFLP) assay to asses the intra-population variation of C. oncophora. Testing 816 individuals revealed the existence of three different haplotypes, having either both (type I) or only one (types II and III) RsaI site. Laboratory maintained individuals obtained at different time points after infection showed no significant difference in the distribution of the three haplotypes. Neither was there a difference in the distribution between male and female worms, confirming that the mitochondrial genome of C. oncophora is also maternally inherited. Nevertheless, there was a significant difference in the prevalence of the RsaI point mutation in the cox1 gene between the laboratory maintained population of C. oncophora and a Dutch field isolate, indicating that these RFLPs can be used to study genetic variation within or among C. oncophora populations.

Long PCR-based amplification of the entire mitochondrial genome from single parasitic nematodes

Mitochondrial genome sequences provide useful markers for investigating population genetic structures because of their maternal inheritance and high evolutionary rates. There is, however, a paucity of information on mitochondrial genomes for many parasitic organisms, including nematodes, which appears to relate mainly to technical limitations and (for modestly funded laboratories) the cost associated with full mitochondrial genome sequencing. In this article, we describe a simple, relatively inexpensive long-PCR approach for the amplification (using two sets of primers) of the entire mitochondrial genome from individual parasitic nematodes for subsequent sequencing, which overcomes these limitations. We employed two species of human hookworm (Ancylostoma duodenale and Necator americanus; order Strongylida) to establish the long-PCR conditions, and then extended its use to a number of other species of parasitic nematode of the class Secernentea (orders Strongylida, Ascaridida and Rhabditida). The long-PCR method for the amplification of the entire mitochondrial genome from single nematodes, coupled with direct sequencing of amplicons, provides a useful tool for the comparative analysis of genome organisation and evolution of a range of nematode groups. It also creates a platform for molecular ecological and population genetic studies.

Microsatellite DNA: a tool for population genetic analysis

Microsatellite deoxyribonucleic acid repeats provide a source of high variability that makes them ideal for use in studies requiring such molecular markers, including large population studies and genetic typing of individuals for kinship investigations. This paper provides reviews of the use of such markers in parasitology. Most studies to date have been carried out using protozoan and vector species. Recent investigations have, however, demonstrated their usefulness in the study of helminths, illustrating their ability to distinguish between individuals within hosts as well as from different hosts. The detection of microsatellites within parasites has provided a tool that will prove invaluable in parasitology and should lead to significant advances in our understanding of the processes that affect the organisms' population genetic structure.

Applications of single-strand conformation polymorphism (SSCP) to taxonomy, diagnosis, population genetics and molecular evolution of parasitic nematodes

The analysis of genetic variation in parasitic nematodes has important implications for studying aspects of taxonomy, diagnosis, population genetics, drug resistance and molecular evolution. This article highlights some applications of PCR-based single-strand conformation polymorphism (SSCP) for the analysis of sequence variation in individual parasites (and their populations) to address some of these areas. It also describes the principles and advantages of SSCP, and provides some examples for future applications in parasitology.

Genetic structure of populations of the human hookworm, Necator americanus, in China

Twenty-one to 58 individual Necator americanus were sampled from each of four villages in south-western China. Each nematode was sequenced for 588 bp of the mitochondrial cytochrome oxidase I gene. Allelic and nucleotide diversity varied two-fold among villages. Overall FST among populations was approximately 0.28, but this large value resulted from one low-diversity population that had a large genetic distance to the other three populations (F(ST) = 0.10 without that population). There was no correlation between geographical and genetic distance among sites. Thus, the genetic structure of this species in China may be characterized by variable effective sizes and uneven movement among sites. We discuss the implications of this genetic structure for vaccine development and the spread of drug resistance in human hookworms, and compare the genetic structure of hookworms with that of other nematodes.

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.

Mitochondrial genome diversity in parasites

Mitochondrial genomes have been sequenced from a wide variety of organisms, including an increasing number of parasites. They maintain some characteristics in common across the spectrum of life-a common core of genes related to mitochondrial respiration being most prominent-but have also developed a great diversity of gene content, organisation, and expression machineries. The characteristics of mitochondrial genomes vary widely among the different groups of protozoan parasites, from the minute genomes of the apicomplexans to amoebae with 20 times as many genes. Kinetoplastid protozoa have a similar number of genes to metazoans, but the details of gene organisation and expression in kinetoplastids require extraordinary mechanisms. Mitochondrial genes in nematodes and trematodes appear quite sedate in comparison, but a closer look shows a strong tendency to unusual tRNA structure and alternative initiation codons among these groups. Mitochondrial genes are increasingly coming into play as aids to phylogenetic and epidemiologic analyses, and mitochondrial functions are being recognised as potential drug targets. In addition, examination of mitochondrial genomes is producing further insights into the diversity of the wide-ranging group of organisms comprising the general category of parasites.