Mitochondrial genomes of parasitic nematodes – progress and perspectives

Comparative mitochondrial genomics in Nematoda reveal astonishing variation in compositional biases and substitution rates indicative of multi-level selection

BACKGROUND

Nematodes are the most abundant and diverse metazoans on Earth, and are known to significantly affect ecosystem functioning. A better understanding of their biology and ecology, including potential adaptations to diverse habitats and lifestyles, is key to understanding their response to global change scenarios. Mitochondrial genomes offer high species level characterization, low cost of sequencing, and an ease of data handling that can provide insights into nematode evolutionary pressures.

RESULTS

Generally, nematode mitochondrial genomes exhibited similar structural characteristics (e.g., gene size and GC content), but displayed remarkable variability around these general patterns. Compositional strand biases showed strong codon position specific G skews and relationships with nematode life traits (especially parasitic feeding habits) equal to or greater than with predicted phylogeny. On average, nematode mitochondrial genomes showed low non-synonymous substitution rates, but also high clade specific deviations from these means. Despite the presence of significant mutational saturation, non-synonymous (dN) and synonymous (dS) substitution rates could still be significantly explained by feeding habit and/or habitat. Low ratios of dN:dS rates, particularly associated with the parasitic lifestyles, suggested the presence of strong purifying selection.

CONCLUSIONS

Nematode mitochondrial genomes demonstrated a capacity to accumulate diversity in composition, structure, and content while still maintaining functional genes. Moreover, they demonstrated a capacity for rapid evolutionary change pointing to a potential interaction between multi-level selection pressures and rapid evolution. In conclusion, this study helps establish a background for our understanding of the potential evolutionary pressures shaping nematode mitochondrial genomes, while outlining likely routes of future inquiry.

Potential new species of pseudaliid lung nematode (Metastrongyloidea) from two stranded neonatal orcas (Orcinus orca) characterized by ITS-2 and COI sequences

Knowledge about parasite species of orcas, their prevalence, and impact on the health status is scarce. Only two records of lungworm infections in orca exist from male neonatal orcas stranded in Germany and Norway. The nematodes were identified as Halocercus sp. (Pseudaliidae), which have been described in the respiratory tract of multiple odontocete species, but morphological identification to species level remained impossible due to the fragile structure and ambiguous morphological features. Pseudaliid nematodes (Metastrongyloidea) are specific to the respiratory tract of toothed whales and are hypothesized to have become almost extinct in terrestrial mammals. Severe lungworm infections can cause secondary bacterial infections and bronchopneumonia and are a common cause of mortality in odontocetes. DNA isolations and subsequent sequencing of the rDNA ITS-2 and mtDNA COI revealed nucleotide differences between previously described Halocercus species from common dolphin (H. delphini) and harbor porpoises (H. invaginatus) that were comparatively analyzed, pointing toward a potentially new species of pseudaliid lungworm in orcas. New COI sequences of six additional metastrongyloid lungworms of seals and porpoises were derived to elucidate phylogenetic relationships and differences between nine species of Metastrongyloidea.

Comprehensive Molecular Characterization of the Mitochondrial Genome of the Takin Lungworm Varestrongylus eleguneniensis (Strongylida: Protostrongylidae)

The takin lungworm Varestrongylus eleguneniensis (Strongylida: Protostrongylidae) causes lethal bronchopneumonia and represents severe threats to captive and wild populations. However, until now there has been very limited information available concerning the molecular epidemiology and evolutionary biology of V. eleguneniensis. Mitochondrial genomes (mtDNAs) can provide resources for investigations in these areas and, therefore, can assist with the surveillance and control of this lungworm. Herein, the complete mtDNA of V. eleguneniensis was sequenced and characterized with Illumina pipeline analyses. This circular genome (13,625 bp) encoded twelve protein-coding genes (PCGs), two rRNAs, and twenty-two tRNAs, with notable levels of AT and GC skews. Comparative genomics revealed a purifying selection among PCGs, with cox1 and nad6 having the lowest and the highest evolutionary rate, respectively. Genome-wide phylogenies showed a close relationship between V. eleguneniensis and Protostrongylus rufescens in Strongylida. Single gene (PCGs or rRNAs)-based phylogenies indicated that cox1 and nad5 genes shared the same family-level topology with that inferred from genomic datasets, suggesting that both genes could be suitable genetic markers for evolutionary and phylogenetic studies of Strongylida species. This was the first mtDNA of any member of the genus Varestrongylus, and its comprehensive molecular characterization represents a new resource for systematic, population genetic and evolutionary biological studies of Varestrongylus lungworms in wildlife.

The Mitochondrial Genome of Cylicocyclus elongatus (Strongylida: Strongylidae) and Its Comparative Analysis with Other Cylicocyclus Species

Simple Summary

We first report the complete mitochondrial genome of C. elongatus, which is circular and 13,875 bp in size, containing 12 PCGs, 22 tRNAs, 2 RNAs, and 2 NCRs. Comparative analyses and phylogenetic analyses show that C. elongatus is a member in Cylicocyclus based on mt genome data.

Abstract

Cylicocyclus elongatus (C. elongatus) is one of the species in Cylicocyclus, subfamily Cyathostominae, but its taxonomic status in Cylicocyclus is controversial. Mitochondrial (mt) genome is an excellent gene marker which could be used to address the taxonomy controversy. In the present study, the complete mt genome of C. elongatus was determined, and sequence and phylogenetic analyses were performed based on mtDNA data to determine the classification of C. elongatus. The circular complete mt genome of C.elongatus was 13875 bp in size, containing 12 protein-coding genes (12 PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and 2 non-coding regions (NCRs). The A + T content of C. elongatus complete mt genome was 76.64%. There were 19 intergenic spacers with lengths of 2–53 bp and 2 overlaps with lengths of 1–2 bp in the impact complete mt genome. ATT and TAA were the most common start and termination codons of 12 PCGs, respectively. Comparative analyses of mt genomes nucleotide sequence and amino acid sequence showed that there were higher identities between C. elongatus and five other Cylicocyclus, rather than with P. imparidentatum. Phylogenetic analyses based on concatenated nucleotide sequences of 12 PCGs of 23 species in the family Strongylidae showed that C. elongatus was closely related to Cylicocyclus species, rather than P. imparidentatum. We concluded that C. elongatus was a member in Cylicocyclus based on comparative and phylogenetic analyses of mt genome sequences. The data of the complete mt genome sequence of C. elongatus provide a new and useful genetic marker for further research on Cyathostominae nematodes.

Inverted base composition skews and discontinuous mitochondrial genome architecture evolution in the Enoplea (Nematoda)

Background

Within the class Enoplea, the earliest-branching lineages in the phylum Nematoda, the relatively highly conserved ancestral mitochondrial architecture of Trichinellida is in stark contrast to the rapidly evolving architecture of Dorylaimida and Mermithida. To better understand the evolution of mitogenomic architecture in this lineage, we sequenced the mitogenome of a fish parasite Pseudocapillaria tomentosa (Trichinellida: Capillariidae) and compared it to all available enoplean mitogenomes.

Results

P. tomentosa exhibited highly reduced noncoding regions (the largest was 98 bp), and a unique base composition among the Enoplea. We attributed the latter to the inverted GC skew (0.08) in comparison to the ancestral skew in Trichinellidae (-0.43 to -0.37). Capillariidae, Trichuridae and Longidoridae (Dorylaimida) generally exhibited low negative or low positive skews (-0.1 to 0.1), whereas Mermithidae exhibited fully inverted low skews (0 to 0.05). This is indicative of inversions in the strand replication order or otherwise disrupted replication mechanism in the lineages with reduced/inverted skews. Among the Trichinellida, Trichinellidae and Trichuridae have almost perfectly conserved architecture, whereas Capillariidae exhibit multiple rearrangements of tRNA genes. In contrast, Mermithidae (Mermithida) and Longidoridae (Dorylaimida) exhibit almost no similarity to the ancestral architecture.

Conclusions

Longidoridae exhibited more rearranged mitogenomic architecture than the hypervariable Mermithidae. Similar to the Chromadorea, the evolution of mitochondrial architecture in enoplean nematodes exhibits a strong discontinuity: lineages possessing a mostly conserved architecture over tens of millions of years are interspersed with lineages exhibiting architectural hypervariability. As Longidoridae also have some of the smallest metazoan mitochondrial genomes, they contradict the prediction that compact mitogenomes should be structurally stable. Lineages exhibiting inverted skews appear to represent the intermediate phase between the Trichinellidae (ancestral) and fully derived skews in Chromadorean mitogenomes (GC skews = 0.18 to 0.64). Multiple lines of evidence (CAT-GTR analysis in our study, a majority of previous mitogenomic results, and skew disruption scenarios) support the Dorylaimia split into two sister-clades: Dorylaimida + Mermithida and Trichinellida. However, skew inversions produce strong base composition biases, which can hamper phylogenetic and other evolutionary studies, so enoplean mitogenomes have to be used with utmost care in evolutionary studies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08607-4.

Complete Mitogenome of Cruznema Tripartitum Confirms Highly Conserved Gene Arrangement within Family Rhabditidae

Mitochondrial genomes have widely been used as molecular markers in understanding the patterns and processes of nematode evolution. The species in genus Cruznema are free-living bacterivores as well as parasites of crickets and mollusks. The complete mitochondrial genome of C. tripartitum was determined through high-throughput sequencing as the first sequenced representative of the genus Cruznema. The genome is comprised of 14,067 bp nucleotides, and includes 12 protein-coding, two rRNA, and 22 tRNA genes. Phylogenetic analyses based on amino acid data support C. tripartitum as a sister to the clade containing Caenorhabditis elegans and Oscheius chongmingensis. The analysis of gene arrangement suggested that C. tripartitum shares the same gene order with O. chongmingensis, Litoditis marina, Diplocapter coronatus, genus Caenorhabditis, and Pristionchus pacificus. Thus, the mitochondrial gene arrangement is highly conserved in the family Rhabditidae as well as some species in Diplogasteridae.

Sequencing and Reconstructing Helminth Mitochondrial Genomes Directly from Genomic Next-Generation Sequencing Data

We present a detailed method for extraction of high-molecular weight genomic DNA suitable for numerous DNA sequencing applications, and a straightforward in silico approach for reconstructing novel mitochondrial (mt) genomes directly from total genomic DNA extracts derived from next-generation sequencing (NGS) data sets. The in silico post-sequencing pipeline described is fast, accurate, and highly efficient, with modest memory requirements that can be performed using a standard desktop computer. The approach is particularly effective for obtaining mitochondrial genomes for species with little or no mitochondrial sequence information currently available and overcomes many of the limitations of traditional strategies. The described methodologies are also applicable for metagenomics sequencing from mixed or pooled samples containing multiple species and subsequent specific assembly of specific mitochondrial genomes.

The mitochondrial genome sequence analysis of Ophidascaris baylisi from the Burmese python (Python molurus bivittatus)

Ophidascaris species are parasitic roundworms that inhabit the python gut, resulting in severe granulomatous lesions or even death. However, the classification and nomenclature of these roundworms are still controversial. Our study aims to identify a snake roundworm from the Burmese python (Python molurus bivittatus) and analyze the mitochondrial genome. We identified this roundworm as Ophidascaris baylisi based on the morphology and cytochrome c oxidase subunit I (cox1) sequence. Ophidascaris baylisi complete mitochondrial genome was 14,784 bp in length, consisting of two non-coding regions and 36 mitochondrial genes (12 protein-coding genes, 22 tRNA genes, and two rRNA genes). The protein-coding genes used TTG, ATG, ATT, or TTA as start codons and TAG, TAA, or T as stop codons. All tRNA genes showed a TV-loop structure, except trnS1^AGN and trnS2^UCN revealed a D-loop structure. The mitochondrial large ribosomal subunit 16S (rrnL) and small ribosomal subunit 12S (rrnS) were 956 bp and 700 bp long, respectively. Phylogenetic analysis based on O. baylisi mitochondrial protein-coding genes demonstrated that O. baylisi clustered with the family Ascarididae members and was most closely related to Ophidascaris wangi. These results may enhance the nematode mitochondrial genome database and provide valuable molecular markers for further research on the taxonomy, phylogeny, and genetic relationships of Ophidascaris nematodes.

Genetic diversity and population structure of Haemonchus contortus in goats from Thailand

Haemonchus contortus is one of the most economically important parasitic nematodes affecting small ruminant livestock worldwide. This study was conducted to elucidate the genetic diversity and population structure of this nematode in Thailand based on mitochondrial DNA markers, the nicotinamide dehydrogenase subunit 4 (nad4) and the cytochrome c oxidase subunit 1 (cox1) genes. One hundred and thirty-six adult worms were obtained from 86 abomasa of slaughtered goats from 13 different localities in 5 regions of Thailand. Identification to the genus Haemonchus was done using morphology. DNA sequences of the nuclear ribosomal second internal transcribed spacer (ITS2) identified each specimen to species: three fixed nucleotide (SNP) differences distinguished H. contortus from H. placei. Genetic analysis defined 118 and 122 unique haplotypes in partial sequences of nad4 (alignment length 723 bp) and cox1 (645 bp) genes, respectively. Nucleotide diversities were 0.031 and 0.043 for nad4 and cox1 genes, respectively. Low genetic differentiation was observed among H. contortus samples from various provinces in Thailand. This is the first study on the genetic diversity and population structure of H. contortus of goats in Thailand. This study has provided insights into the transmission dynamics of this parasitic nematode, information which is essential for farm management and parasite control.

First report of Spirocerca lupi larva in dung beetles (Scarabaeus armeniacus) in the central region of Iran: A morphological and molecular identification

Dung beetles as detritivores insects, naturally use feces of vertebrates as foods and reproduction beds. This leads to frequent contacts between dung beetles and parasitic helminths. The current study was carried out to assess infections of dung beetles with larval stages of helminths in rural areas of Taleqan County, Alborz Province, Iran. A total number of 200 dung beetles were collected randomly in June 2017 from the highlands of Taleqan County. Beetles were dissected in normal saline and carefully studied using a stereomicroscope. Morphological characteristics of the recovered larvae were drawn using a camera lucida equipped microscope at 400× magnification. Then, genomic DNAs of the recovered larvae extracted and PCR amplifications of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene were carried out and the amplicons were sequenced. All collected dung beetles identified as Scarabaeus armeniacus from the Scarabaeidae family (55.5 % were male and 44.5 % female). Three females of the beetles have been found to be naturally infected with the third stage larvae of Spirocerca lupi. The average length and width of the larvae were 2.95 (2.81-3.15; CI 95 %) and 0.12 (0.1-0.15; CI 95 %) mm, respectively. The phylogenetic analysis showed that S. lupi belonged to a clade within the Spirocercidae family. In the current study, S. armeniacus introduced as a potential biological vector for transmission of S. lupi to vertebrates in the region. To the best of the authors' knowledge, this is the first report on the larval stages of S. lupi in S. armeniacus.

The complete mitogenome of Toxascaris leonina from the Siberian tiger (Panthera tigris altaica)

Toxascaris leonina is a polyxenical parasite and commonly found in canids and felids. In this study, we used the Illumina high throughput sequencing and assembly to determine the complete mitogenome of a representative of this parasite from the Siberian tiger (Panthera tigris altaica). The genome was 14,248 bp in size and encoded 12 protein-coding genes, 22 transfer RNAs, and two ribosomal RNAs. Phylogeny showed that two canid (dog)-originated T. leonina were phylogenetically distinct from two felid-originated T. leonina (tiger isolate and cheetah isolate), suggesting at least two distinct subclades of T. leonina infecting these hosts and supporting once again that T. leonina represents a species complex. Furthermore, four isolates of T. leonina grouped together and were more closely related to other species from the family Ascarididae than species of families Toxocaridae, Anisakidae and Ascaridiidae, demonstrating phylogenetic stability of these paraphyletic groups characterized in this study. These cumulative mitochondrial DNA data provide a better understanding of phylogenetic relationships of this polyxenical and zoonotic roundworm species.

The mitogenome of Ophidascaris wangi isolated from snakes in China

Different species of the genus Ophidascaris (Baylis, 1921; Nematoda: Ascaridida, Ascaridoidea) are intestinal parasites of various snake species. More than 30 Ophidascaris species have been reported worldwide; however, few molecular genetic studies have been conducted on this genus. We sequenced the complete mitogenome of Ophidascaris wangi parasitizing two snake species of the family Colubridae, i.e., Elaphe carinata (Günther, 1864) and Dinodon rufozonatum. The mitogenome sequence of O. wangi was approximately 14,660 base pairs (bp) long and encoded 36 genes, including 12 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, and 22 transfer RNA genes. Gene arrangement, genome content, and transcription direction were in line with those in Toxascaris leonina (Linstow, 1902; Ascaridida: Ascarididae). Phylogenetics of O. wangi and other ascaridoids were reconstructed based on the concatenated amino acid sequences of 12 PCGs, and on nucleotide sequences of 12 PCGs and two rRNA genes. Phylogenetic analyses were performed using maximum likelihood and Bayesian inference methods, and the results suggested that O. wangi constitutes a sister clade of Ascaris, Parascaris, Baylisascaris, and Toxascaris within the family Ascarididae, which is a sister clade of Toxocaridae. The mitogenome sequence of O. wangi obtained from the present study will be useful for future identification of the nematode worms in the genus Ophidascaris and will increase the understanding of population genetics, molecular epidemiology, and phylogenetics of ascaridoid nematodes in snakes.

The complete mitochondrial genome of the beef cattle hookworm Bunostomum phlebotomum (Nematoda: Bunostominae)

The bovine hookworm Bunostomum phlebotomum (Nematoda: Bunostominae) is a blood-feeding nematode with important socioeconomic impact in the cattle breeding industry. In the present study, the complete mitochondrial genome sequence of a representative individual of B. phlebotomum from beef cattle in Southwest China was determined using the next generation sequencing technology. The genome was 13,799 bp in size and encoded 12 protein-coding genes, 22 tRNA genes and two rRNA genes. The phylogeny revealed that although B. phlebotomum from Chinese beef cattle and yaks were more closely related to each other than to that from Australian cows, these three bovine-originated B. phlebotomum grouped together and formed paraphyletic relationships with Bunostomum trigonocephalum (goat/sheep hookworm) and Necator americanus (human hookworm), supporting their sister-species relationships within Bunostominae. The cumulative mitochondrial DNA data provides a better understanding of phylogenetic relationships of this species in cattle.

The mitochondrial genome of the sheep roundworm Ascaris ovis (Ascaridida: Nematoda) from Southwest China

The Ascaris roundworms (Ascaridida: Nematoda), one of the commonest soil-transmitted helminths (STHs), can cause ascariasis with significant socioeconomic and public health impact. In this study, the mitochondrial genome of Ascaris ovis, a representative of this genus from the sheep in Southwest China was determined using Illumina sequencing technology. The assembled genome was 14,205 bp in size and encoded 36 genes, including 12 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes. Phylogenetic analysis showed that A. ovis grouped with the congeneric Ascaris lumbricoides of humans, Ascaris spp. of non-human primates and Ascaris suum of pigs and together formed a monophyletic group relationship with either species of Baylisascaris/Toxascaris/Parascaris, species of Toxocara, species of Anisakis/Pseudoterranova or species of Ascaridia/Heterakis in the order Ascaridida, supporting its genetic similarity with A. lumbricoides, A. suum, and other congeneric species. The cumulative mitochondrial DNA data of this genus should contribute to a better understanding of the phylogenetic relationships among these roundworms.

A new root-knot nematode, Meloidogyne vitis sp. nov. (Nematoda: Meloidogynidae), parasitizing grape in Yunnan

An unknown root-knot nematode was found at high density on grape roots collected from Yunnan Province. Morphometric traits and measurements, isozyme phenotypes, and molecular analysis clearly differentiated this nematode from previously described root-knot nematodes. This new species is described, illustrated and named Meloidogyne vitis sp. nov. The new species can be distinguished from other Meloidogyne spp. by a unique combination of characters. Females display a prominent neck, an excretory pore is located on the ventral region between 23rd and 25th annule behind lips, an EP/ST ratio of approximately 2.5 (1.98-2.96), a perineal pattern with two large and prominent phasmids, and a labial disc fused with the medial lips to form a dumbbell-shaped structure. Males display an obvious head region, a labial disc fused with the medial lips to form a dumbbell-shaped structure, no lateral lips, a prominent slit-like opening between the labial disc and medial lips, a distinct sunken appearance of the middle of the medial lips, and four incisures in the lateral field. Second-stage juveniles are characterized by a head region with slightly wrinkled mark, a labial disc fused with the medial lips to form a dumbbell-shaped structure, a slightly sunken appearance of the middle of the medial lips, a slit-like amphidial openings between the labial disc and lateral lips, and four incisures in the lateral field. The new species has rare Mdh (N3d) and Est phenotypes (VF1). Phylogenetic analysis based on ITS1-5.8S-ITS2, D2D3 fragments of rDNA, and coxI and coxII fragments of mtDNA sequences clearly separated the new species from other root-knot nematodes, and the closest relative was Meloidogyne mali. Meloidogyne mali was collected for amplifying these sequences as mentioned above, which were compared with the corresponding sequences of new species, the result showed that all of these sequences with highly base divergence (48-210 base divergence). Moreover, sequence characterized amplified region (SCAR) primers for rapid identification of this new species were designed.

Occurrence and molecular characterization of Meloidogyne graminicola on rice in Central Punjab, Pakistan

Meloidogyne graminicola threatens global rice production, yet is understudied for many areas where it is cultivated. To better understand the prevalence and incidence of M. graminicola in central Punjab, Pakistan, we carried out field surveys of rice fields in the districts of Faisalabad and Chiniot. M. graminicola isolates were recovered from soil and root samples and identified on the basis of perineal patterns and rDNA ITS-based sequencing. The severity of nematode attack on rice roots and infested fields at various locations was based on galling index, root-knot nematode juveniles per root system, juveniles per 100 ml of soil, and prevalence of stylet-bearing nematodes and non-stylet-bearing nematodes. Maximum prevalence (22.5 and 27.5%) and minimum prevalence (17.5 and 20%) of M. graminicola was observed in Chiniot and Faisalabad, respectively. Eleven alternate host-plant species were examined in this study revealing varying degrees of M. graminicola infestation. ITS sequencing and phylogenetic analysis indicated that isolates from this study form a well-resolved clade with others from Asia, while another isolate falls outside of this clade in an unresolved polytomy with those from Europe and South America. Though monophyletic with the other M. graminicola, the isolates from Pakistan are distinguished by their high genetic variability and long branch lengths relative to the other isolates of M. graminicola, suggesting Pakistan as a possible ancestral area. Our results indicate that rice is severely attacked by a genetically diverse and aggressive M. graminicola, necessitating the development of appropriate control measures for its management in rice and other graminaceous crops.

Characterization of the complete mitochondrial genomes of Coronocyclus labiatus and Cylicodontophorus bicoronatus: Comparison with Strongylidae species and phylogenetic implication

Coronocyclus labiatus and Cylicodontophorus bicoronatus are two significant horse parasitic nematodes which are classified into subfamily Cyathostominae, family Strongylidae, however, the classification of these nematodes has been controversial for more than a century. Mitochondrial (mt) genomes are considered valuable sources for parasite taxonomy, population genetics, and systematics studies. In the present study, the mt genomes of Co. labiatus and Cd. bicoronatus (type species) were determined and subsequently compared with those from closely related species by phylogenetic analysis based on concatenated datasets of amino acid sequences predicted from mt protein-coding genes. The complete mt genomes of Co. labiatus and Cd. bicoronatus were circular with 13,827 bp and 13,753 bp in size, respectively. Both mt genomes consisted of a total of 12 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and two non-coding regions. All protein coding genes were transcribed in the same direction, and the gene order in both mt genomes belonged to the gene arrangement type 3 (GA3). There were 19 intergenic spacers with 1 bp to 35 bp and one overlap with 4 bp in mt genome of Co. labiatus, and 22 intergenic spacers with 1-29 bp in size but no overlap in the mt genome of Cd. bicoronatus. The A + T content of Co. labiatus and Cd. bicoronatus mt genomes were 75.87 % and 75.16 %, respectively. Similar to mt genones of other Strongylidae species published in GenBank, they also exhibited a strong A + T bias not only in the nucleotide composition but also in codon usage. Comparative analyses of mt genomes nucleotide sequence showed that mt genomes of Co. labiatus and Cd. bicoronatus had higher identities to that of Cylicostephanus goldi (90.3 % and 86.9 %, respectively), followed by those of two Cyathostomum species (89.9∼90.0 %; 86.4 %), respectively. Phylogenetic analyses using mt genomes of 26 Strongyloidea nematodes revealed that Co. labiatus was closely related to Cyathostomum species, and Cd. bicoronatus formed a distinct branch with Cyathostominae species, which was closer to Triodontophorus than Poteriostomum imparidentatum. We concluded Coronocyclus might be closely related with Cyathostomum but represent a distinct genus based on comparative mt genome sequences and phylogenetic analyses. The availability of complete mt genome sequences of Co. labiatus and Cd. bicoronatus provides new and useful genetic markers for further studies on Strongylidae nematodes.

Evidence for mitochondrial pseudogenes (numts) as a source of contamination in the phylogeny of human whipworms

Trichuris trichiura and T. suis are whipworms of humans and pigs, respectively, but it has recently been suggested that humans may be infected with multiple genotypes or species of Trichuris and cross-infection with Trichuris of pig origin has also been reported. In addition, the species status of Trichuris in non-human primates is unsettled and it is unknown how many whipworm species we share with other primates. Herein, we inferred the phylogeny of Trichuris collected from human, baboon and pig based on nuclear (18S and beta-tubulin) and mitochondrial (cox1) genes and evaluated the use of three PCR linked restriction fragment length polymorphism (PCR-RFLP) to identify worms. We found that all baboon worms clustered with human worms and that all these primate worms are different from T. suis. In general, there was an agreement between the phylogeny established based on the nuclear and mtDNA genes. However, we found evidence for non-targeted cox1 gene amplification for a subset of the human worms and suggest the presence of mitochondrial pseudogenes (numts) of pig cox1 gene in the human Trichuris genome. In conclusion, phylogenetic characterization of human whipworm based on the cox1 gene alone may be problematic without suitable preceded measures to avoid the numts amplification.

Characterization of the Complete Mitochondrial Genomes of Two Sibling Species of Parasitic Roundworms, Haemonchus contortus and Teladorsagia circumcincta

Haemonchus contortus and Teladorsagia circumcincta are among the two most pathogenic internal parasitic nematodes infecting small ruminants, such as sheep and goats, and are a global animal health issue. Accurate identification and delineation of Haemonchidae species is essential for development of diagnostic and control strategies with high resolution for Trichostrongyloidea infection in ruminants. Here, we describe in detail and compare the complete mitochondrial (mt) genomes of the New Zealand H. contortus and T. circumcincta field strains to improve our understanding of species- and strain-level evolution in these closely related roundworms. In the present study, we performed extensive comparative bioinformatics analyses on the recently sequenced complete mt genomes of the New Zealand H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP field strains. Amino acid sequences inferred from individual genes of each of the two mt genomes were compared, concatenated and subjected to phylogenetic analysis using Bayesian inference (BI), Maximum Likelihood (ML), and Maximum Parsimony (MP). The AT-rich mt genomes of H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP are 14,001 bp (A+T content of 77.4%) and 14,081 bp (A+T content of 77.3%) in size, respectively. All 36 of the typical nematode mt genes are transcribed in the forward direction in both species and comprise of 12 protein-encoding genes (PCGs), 2 ribosomal RNA (rrn) genes, and 22 transfer RNA (trn) genes. The secondary structures for the 22 trn genes and two rrn genes differ between H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP, however the gene arrangements of both are consistent with other Trichostrongylidea sequenced to date. Comparative analyses of the complete mitochondrial nucleotide sequences, PCGs, A+T rich and non-coding repeat regions of H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP further reinforces the high levels of diversity and gene flow observed among Trichostrongylidea, and supports their potential as ideal markers for strain-level identification from different hosts and geographical regions with high resolution for future studies. The complete mt genomes of H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP presented here provide useful novel markers for further studies of the meta-population connectivity and the genetic mechanisms driving evolution in nematode species.

Mitochondrial phylogenomics of human-type Ascaris, pig-type Ascaris, and hybrid Ascaris populations

Ascaris lumbricoides and Ascaris suum are parasitic nematodes in human and pig intestines. The two species can cross infect and produce hybrids, which contribute to the controversy concerning the taxonomy of A. lumbricoides and A. suum. The purpose of this study was to investigate the microevolutionary process and evolutionary history of human-type Ascaris, pig-type Ascaris, and hybrid Ascaris and provide a theoretical basis for the prevention and control of human and animal ascariasis. The mitochondrial phylogenomics of human-type Ascaris (n = 5), pig-type Ascaris (n = 6), and hybrid Ascaris (n = 6) populations were analyzed using high-throughput sequencing technology. The mitochondrial genomes of human-type Ascaris, pig-type Ascaris, and hybrid Ascaris contained 36 genes (atp8 was missing), including 12 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. All genes were located on the heavy chain. The initiation codons used for protein-coding genes were ATT and TTG and the termination codons were TAA and TAG. The base distribution showed obvious AT preference. The phylogenetic tree based on the Ascaris mitochondrial genomes showed three main clusters (A, B, and C). The Ascaris populations sequenced in this study were all gathered in cluster B. The human-type and hybrid Ascaris populations belonged to different sub-clusters, but the pig-type Ascaris population was more scattered. The mitochondrial genome sequences of the 17 Ascaris individuals in this study did not differ much. The results of this study indicate that Ascaris populations were geographically isolated before host shift. In addition, the data show that there are differences between hybrid Ascaris, human-type Ascaris, and pig-type Ascaris. The information has important theoretical significance and application value.

First record of a tandem-repeat region within the mitochondrial genome of Clonorchis sinensis using a long-read sequencing approach

Background

Mitochondrial genomes provide useful genetic markers for systematic and population genetic studies of parasitic helminths. Although many such genome sequences have been published and deposited in public databases, there is evidence that some of them are incomplete relating to an inability of conventional techniques to reliably sequence non-coding (repetitive) regions. In the present study, we characterise the complete mitochondrial genome—including the long, non-coding region—of the carcinogenic Chinese liver fluke, Clonorchis sinensis, using long-read sequencing.

Methods

The mitochondrial genome was sequenced from total high molecular-weight genomic DNA isolated from a pool of 100 adult worms of C. sinensis using the MinION sequencing platform (Oxford Nanopore Technologies), and assembled and annotated using an informatic approach.

Results

From > 93,500 long-reads, we assembled a 18,304 bp-mitochondrial genome for C. sinensis. Within this genome we identified a novel non-coding region of 4,549 bp containing six tandem-repetitive units of 719–809 bp each. Given that genomic DNA from pooled worms was used for sequencing, some variability in length/sequence in this tandem-repetitive region was detectable, reflecting population variation.

Conclusions

For C. sinensis, we report the complete mitochondrial genome, which includes a long (> 4.5 kb) tandem-repetitive region. The discovery of this non-coding region using a nanopore-sequencing/informatic approach now paves the way to investigating the nature and extent of length/sequence variation in this region within and among individual worms, both within and among C. sinensis populations, and to exploring whether this region has a functional role in the regulation of replication and transcription, akin to the mitochondrial control region in mammals. Although applied to C. sinensis, the technological approach established here should be broadly applicable to characterise complex tandem-repetitive or homo-polymeric regions in the mitochondrial genomes of a wide range of taxa.

In the present study, we characterised the complete mitochondrial genome of Clonorchis sinensis—a carcinogenic liver fluke. To do this, we sequenced from total genomic DNA from multiple adult worms using a new method (Oxford Nanopore technology) to obtain data for long stretches of DNA, and then assembled these data to construct a mitochondrial genome of 18,304 bp, containing a > 4.5 kb-long tandem-repetitive region—not previously detected in this species. The results demonstrate that this method is effective at sequencing long and complex non-coding elements—not achievable using conventional techniques. The discovery of this long tandem-repetitive region in C. sinensis provides an opportunity to now explore its origin(s) and length/sequence diversity in populations of this species, and also to characterise its function(s). The technological approach employed here should have broad applicability to characterise previously-elusive non-coding mitochondrial genomic regions in a wide range of taxa.

Molecular characterization of ascaridoid parasites from captive wild carnivores in China using ribosomal and mitochondrial sequences

BACKGROUND

Despite the public health importance of toxocariasis/toxascariasis, only a few species of these ascaridoid parasites from wild canine and feline carnivores have been studied at the molecular level so far. Poor understanding of diversity, host distribution and the potential (zoonotic) transmission of the ascaridoid species among wild animals negatively affects their surveillance and control in natural settings. In this study, we updated previous knowledge by profiling the genetic diversity and phylogenetic relationships of ascaridoid species among eleven wild canine and feline animals on the basis of a combined analysis of the ribosomal internal transcribed spacer region (ITS) gene and the partial mitochondrial cytochrome c oxidase subunit 2 (cox2) and NADH dehydrogenase subunit 1 (nad1) genes.

RESULTS

In total, three genetically distinct ascaridoid lineages were determined to be present among these wild carnivores sampled, including Toxocara canis in Alopex lagopus and Vulpes vulpes, Toxocara cati in Felis chaus, Prionailurus bengalensis and Catopuma temmincki and Toxascaris leonina in Canis lupus, Panthera tigris altaica, Panthera tigris amoyensis, Panthera tigris tigris, Panthera leo and Lynx lynx. Furthermore, it was evident that T. leonina lineage split into three well-supported subclades depending on their host species, i.e. wild felids, dogs and wolves and foxes, based on integrated genetic and phylogenetic evidence, supporting that a complex of T. leonina other than one species infecting these hosts.

CONCLUSIONS

These results provide new molecular insights into classification, phylogenetic relationships and epidemiological importance of ascaridoids from wild canids and felids and also highlight the complex of the taxonomy and genetics of Toxascaris in their wild and domestic carnivorous hosts.

Molecular Characterization and Phylogenetic Analysis of Toxocara Species in Dogs, Cattle and Buffalo in Egypt

Toxocara canis of dogs and Toxocara vitulorum of cattle and buffalo are nematode parasites that cause serious economic and public health problems all over the world. This study aims to provide molecular data to identify and distinguish between Toxocara spp. from dogs, cattle and buffalo in Egypt. Moreover, constructing a phylogeny and phylogenetic relationships among these Toxocara spp. were performed through an analytic study of ATPase-6, a mitochondrial gene; 12S, small subunit ribosomal RNA gene and ITS-2, the second internal transcribed spacer nuclear ribosomal gene. T. vitulorum from cattle and buffalo were found to be almost identical. The ATPase- 6 and 12S regions showed 87.78 % and 90.38 % nucleotide similarity between T. canis and T. vitulorum, while for the ITS-2 region, only 78.38 % was found. Analysis of the three studied genes revealed that each Toxocara spp. has distinct molecular characteristics. Moreover, it was revealed that these genes, especially the ITS-2 gene, are useful and sensitive molecular markers for classifying and studying the phylogenetic analysis and relationships among closely related Toxocara spp. All sequences obtained in this study were registered in the GenBank under the accession numbers: MG214149 -MG214157.

The mitochondrial genome of Acrobeloides varius (Cephalobomorpha) confirms non-monophyly of Tylenchina (Nematoda)

The infraorder Cephalobomorpha is a diverse and ecologically important nematode group found in almost all terrestrial environments. In a recent nematode classification system based on SSU rDNA, Cephalobomorpha was classified within the suborder Tylenchina with Panagrolaimomorpha, Tylenchomorpha and Drilonematomorpha. However, phylogenetic relationships among species within Tylenchina are not always consistent, and the phylogenetic position of Cephalobomorpha is still uncertain. In this study, in order to examine phylogenetic relationships of Cephalobomorpha with other nematode groups, we determined the complete mitochondrial genome sequence of Acrobeloides varius, the first sequenced representative of Cephalobomorpha, and used this sequence for phylogenetic analyses along with 101 other nematode species. Phylogenetic analyses using amino acid and nucleotide sequence data of 12 protein-coding genes strongly support a sister relationship between the two cephalobomorpha species A. varius and Acrobeles complexus (represented by a partial mt genome sequence). In this mitochondrial genome phylogeny, Cephalobomorpha was sister to all chromadorean species (excluding Plectus acuminatus of Plectida) and separated from Panagrolaimomorpha and Tylenchomorpha, rendering Tylenchina non-monophyletic. Mitochondrial gene order among Tylenchina species is not conserved, and gene clusters shared between A. varius and A. complexus are very limited. Results from phylogenetic analysis and gene order comparison confirms Tylenchina is not monophyletic. To better understand phylogenetic relationships among Tylenchina members, additional mitochondrial genome information is needed from underrepresented taxa representing Panagrolaimomorpha and Cephalobomorpha.

The mitochondrial genome of Angiostrongylus mackerrasae is distinct from A. cantonensis and A. malaysiensis

The native rat lungworm (Angiostrongylus mackerrasae) and the invasive rat lungworm (Angiostrongylus cantonensis) occur in eastern Australia. The species identity of A. mackerrasae remained unquestioned until relatively recently, when compilation of mtDNA data indicated that A. mackerrasae sensu Aghazadeh et al. (2015b) clusters within A. cantonensis based on their mitochondrial genomes (mtDNA). To re-evaluate the species identity of A. mackerrasae, we sought material that would be morphologically conspecific with A. mackerrasae. We combined morphological and molecular approaches to confirm or refute the specific status of A. mackerrasae. Nematodes conspecific with A. mackerrasae from Rattus fuscipes and Rattus rattus were collected in Queensland, Australia. Morphologically identified A. mackerrasae voucher specimens were characterized using amplification of cox1 followed by the generation of reference complete mtDNA. The morphologically distinct A. cantonensis, A. mackerrasae and A. malaysiensis are genetically distinguishable forming a monophyletic mtDNA lineage. We conclude that A. mackerrasae sensu Aghazadeh et al. (2015b) is a misidentified specimen of A. cantonensis. The availability of the mtDNA genome of A. mackerrasae enables its unequivocal genetic identification and differentiation from other Angiostrongylus species.

The Complete Mitochondrial Genome of the Caecal Fluke of Poultry, Postharmostomum commutatum, as the First Representative from the Superfamily Brachylaimoidea

Postharmostomum commutatum (Platyhelminthes: Brachylaimoidea), a parasite of the caeca of poultry, has been frequently reported from many countries and regions, including China. However, the molecular epidemiology, population genetics and phylogenetics of this parasite are poorly understood. In the present study, we determined and characterized the complete mitochondrial (mt) genome of P. commutatum, as the first representative from the superfamily Brachylaimoidea. The mt genome of P. commutatum is a circular DNA molecule of 13,799 bp in size and encodes the complete set of 36 genes (12 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes) as well as a typical control region. The mt genome of P. commutatum presents a clear bias in nucleotide composition with a negative AT-skew on average (-0.306) and a positive GC-skew on average (0.466). Phylogenetic analyses showed that P. commutatum (superfamily Brachylaimoidea) and other ten members of the order Diplostomida were recovered as sister groups of the order Plagiorchiida, indicating that the order Diplostomida is paraphyletic. This is the first mt genome of any member of the superfamily Brachylaimoidea and should represent a rich source of genetic markers for molecular epidemiological, population genetic and phylogenetic studies of parasitic flukes of socio-economic importance in poultry.

Characterization of the complete mitochondrial genome sequence of the dog roundworm Toxascaris leonina (Nematoda, Ascarididae) from China

Toxascaris leonina (Nematoda, Ascarididae) is a cosmopolitan nematode of canids and felids and poses potential threats to public health due to aberrant larva migrans. Herein, the complete mitochondrial genome sequence of a representative of this nematode from the dog in China was determined using next-generation sequencing technology. The assembled genome was 14,357 bp in length and encoded 36 genes, including 12 protein-coding genes, 22 transfer RNAs and 2 ribosomal RNAs. The phylogeny revealed that the canid-originated T. leonina were phylogenetic distinctiveness from the felid-originated T. leonina within the genus Toxascaris of Ascarididae, supporting that T. leonina may represent a species complex.

The mitochondrial genome of the dog hookworm Ancylostoma caninum (Nematoda, Ancylostomatidae) from Southwest China

The dog hookworm Ancylostoma caninum (Nematoda, Ancylostomatidae) is a blood-feeding intestinal parasitic nematode and can cause ancylostomiasis in humans. In this study, the complete mitochondrial genome of this anthropozoonotic hookworm was sequenced through Illumina deep sequencing technology. The whole genome was 13,721 bp in length and encoded 36 genes including 12 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs. Phylogeny revealed that A. caninum grouped with species from Ancylostomatinae and separated from species of Bunostominae in the family Ancylostomatidae. Amongst the subfamily Ancylostomatinae, three dog-originated A. caninum, regardless of isolate origins, clustered together and were more closely related to the cat hookworm A. tubaeforme and the human hookworm A. duodenale than to the dog/cat hookworm A. ceylanicum and the sea lion hookworm Uncinaria sanguinis. Taken together, the cumulative mitochondrial DNA data provides insights into phylogenetic studies among Ancylostomatidae nematodes.

Sequencing and analysis of the complete mitochondrial genome of dog roundworm Toxocara canis (Nematoda: Toxocaridae) from USA

The dog roundworm Toxocara canis (Nematoda: Toxocaridae) is an important zoonotic parasitic nematode and cause toxocariasis in human with a worldwide distribution. Herein, the complete mitochondrial genome of a representative of this nematode from USA was determined through next generation sequencing platform. The whole genome was 14,309 bp in size and encoded 12 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs. Phylogeny showed that although T. canis from USA and Australia were more closely related to each other than to that from Chinese, three T. canis isolates clustered together and formed paraphyletic relationships with T. cati and T. malayensis, supporting them as sister species among the family Toxocaridae. These cumulative mitochondrial DNA data should contribute to a better understanding of the phylogenetic relationship of this species.

Characterization of the complete mitochondrial genome of Spirometra decipiens (Cestoda: Diphyllobothriidae) from China

The plerocercoid larvae (spargana) of Spirometra decipiens (Cestoda: Diphyllobothriidae) can parasitize humans, causing the zoonotic sparganosis. In this study, the complete mitochondrial genome of this tapeworm was determined using an Illumina sequencing platform. The entire genome was 13,642 bp in length and contained 12 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and two non-coding regions. The phylogeny indicated that S. decipiens was closely related to Spirometra erinaceieuropaei and supported the monophyletic relationships between Spirometra, Diphyllobothrium, and Diplogonoporus within the Dipyllobothriidae. These results should contribute to a better understanding of the phylogenetic position of this species.

Human toxocariasis - A look at a neglected disease through an epidemiological 'prism'

Toxocariasis, a disease caused by infection with larvae of Toxocara canis, T. cati and/or congeners, represents clinical syndromes in humans including visceral and ocular larva migrans, neurotoxocariasis and covert/common toxocariasis. It is reported to be one of the most widespread public health and economically important zoonotic parasitic infections that humans share with dogs, wild canids, including foxes, and possibly other mammals. Humans become infected by accidental ingestion of embryonated Toxocara eggs, or larvae from tissues from domestic or wild paratenic hosts. Most infections are asymptomatic, and human disease may go unnoticed, as clinical investigation is often not pursued and/or diagnostic testing not conducted. Sometimes toxocariasis can be associated with complications, such as allergic and/or neurological disorders, possibly including cognitive or developmental delays in children. There is no anti-toxocariasis vaccine, and chemotherapy in humans varies, depending on symptoms and location of larvae, and may include the administration of albendazole or mebendazole, together with anti-inflammatory corticosteroids. Some recent studies indicate that toxocariasis is having an increased, adverse impact on human health in some, particularly underprivileged, tropical and subtropical communities around the world. Although tens of millions of people, especially children, are expected to be exposed to, or infected with Toxocara species, there is limited precise epidemiological data or information on the relationship between seropositivity and disease (toxocariasis) on a global scale. To gain an improved insight into this area, the present article reviews salient clinical aspects of human toxocariasis and the epidemiology of this disease, with particular reference to seroprevalence, and discusses future research and approaches/measures to understand and prevent/control this socioeconomically important, yet neglected zoonosis.

Complete mitogenome of the dog cucumber tapeworm Dipylidium caninum (Cestoda, Dilepididae) from Southwest China

The cucumber tapeworm Dipylidium caninum (Cestoda, Dilepididae) is a common intestinal parasite of dogs and cats and can cause dipylidiasis in humans, especially in infants and children. In this study, the complete mitogenome of this tapeworm was sequenced using next-generation sequencing technology. The entire genome was 14,226 bp in size and encoded 36 genes, including 12 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes. The phylogeny revealed that D. caninum grouped with other species from the order Cyclophyllidea and separated from species of Pseudophyllidea. Within the Dipylidiidae, both dog-originated D. caninum were phylogenetic distinctiveness from cat-originated D. caninum, suggesting that D. caninum may represent a species complex. Altogether, the complete mitogenome of D. caninum sequenced here should contribute to a better understanding of the phylogenetic and taxonomic placement of this species.

The complete mitochondrial genome of the New Zealand parasitic roundworm Haemonchus contortus (Trichostrongyloidea: Haemonchidae) field strain NZ_Hco_NP

The complete mitochondrial genome of the New Zealand parasitic nematode Haemonchus contortus field strain NZ_Hco_NP was sequenced and annotated. The 14,001 bp-long mitogenome contains 12 protein-coding genes (atp8 gene missing), two ribosomal RNAs, 22 transfer RNAs, and a 583 bp non-coding region. Phylogenetic analysis showed that H. contortus NZ_Hco_NP forms a monophyletic cluster with the remaining three Haemonchidae species, and further illustrates the high levels of diversity and gene flow among Trichostrongylidae.

The Genome Sequence of the Anthelmintic-Susceptible New Zealand Haemonchus contortus

Internal parasitic nematodes are a global animal health issue causing drastic losses in livestock. Here, we report a H. contortus representative draft genome to serve as a genetic resource to the scientific community and support future experimental research of molecular mechanisms in related parasites. A de novo hybrid assembly was generated from PCR-free whole genome sequence data, resulting in a chromosome-level assembly that is 465 Mb in size encoding 22,341 genes. The genome sequence presented here is consistent with the genome architecture of the existing Haemonchus species and is a valuable resource for future studies regarding population genetic structures of parasitic nematodes. Additionally, comparative pan-genomics with other species of economically important parasitic nematodes have revealed highly open genomes and strong collinearities within the phylum Nematoda.

Mitochondrial DNA, a Powerful Tool to Decipher Ancient Human Civilization from Domestication to Music, and to Uncover Historical Murder Cases

Mitochondria are unique organelles carrying their own genetic material, independent from that in the nucleus. This review will discuss the nature of mitochondrial DNA (mtDNA) and its levels in the cell, which are the key elements to consider when trying to achieve molecular identification in ancient and degraded samples. mtDNA sequence analysis has been appropriately validated and is a consistent molecular target for the examination of biological evidence encountered in forensic cases—and profiling, in certain conditions—especially for burnt bodies and degraded samples of all types. Exceptional cases and samples will be discussed in this review, such as mtDNA from leather in Beethoven’s grand piano, mtDNA in mummies, and solving famous historical criminal cases. In addition, this review will be discussing the use of ancient mtDNA to understand past human diet, to trace historical civilizations and ancient trade routes, and to uncover geographical domestication origins and lineage relationships. In each topic, we will present the power of mtDNA and how, in many cases, no nuclear DNA was left, leaving mitochondrial DNA analysis as a powerful alternative. Exploring this powerful tool further will be extremely useful to modern science and researchers, due to its capabilities in providing us with previously unattainable knowledge.

Comparative analysis of mitochondrial DNA datasets indicates that Toxascaris leonina represents a species complex

Background

Toxascaris leonina is one of the most common intestinal parasites of canids and felids. In this study, we characterised the entire mitochondrial (mt) genome sequence of T. leonina from the cheetah and compared it with that of T. leonina from the dog.

Results

The entire mt genome sequence of T. leonina from the cheetah is 14,685 bp in size, which is 375 bp longer than that from the dog, and it is 408 bp longer than that from the South China tiger. The overall nucleotide sequence (except for the non-coding region) identity was 92.8% between the two mt genomes of T. leonina from the cheetah and the dog. For the 12 protein-coding genes, sequence difference between T. leonina from the cheetah and the dog was 5.0–9.7% at the nucleotide level and 1.0–7.2% at the amino acid level. Moreover, comparison of mt cox1 sequences among T. leonina isolates (n = 23) from different hosts revealed substantial nucleotide differences (10.6%). Phylogenetic analysis showed the separation of T. leonina from canid and felid hosts into three distinct clades.

Conclusions

Taken together, these mtDNA datasets indicate that T. leonina from canid and felid hosts represents a species complex. Our results have implications for further studies of the molecular epidemiology, systematics and population genetics of this nematode.

Electronic supplementary material

The online version of this article (10.1186/s13071-019-3447-2) contains supplementary material, which is available to authorized users.

Genetic Variability among Different Populations of Root Knot Nematodes Based on Their Encumbrance Response to Pasteuria Isolates Using PCR-RFLP

A great variable response was observed when PP-3 and PP-J encumbered with 116 populations of root knot nematode (RKN) at two different temperatures (25 ± 2°C and 30 ± 2°C) and concentrations (10⁴ and 10⁵ spores/ml). The PCR reaction amplified intergenic region between cytochrome oxidase subunit II gene (COII) and large subunit of rRNA gene (lrRNA) of the mitochondrial genome of different RKN species. The primer C2F3 and 1108 identified M. incognita with the highest frequency (52.6%) followed by M. javanica (36.8%) and M. arenaria (10.5%). The sizes of PCR products were 1.7 kb for M. incognita and M. javanica populations while populations of M. arenaria produced 1.1 kb fragment. The digestion with Hinf I yielded three different fragment length patterns on 1.5 % agarose gel. From current research it is concluded that intra-Meloidogyne genetic variability exist in RKN populations which have better encumbrance with P. penetrans.

The mitochondrial genome of Dipetalonema gracile from a squirrel monkey in China

Dipetalonema gracile is a common parasite in squirrel monkeys (Saimiri sciureus), which can cause malnutrition and progressive wasting of the host, and lead to death in the case of massive infection. This study aimed to identify a suspected D. gracile worm from a dead squirrel monkey by means of molecular biology, and to amplify its complete mitochondrial genome by polymerase chain reaction (PCR) and sequence analysis. The results identified the worm as D. gracile, and the full length of its complete mitochondrial genome was 13,584 bp, which contained 22 tRNA genes, 12 protein-coding genes, two rRNA genes, one AT-rich region and one small non-coding region. The nucleotide composition included A (16.89%), G (20.19%), T (56.22%) and C (6.70%), among which A + T = 73.11%. The 12 protein-coding genes used TTG and ATT as start codons, and TAG and TAA as stop codons. Among the 22 tRNA genes, only trnS1AGN and trnS2UCN exhibited the TΨC-loop structure, while the other 20 tRNAs showed the TV-loop structure. The rrnL (986 bp) and rrnS (685 bp) genes were single-stranded and conserved in secondary structure. This study has enriched the mitochondrial gene database of Dipetalonema and laid a scientific basis for further study on classification, and genetic and evolutionary relationships of Dipetalonema nematodes.

The bipartite mitochondrial genome of Ruizia karukerae (Rhigonematomorpha, Nematoda)

Mitochondrial genes and whole mitochondrial genome sequences are widely used as molecular markers in studying population genetics and resolving both deep and shallow nodes in phylogenetics. In animals the mitochondrial genome is generally composed of a single chromosome, but mystifying exceptions sometimes occur. We determined the complete mitochondrial genome of the millipede-parasitic nematode Ruizia karukerae and found its mitochondrial genome consists of two circular chromosomes, which is highly unusual in bilateral animals. Chromosome I is 7,659 bp and includes six protein-coding genes, two rRNA genes and nine tRNA genes. Chromosome II comprises 7,647 bp, with seven protein-coding genes and 16 tRNA genes. Interestingly, both chromosomes share a 1,010 bp sequence containing duplicate copies of cox2 and three tRNA genes (trnD, trnG and trnH), and the nucleotide sequences between the duplicated homologous gene copies are nearly identical, suggesting a possible recent genesis for this bipartite mitochondrial genome. Given that little is known about the formation, maintenance or evolution of abnormal mitochondrial genome structures, R. karukerae mtDNA may provide an important early glimpse into this process.

Comparative analysis of Ancylostoma ceylanicum mitochondrial genome with other Ancylostoma species

Ancylostoma ceylanicum may inhabit the small intestine of canids, felids and humans, can pose a potential risk to public health. This study is the first time to amplify complete mitochondrial genome sequence of A. ceylanicum from dog and to compare it with Ancylostoma tubaeforme, Ancylostoma duodenale and Ancylostoma caninum. The results showed that the complete mitochondrial genome of A. ceylanicum was 13,660 bp in length, including 12 protein-coding genes, 2 rRNA genes and 22 tRNA genes and 3 non-coding regions (AT-rich region, SNCR and LNCR). Its mtDNA was the shortest, biased toward A and T at base composition, and higher than other three Ancylostoma species at total AT content. Its nad5 and nad6 genes used TTG and ATT as initiation codons, while other three Ancylostoma species used ATT and GTG or ATG. The 22 tRNA genes were different in length among four Ancylostoma species, but their anticodons were the same. Among 12 protein-coding genes, the cox1 gene was the lowest at AT content and minimum at Ka/Ks while the nad2 gene was the opposite. The phylogenetic tree showed that in the lineage of Ancylostoma, A. ceylanicum occurred on a branch external to other three Ancylostoma species, and A. caninum and A. tubaeforme had closer phylogenetic relationship than A. duodenale. This study not only enhances the mitochondrial genome database of Ancylostomatidae nematodes, but also provides new data for further phylogenetic studies among Ancylostomatidae nematodes.

Full mitochondrial and nuclear genome comparison confirms that Onchocerca sp. "Siisa" is Onchocerca ochengi

Onchocerca ochengi is a nodule-forming filarial nematode parasite of cattle. It is the closest known relative of the human parasite Onchocerca volvulus, with which it shares the black fly vector Simulium damnosum. Onchocerca sp. "Siisa" was described in black flies and in cattle and, based on limited mitochondrial sequence information, appeared to be about equally phylogenetically distant from O. ochengi and O. volvulus. Based on molecular genetic markers and apparent interbreeding, we later proposed that O. sp. "Siisa" belongs to the species O. ochengi. However, we did not demonstrate directly that the hybrids were fertile, and we were still unable to resolve the phylogenetic relationship of O. ochengi, O. sp. "Siisa," and O. volvulus, leaving some concerns with the conclusion mentioned above. Here, we present fully assembled, manually curated mitochondrial genomes of O. ochengi and O. sp. "Siisa," and we compare multiple individuals of these two taxa with respect to their whole mitochondrial and nuclear genomes. Based on the mitochondrial genomes, O. ochengi and O. sp. "Siisa" are phylogenetically much closer to each other than to O. volvulus. The differences between them are well within the range of what is expected for within-species variation. The nuclear genome comparison provided no indication of genetic separation of O. ochengi and O. sp. "Siisa." From this, in combination with the earlier literature, we conclude that O. ochengi and O. sp. "Siisa" should be considered one species.

The complete mitochondrial genome of parasitic nematode Camallanus cotti: extreme discontinuity in the rate of mitogenomic architecture evolution within the Chromadorea class

BACKGROUND

Complete mitochondrial genomes are much better suited for the taxonomic identification and phylogenetic studies of nematodes than morphology or traditionally-used molecular markers, but they remain unavailable for the entire Camallanidae family (Chromadorea). As the only published mitogenome in the Camallanina suborder (Dracunculoidea superfamily) exhibited a unique gene order, the other objective of this research was to study the evolution of mitochondrial architecture in the Spirurida order. Thus, we sequenced the complete mitogenome of the Camallanus cotti fish parasite and conducted structural and phylogenomic comparative analyses with all available Spirurida mitogenomes.

RESULTS

The mitogenome is exceptionally large (17,901 bp) among the Chromadorea and, with 46 (pseudo-) genes, exhibits a unique architecture among nematodes. Six protein-coding genes (PCGs) and six tRNAs are duplicated. An additional (seventh) tRNA (Trp) was probably duplicated by the remolding of tRNA-Ser2 (missing). Two pairs of these duplicated PCGs might be functional; three were incomplete and one contained stop codons. Apart from Ala and Asp, all other duplicated tRNAs are conserved and probably functional. Only 19 unique tRNAs were found. Phylogenomic analysis included Gnathostomatidae (Spirurina) in the Camallanina suborder.

CONCLUSIONS

Within the Nematoda, comparable PCG duplications were observed only in the enoplean Mermithidae family, but those result from mitochondrial recombination, whereas characteristics of the studied mitogenome suggest that likely rearrangement mechanisms are either a series of duplications, transpositions and random loss events, or duplication, fragmentation and subsequent reassembly of the mitogenome. We put forward a hypothesis that the evolution of mitogenomic architecture is extremely discontinuous, and that once a long period of stasis in gene order and content has been punctuated by a rearrangement event, such a destabilised mitogenome is much more likely to undergo subsequent rearrangement events, resulting in an exponentially accelerated evolutionary rate of mitogenomic rearrangements. Implications of this model are particularly important for the application of gene order similarity as an additive source of phylogenetic information. Chromadorean nematodes, and particularly Camallanina clade (with C. cotti as an example of extremely accelerated rate of rearrangements), might be a good model to further study this discontinuity in the dynamics of mitogenomic evolution.

Infection of the lesser spotted dogfish with Proleptus obtusus Dujardin, 1845 (Nematoda: Spirurida) reflects ontogenetic feeding behaviour and seasonal differences in prey availability

Proleptus obtusus Dujardin, 1845 is the most common parasite infecting the gut of the lesser spotted dogfish (Scyliorhinus canicula, Linnaeus). This nematode is trophically transmitted from an intermediate crustacean host to the definitive elasmobranch host. Sexual and age-related differences in habitat occupancy and feeding behaviour of the lesser spotted dogfish make this parasite-host dyad ideal for testing which aspects of host biology influence parasite transmission. Here, the relationship between P. obtusus burden and host condition, sex and age were investigated in lesser spotted dogfish captured in the Northeast Atlantic. Prevalence of P. obtusus was of 94.8% with a mean abundance of 23.3 worms per host. Our results indicate that parasite burden is best explained by the interaction between ontogenetic differences in foraging behaviour of the lesser spotted dogfish and seasonal differences in prey availability.

Duplication of Drosophila melanogaster mitochondrial EF-Tu: pre-adaptation to T-arm truncation and exclusion of bulky aminoacyl residues

Translation elongation factor Tu (EF-Tu) delivers aminoacyl-tRNA (aa-tRNA) to ribosomes in protein synthesis. EF-Tu generally recognizes aminoacyl moieties and acceptor- and T-stems of aa-tRNAs. However, nematode mitochondrial (mt) tRNAs frequently lack all or part of the T-arm that is recognized by canonical EF-Tu. We previously reported that two distinct EF-Tu species, EF-Tu1 and EF-Tu2, respectively, recognize mt tRNAs lacking T-arms and D-arms in the mitochondria of the chromadorean nematode Caenorhabditis elegansC. elegans EF-Tu2 specifically recognizes the seryl moiety of serylated D-armless tRNAs. Mitochondria of the enoplean nematode Trichinella possess three structural types of tRNAs: T-armless tRNAs, D-armless tRNAs, and cloverleaf tRNAs with a short T-arm. Trichinella mt EF-Tu1 binds to all three types and EF-Tu2 binds only to D-armless Ser-tRNAs, showing an evolutionary intermediate state from canonical EF-Tu to chromadorean nematode (e.g. C. elegans) EF-Tu species. We report here that two EF-Tu species also participate in Drosophila melanogaster mitochondria. Both D. melanogaster EF-Tu1 and EF-Tu2 bound to cloverleaf and D-armless tRNAs. D. melanogaster EF-Tu1 has the ability to recognize T-armless tRNAs that do not evidently exist in D. melanogaster mitochondria, but do exist in related arthropod species. In addition, D. melanogaster EF-Tu2 preferentially bound to aa-tRNAs carrying small amino acids, but not to aa-tRNAs carrying bulky amino acids. These results suggest that the Drosophila mt translation system could be another intermediate state between the canonical and nematode mitochondria-type translation systems.

The mitochondrial genome of Ancylostoma tubaeforme from cats in China

Ancylostoma tubaeforme may infect canids, felids and humans, and pose a potential risk to public health. Polymerase chain reaction (PCR) techniques were used to amplify the complete mitochondrial (mt) genome sequence of A. tubaeforme from cats and to analyse its sequence characteristics after molecular identification based on the internal transcribed spacer ITS1+ sequence. The results show that the complete mt genome sequence (GenBank accession number KY070315) of A. tubaeforme from cats was 13,730 bp in length, including 12 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, two non-coding regions and an AT-rich region. The nucleotide content of A and T was 77.93%, biased toward A and T. Twelve protein-coding genes used ATT, TTG and GTG as initiation codons, and TAA, TAG, TA and T as termination codons. The length of the 22 tRNA genes ranged from 52 to 62 bp, their predicted secondary structures were D loops and V loops. The lengths of the two rRNAs were 958 and 697 bp. Phylogenetic analyses showed that A. tubaeforme from cats was in the lineage of Ancylostoma, having a close phylogenetic relationship with A. caninum. This study reports for the first time the mt genome of A. tubaeforme from cats in China, which could enhance the mt genome database of Ancylostomatidae nematodes, and it offers the scientific basis for further studies in the genetic diversity of hookworms among different hosts.

Annotated mitochondrial genome with Nanopore R9 signal for Nippostrongylus brasiliensis

Nippostrongylus brasiliensis, a nematode parasite of rodents, has a parasitic life cycle that is an extremely useful model for the study of human hookworm infection, particularly in regards to the induced immune response. The current reference genome for this parasite is highly fragmented with minimal annotation, but new advances in long-read sequencing suggest that a more complete and annotated assembly should be an achievable goal. We de-novo assembled a single contig mitochondrial genome from N. brasiliensis using MinION R9 nanopore data. The assembly was error-corrected using existing Illumina HiSeq reads, and annotated in full (i.e. gene boundary definitions without substantial gaps) by comparing with annotated genomes from similar parasite relatives. The mitochondrial genome has also been annotated with a preliminary electrical consensus sequence, using raw signal data generated from a Nanopore R9 flow cell.

The complete mitochondrial genome of a parasitic flatworm Senga ophiocephalina (Cestoda: Bothriocephalidae)

Mitochondrial DNA of nematodes undergoes frequent rearrangements, so it is a very good model for studying the mitochondrial genome evolution. The complete mitochondrial genome of a parasitic nematode Senga ophiocephalina was sequenced and annotated. The 13,816 bp-long genome contained 12 protein-coding genes (atp8 gene was missing), two ribosomal RNAs, 22 transfer RNAs, and a 391 bp non-coding region. Phylogenetic analysis showed that S. ophiocephalina forms a monophyletic cluster with the remaining two Bothriocephalidae species.