The complete mitochondrial genomes of three parasitic nematodes of birds: a unique gene order and insights into nematode phylogeny

Morphology, complete mitochondrial genome and molecular phylogeny of Heterakis pucrasia sp. n. (Nematoda: Ascaridida) from the koklass pheasant Pucrasia macrolopha (Lesson) (Galliformes: Phasianidae) in Pakistan

Species of Heterakis (Ascaridida: Heterakoidea) are commonest nematode parasites occurring in the alimentary canal of wild and domestic birds, which are of major socio-economic importance, due to some Heterakis species causing Heterakidosis in wild birds and poultry. In the present study, a new species of Heterakis, H. pucrasia sp. n., was described using integrated methods based on specimens collected from the koklass pheasant Pucrasia macrolopha (Lesson) (Galliformes: Phasianidae) in Pakistan. The complete mitochondrial genome of H. pucrasia sp. n. was sequenced and annotated for the first time to enrich the mitogenomic data, and reveal the pattern of mitogenomic evolution of the family Heterakidae. Moreover, phylogenetic analyses of the orders Ascaridida, Spirurida, Oxyurida and Rhigonematida based on the amino acid sequences of 12 protein coding genes (PCGs) of mitochondrial genomes, revealed that the order Ascaridida is not monophyletic, and the superfamily Heterakoidea has a closer affinity with Rhigonematida + Oxyurida + Spirurida, than the superfamily Ascaridoidea in Ascaridida. The present findings enriched the global species composition of heterakid nematodes and their mitogenomic data, and also provided novel insight on the phylogenetic relationships between Heterakoidea and its related groups.

Genome-wide analyses provide insights into genetic variation, phylo- and co-phylogenetic relationships, and biogeography of the entomopathogenic nematode genus Heterorhabditis

Multigene, genus-wide phylogenetic studies have uncovered the limited taxonomic resolution power of commonly used gene markers, particularly of rRNA genes, to discriminate closely related species of the nematode genus Heterorhabditis. In addition, conflicting tree topologies are often obtained using the different gene markers, which limits our understanding of the phylo- and co-phylogenetic relationships and biogeography of the entomopathogenic nematode genus Heterorhabditis. Here we carried out phylogenomic reconstructions using whole nuclear and mitochondrial genomes, and whole ribosomal operon sequences, as well as multiple phylogenetic reconstructions using various single nuclear and mitochondrial genes. Using the inferred phylogenies, we then investigated co-phylogenetic relationships between Heterorhabditis and their Photorhabdus bacterial symbionts and biogeographical patterns. Robust, well-resolved, and highly congruent phylogenetic relationships were reconstructed using both whole nuclear and mitochondrial genomes. Similarly, whole ribosomal operon sequences proved valuable for phylogenomic reconstructions, though they have limited value to discriminate closely related species. In addition, two mitochondrial genes, the cytochrome c oxidase subunit I (cox-1) and the NADH dehydrogenase subunit 4 (nad-4), and two housekeeping genes, the fanconi-associated nuclease 1 (fan-1) and the serine/threonine-protein phosphatase 4 regulatory subunit 1 (ppfr-1), provided the most robust phylogenetic reconstructions compared to other individual genes. According to our findings, whole nuclear and/or mitochondrial genomes are strongly recommended for reconstructing phylogenetic relationships of the genus Heterorhabditis. If whole nuclear and/or mitochondrial genomes are unavailable, a combination of nuclear and mitochondrial genes can be used as an alternative. Under these circumstances, sequences of multiple conspecific isolates in a genus-wide phylogenetic context should be analyzed to avoid artefactual species over-splitting driven by the high intraspecific sequence divergence of mitochondrial genes and to avoid artefactual species lumping driven by the low interspecific sequence divergence of some nuclear genes. On the other hand, we observed that the genera Heterorhabditis and Photorhabdus exhibit diverse biogeographic patterns, ranging from cosmopolitan species to potentially endemic species, and show high phylogenetic congruence, although host switches have also occurred. Our study contributes to a better understanding of the biodiversity and phylo- and co-phylogenetic relationships of an important group of biological control agents and advances our efforts to develop more tools that are compatible with sustainable and eco-friendly agricultural practices.

The complete mitochondrial genome of Cylicocyclus ultrajectinus (Ihle, 1920)

In this study, the mitochondrial genome of Cylicocyclus ultrajectinus (Ihle, 1920) was sequenced for the first time using next-generation sequencing technology, and its compositional characteristics, structure, and phylogenetic relationship with other strongylid nematodes were analyzed by biological software. The results showed that these sequences contained 12 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 non-coding regions, all exhibiting a significant AT bias. Phylogenetic studies showed that C. ultrajectinus formed a distinct branch form other Cylicocyclus nematodes. This study contributes to the mitochondrial genome database of Strongylidae, laying a foundation for genetic variation, molecular classification, and evolutionary studies of strongylid nematodes.

Characterization and phylogenetic analysis of the mitochondrial genome of Cylicostephanus longibursatus

Cylicostephanus longibursatus is a common parasite in equine animals. Hosts infected by these nematodes might face disease or death. This study utilized next-generation sequencing technology to sequence the complete mitochondrial genome (mt genome) of C. longibursatus. Through bioinformatics techniques, the genomic base composition, codon usage, tRNA secondary structures, evolutionary relationships, and taxonomic status were analyzed. The results revealed that the mitochondrial genome of C. longibursatus is a double-stranded, 13,807-bp closed circular molecule with an AT content of 76.0%, indicating a clear preference for AT bases. The mitochondrial genome consisted of a total of 12 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 non-coding regions. Among the 12 protein-coding genes, TTG and ATT were the common start codons. TAA was the predominant termination codon, except for the ND3 and ND6 coding genes, and the COШ genes used TAG and "T" as termination codons, respectively. All tRNAs exhibited atypical clover-leaf secondary structures, except for tRNALys and tRNALeu2, where two tRNASer genes lacked DHU arms and DHU loops, tRNAmet lacked the TΨC-arm, tRNAIle lacked the TΨC-loop, and the remaining 16 tRNAs lacked the TΨC-arm and TΨC loop, which were substituted by the "TV-replacement loop". Phylogenetic analyses, based on the 12 protein-coding genes and utilizing maximum likelihood (ML) and Bayesian inference (BI) analyses, indicated that C. longibursatus did not form a monophyletic group with other Cylicostephanus but was instead more closely related to Cyathostomum. These research findings provide fundamental data for exploring the population classification and phylogeny of strongylid nematodes.

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.

Characterisation of the mitochondrial genome and phylogenetic analysis of Toxocara apodemi (Nematoda: Ascarididae)

We first sequenced and characterised the complete mitochondrial genome of Toxocara apodeme, then studied the evolutionary relationship of the species within Toxocaridae. The complete mitochondrial genome was amplified using PCR with 14 specific primers. The mitogenome length was 14303 bp in size, including 12 PCGs (encoding 3,423 amino acids), 22 tRNAs, 2 rRNAs, and 2 NCRs, with 68.38% A+T contents. The mt genomes of T. apodemi had relatively compact structures with 11 intergenic spacers and 5 overlaps. Comparative analyses of the nucleotide sequences of complete mt genomes showed that T. apodemi had higher identities with T. canis than other congeners. A sliding window analysis of 12 PCGs among 5 Toxocara species indicated that nad4 had the highest sequence divergence, and cox1 was the least variable gene. Relative synonymous codon usage showed that UUG, ACU, CCU, CGU, and UCU most frequently occurred in the complete genomes of T. apodemi. The Ka/Ks ratio showed that all Toxocara mt genes were subject to purification selection. The largest genetic distance between T. apodemi and the other 4 congeneric species was found in nad2, and the smallest was found in cox2. Phylogenetic analyses based on the concatenated amino acid sequences of 12 PCGs demonstrated that T. apodemi formed a distinct branch and was always a sister taxon to other congeneric species. The present study determined the complete mt genome sequences of T. apodemi, which provide novel genetic markers for further studies of the taxonomy, population genetics, and systematics of the Toxocaridae nematodes.

Genome assembly and annotation of the mermithid nematode Mermis nigrescens

Genetic studies of nematodes have been dominated by Caenorhabditis elegans as a model species. A lack of genomic resources has limited the expansion of genetic research to other groups of nematodes. Here, we report a draft genome assembly of a mermithid nematode, Mermis nigrescens. Mermithidae are insect parasitic nematodes with hosts including a wide range of terrestrial arthropods. We sequenced, assembled, and annotated the whole genome of M. nigrescens using nanopore long reads and 10X Chromium link reads. The assembly is 524 Mb in size consisting of 867 scaffolds. The N50 value is 2.42 Mb, and half of the assembly is in the 30 longest scaffolds. The assembly BUSCO score from the eukaryotic database (eukaryota_odb10) indicates that the genome is 86.7% complete and 5.1% partial. The genome has a high level of heterozygosity (6.6%) with a repeat content of 83.98%. mRNA-seq reads from different sized nematodes (≤2 cm, 3.5-7 cm, and >7 cm body length) representing different developmental stages were also generated and used for the genome annotation. Using ab initio and evidence-based gene model predictions, 12,313 protein-coding genes and 24,186 mRNAs were annotated. These genomic resources will help researchers investigate the various aspects of the biology and host-parasite interactions of mermithid nematodes.

A filarial parasite potentially associated with the health burden on domestic chickens in Japan

Chickens in free-range environments are at risk of exposure to various pathogens, such as filarioids transmitted via hematophagous vectors. However, the study of filarioids in poultry has been largely neglected compared to the extensive studies focused on viruses, bacteria, and protozoa. Here, we performed histological and molecular investigations of the filarioids detected in domestic chickens from two different flocks in Hiroshima Prefecture, Japan. In the first case, adult worms were present in the pulmonary artery and right ventricle, and microfilariae were present in multiple organs of deceased chickens. In the second case, similar filarioids were detected in the organs and blood of one necropsied layer. Phylogenetic analysis using 18S rRNA gene fragments positioned the filarioid in the same clade as that of Onchocercidae sp., previously identified in a deceased chicken from Chiba Prefecture, Japan, that is located 500 km away from Hiroshima Prefecture. Based on 28S rRNA and mitochondrial COI gene fragments, the filarioid was positioned distinctly from previously reported genera of avian filarioids. These results suggest that the filarioids are potentially associated with the health burden on domestic chickens and belong to the genus Paronchocerca. Furthermore, we developed a nested PCR assay targeting mitochondrial COI and detected the parasite DNA from the biting midge Culicoides arakawae captured near the flock, suggesting that it serves as a vector. Our findings fill the knowledge gap regarding avian filarioids, laying the groundwork for future studies examining the epidemiology, life cycle, and species diversity of this neglected parasite group.

Molecular phylogeny of the family Rhabdiasidae (Nematoda: Rhabditida), with morphology, genetic characterization and mitochondrial genomes of Rhabdias kafunata and R. bufonis

BACKGROUND

The family Rhabdiasidae (Nematoda: Rhabditida) is a globally distributed group of nematode parasites, with over 110 species parasitic mainly in amphibians and reptiles. However, the systematic position of the family Rhabdiasidae in the order Rhabditida remains unsolved, and the evolutionary relationships among its genera are still unclear. Moreover, the present knowledge of the mitochondrial genomes of rhabdiasids remains limited.

METHODS

Two rhabdiasid species: Rhabdias kafunata Sata, Takeuchi & Nakano, 2020 and R. bufonis (Schrank, 1788) collected from the Asiatic toad Bufo gargarizans Cantor (Amphibia: Anura) in China, were identified based on morphology (light and scanning electron microscopy) and molecular characterization (sequencing of the nuclear 28S and ITS regions and mitochondrial cox1 and 12S genes). The complete mitochondrial genomes of R. kafunata and R. bufonis were also sequenced and annotated for the first time. Moreover, phylogenetic analyses based on the amino acid sequences of 12 protein-coding genes (PCGs) of the mitochondrial genomes were performed to clarify the systematic position of the family Rhabdiasidae in the order Rhabditida using maximum likelihood (ML) and Bayesian inference (BI). The phylogenetic analyses based on the 28S + ITS sequences, were also inferred to assess the evolutionary relationships among the genera within Rhabdiasidae.

RESULTS

The detailed morphology of the cephalic structures, vulva and eggs in R. kafunata and R. bufonis was revealed using scanning electron microscopy (SEM) for the first time. The characterization of 28S and ITS regions of R. kafunata was reported for the first time. The mitogenomes of R. kafunata and R. bufonis are 15,437 bp and 15,128 bp long, respectively, and both contain 36 genes, including 12 PCGs (missing atp8). Comparative mitogenomics revealed that the gene arrangement of R. kafunata and R. bufonis is different from all of the currently available mitogenomes of nematodes. Phylogenetic analyses based on the ITS + 28S data showed Neoentomelas and Kurilonema as sister lineages, and supported the monophyly of Entomelas, Pneumonema, Serpentirhabdias and Rhabdias. Mitochondrial phylogenomic results supported Rhabdiasidae as a member of the superfamily Rhabditoidea in the suborder Rhabditina, and its occurrance as sister to the family Rhabditidae.

CONCLUSIONS

The complete mitochondrial genome of R. kafunata and R. bufonis were reported for the first time, and two new gene arrangements of mitogenomes in Nematoda were revealed. Mitogenomic phylogenetic results indicated that the family Rhabdiasidae is a member of Rhabditoidea in Rhabditina, and is closely related to Rhabditidae. Molecular phylogenies based on the ITS + 28S sequence data supported the validity of Kurilonema, and showed that Kurilonema is sister to Neoentomelas. The present phylogenetic results also indicated that the ancestors of rhabdiasids seem to have initially infected reptiles, then spreading to amphibians.

The complete mitochondrial genome of the chicken roundworm Ascaridia galli (Nematoda: Ascaridiidae)

Ascaridia galli (Nematoda: Ascaridiidae), infecting mainly the small intestine of chickens, is one of the most common nematodes in poultry worldwide. The complete mitochondrial genome sequence of A. galli was 13,981 bp in total length with 36 coding genes, namely, 12 protein-coding genes (PCGs), two ribosomal RNAs, and 22 transfer RNAs. All PCGs were transcribed in one direction. Phylogenetic analysis of the mitogenome of A. galli would further contribute to resolving its phylogenetic position and offer novel perspectives on phylogenetic studies of A. galli.

Evolution of mitogenomic gene order in Orthoptera

Mitochondrial gene order has contributed to the elucidation of evolutionary relationships in several animal groups. It generally has found its application as a phylogenetic marker for deep nodes. Yet, in Orthoptera limited research has been performed on the gene order, although the group represents one of the oldest insect orders. We performed a comprehensive study on mitochondrial genome rearrangements (MTRs) within Orthoptera in the context of mitogenomic sequence-based phylogeny. We used 280 published mitogenome sequences from 256 species, including three outgroup species, to reconstruct a molecular phylogeny. Using a heuristic approach, we assigned MTR scenarios to the edges of the phylogenetic tree and reconstructed ancestral gene orders to identify possible synapomorphies in Orthoptera. We found all types of MTRs in our dataset: inversions, transpositions, inverse transpositions, and tandem-duplication/random loss events (TDRL). Most of the suggested MTRs were in single and unrelated species. Out of five MTRs which were unique in subgroups of Orthoptera, we suggest four of them to be synapomorphies; those were in the infraorder Acrididea, in the tribe Holochlorini, in the subfamily Pseudophyllinae, and in the two families Phalangopsidae and Gryllidae or their common ancestor (leading to the relationship ((Phalangopsidae + Gryllidae) + Trigonidiidae)). However, similar MTRs have been found in distant insect lineages. Our findings suggest convergent evolution of specific mitochondrial gene orders in several species, deviant from the evolution of the mitogenome DNA sequence. As most MTRs were detected at terminal nodes, a phylogenetic inference of deeper nodes based on MTRs is not supported. Hence, the marker does not seem to aid resolving the phylogeny of Orthoptera, but adds further evidence for the complex evolution of the whole group, especially at the genetic and genomic levels. The results indicate a high demand for more research on patterns and underlying mechanisms of MTR events in Orthoptera.

The Complete Mitogenome of Toxocara vitulorum: Novel In-Sights into the Phylogenetics in Toxocaridae

Toxocara vitulorum (Ascaridida: Nematoda) is one of the most common intestinal nematodes of cattle and buffalos and, therefore, represents a serious threat to their populations worldwide. Despite its significance in veterinary health the epidemiology, population genetics, and molecular ecology of this nematode remain poorly understood. The mitogenome can yield a foundation for studying these areas and assist in the surveillance and control of T. vitulorum. Herein, the first whole mitogenome of T. vitulorum was sequenced utilizing Illumina technology and characterized with bioinformatic pipeline analyses. The entire genome of T. vitulorum was 15,045 bp in length and contained 12 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and two ribosomal RNAs (rRNAs). The gene arrangement (GA) of T. vitulorum was similar to those of other Toxocara species under GA3. The whole genome showed significant levels of AT and GC skew. Comparative mitogenomics including sequence identities, Ka/Ks, and sliding window analysis, indicated a purifying selection of 12 PCGs with cox1 and nad6 having the lowest and highest evolutionary rate, respectively. Whole amino acid sequence-based phylogenetic analysis supported a novel sister-species relationship of T. vitulorum with the congeneric species Toxocara canis, Toxocara cati, and Toxocara malaysiensis in the family Toxocaridae. Further, 12 (PCGs) single gene-based phylogenies suggested that nad4 and nad6 genes shared same topological trees with that of the whole genome, suggesting that these genes were suitable as novel genetic markers for phylogenetic and evolutionary studies of Ascaridida species. This complete mitogenome of T. vitulorum refined phylogenetic relationships in Toxocaridae and provided the resource of markers for population genetics, systematics, and epidemiology of this bovine nematode.

Complete Mitochondrial Genome of Contracaecum sp. (Nematoda: Ascarididae) from night herons in China

Contracaecum species are zooparasitic anisakid nematodes and occur in gastrointestinal tracts of vertebrate/invertebrate animals, including humans, causing gastrointestinal pain, diarrhea, and increasingly severe vomiting. Although the complete mitochondrial (mt) genome (mitogenome) of Contracaecum sp. isolated from night herons in Beijing has been reported, the detailed information about this mt sequence is still puzzling. In the present study, we described the detailed characteristics across the complete mt DNA of Contracaecum sp., which includes 36 genes consisting of 12 protein genes, 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and 2 noncoding regions (NCRs), and all genes have the same orientation of transcription. The AT content in the complete mitogenome of Contracaecum sp. was 72.2%, and it was the least value (66.7%) in the cox1 gene but was the highest rate (84.1%) in NCRs. The highest nucleotide diversity (Pi) among the genus Contracaecum was nad4 (0.190) and the least was cox1 (0.125), which indicates that nad4 might have the potential ability as useful markers to detect cryptic species in the genus Contracaecum or subspecies. Based on the maximum likelihood (ML) and Bayesian inference (BI) computational algorithms within subfamilies Ascaridoidea and Heterakoidea, the results supported that Contracaecum sp. was a new species and the family Ascaridiidae was paraphyletic. The complete mitogenome sequence of Contracaecum sp. supported a clear recognition of Contracaecum species and provided the potential existence of cryptic species in the genus Contracaecum. Our findings would better contribute to the surveillance, molecular epidemiology, and control of Contracaecum.

Gene rearrangements in the mitochondrial genome of ten ascaris species and phylogenetic implications for Ascaridoidea and Heterakoidea families

The Ascaridoidea family and Heterakoidea family are the most common and typical representative of large parasites. Although our understanding of these parasites' diversity has expanded by analyses of some mitochondrial genes, there is limited information on these species' evolutionary rates. Here we determined ten complete mitogenome sequences of five subfamilies of Ascaridoidea and one subfamily of Heterakoidea. The phylogenetic tree divided the Ascaridoidea into six monophyletic major clades, and the divergence time of Heterakoidea family and Ascaridoidea family can be placed during the early Carboniferous Period (300-360 Mya). The reconstruction of the ancestral state showed that the gene orders of all species in Ascaridoidea were conserved, and the Heterakoidea had obvious genome rearrangement. The conserved blocks between them were divided into five and the main types are tandem-duplication/random loss (TDRL). These results will help to better understand the gene rearrangements and evolutionary position of ascaris species.

Subulura eliseae sp. n. (Ascaridida: Subuluroidea), a parasite of Marmosa spp. from Amazon rainforest, Brazil

The parasite biodiversity of mouse opossums in Brazil remains incompletely explored. We describe a new species of Subulura (Ascaridida: Subuluroidea) from the large intestine of the white-bellied woolly mouse opossum, Marmosa constantiae, based on the results of light and scanning electron microscopy (SEM). We also partially sequenced the mitochondrial cytochrome c oxidase I (MT-CO1) gene of the new species, using molecular phylogenetic analyses to determine its relationships within the Subuluroidea superfamily. As molecular data on subuluroid species are extremely limited, few inferences could be drawn from our phylogenies. Our SEM observations showed the detailed morphology of the cephalic extremity, precloacal pseudo-sucker, caudal papillae, phasmids and vulva. Subulura eliseae sp. n. differs from the other four Subulura parasites species of marsupials by the number of caudal papillae and the structure dimensions, and size of the spicule. Moreover, S. eliseae sp. n. has ten pairs of caudal papillae, which is unique compared to other species. We present morphometric and molecular data on this new species, contributing to future studies on subuluroids.

Complete mitochondrial genome of cylicocyclus auriculatus: molecular structure and phylogenetic analysis

Cylicocyclus spp. (Nematoda: Strongylida: Cyathostominae) are the common and important parasitic nematodes found in horses and donkeys worldwide. In this study, the complete mitochondrial genome of Cylicocyclus auriculatus Looss 1900, a representative member of this genus from the donkey in Southwest China was determined using the next-generation DNA sequencing technology. The genome was 13,851 bp in size and consisted of 36 genes including 12 protein-coding genes (atp6, cox1-3, cytb, nad1-6 and nad4L), 22 transfer RNA genes and two ribosomal RNA genes (rrnL and rrnS), as well as two non-coding regions. Phylogenetic analysis showed that C. auriculatus and Cylicocyclus insigne Boulenger 1917 were closely related, and then both grouped with other congeneric species and formed a monophyletic relationship with either species of Cyathostomum, Coronocyclus, Cyathostomum, Cylicostephanus or Cylicodontophorus, demonstrating their phylogenetic stability within Cyathostominae. These cumulative mitochondrial DNA data provide novel and useful genetic markers for molecular diagnostic, systematic and evolutionary biological studies of Cyathostominae nematodes.

The re-description of Synoecnemahirsutum Timm, 1959 (Synoecneminae, Ungellidae, Drilonematoidea) from a pheretimoid earthworm in Vietnam with the analysis of its phylogenetic relationships

Synoecnemahirsutum Timm, 1959 (Ungellidae, Drilonematoidea), found in the body cavity of the pheretimoid earthworm at the border of Laos and Vietnam, was re-described and illustrated. The mitochondrial genome of S.hirsutum obtained with Illumina HiSeq sequencing is the first annotated mitochondrial genome as a representative of the superfamily Drilonematoidea. The phylogeny inferred from the analysis of 12 mitochondrial genes has shown some similarity of S.hirsutum with a cephalobid Acrobeloidesvarius.

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.

Isopentenyltransferases as master regulators of crop performance: their function, manipulation, and genetic potential for stress adaptation and yield improvement

Isopentenyltransferase (IPT) in plants regulates a rate-limiting step of cytokinin (CTK) biosynthesis. IPTs are recognized as key regulators of CTK homeostasis and phytohormone crosstalk in both biotic and abiotic stress responses. Recent research has revealed the regulatory function of IPTs in gene expression and metabolite profiles including source-sink modifications, energy metabolism, nutrient allocation and storage, stress defence and signalling pathways, protein synthesis and transport, and membrane transport. This suggests that IPTs play a crucial role in plant growth and adaptation. In planta studies of IPT-driven modifications indicate that, at a physiological level, IPTs improve stay-green characteristics, delay senescence, reduce stress-induced oxidative damage and protect photosynthetic machinery. Subsequently, these improvements often manifest as enhanced or stabilized crop yields and this is especially apparent under environmental stress. These mechanisms merit consideration of the IPTs as 'master regulators' of core cellular metabolic pathways, thus adjusting plant homeostasis/adaptive responses to altered environmental stresses, to maximize yield potential. If their expression can be adequately controlled, both spatially and temporally, IPTs can be a key driver for seed yield. In this review, we give a comprehensive overview of recent findings on how IPTs influence plant stress physiology and yield, and we highlight areas for future research.

The complete mitochondrial genome of capillariid nematodes (Eucoleus annulatus): A novel gene arrangement and phylogenetic implications

Capillariid nematode is a group of endoparasites of vertebrates with a complex taxonomy, causing significant economic losses to poultry industry. The taxonomic status of the genus Eucoleus remained controversial for several decades. Mitochondrial (mt) DNA provides useful genetic markers for accurate identification of species, but complete mt genome sequences have been lacking for any Capillariid nematodes. In the present study, we decoded the complete mt genome of E. annulatus and examined its phylogenetic relationship with selected members of the class Enoplea nematodes. The circular mt genome of E. annulatus was 14,118 bp, encoded 37 genes with a single non-coding region and showed substantial gene rearrangements (especially tRNA genes) compared to other nematodes studied to date. The complete mt genome of E. annulatus showed a clear A + T bias in nucleotide composition. The number of A (5404) was approximately equal to T (5405) and the GC-skew was negative on average (-0.073). Phylogenetic analyses based on 18S rDNA placed Eucoleus spp. well apart from each other and supported the proposal that Eucoleus and Capillaria are two distinct genera. Similarly, Bayesian inference (BI) and Maximum likelihood (ML) phylogenies based on mtDNA sequences revealed that the family Capillariidae is more closely related to the family Trichuridae than to the family Trichinellidae. This is the first report of the complete mt genome of capillariid nematodes, and it will provide additional genetic markers for studying the molecular epidemiology, population genetics and systematics of capillariid nematodes and should have implications for the molecular diagnosis, prevention, and control of capillariosis in animals.

Characterization of the complete mitochondrial genome of the swine kidney worm Stephanurus dentatus (Nematoda: Syngamidae) and phylogenetic implications

Swine stephanuriasis caused by kidney worm Stephanurus dentatus is a parasitic disease in tropical and subtropical countries, leading to economic losses. Despite its significance as a pathogen, the phylogenetic position and taxonomic status of this nematode remain poorly understood. Mitochondrial (mt) genome sequences are known to provide useful genetic markers for investigations in these areas, but mt genome sequences are lacking for S. dentatus. In the present study, we determined the complete mt genome sequences of S. dentatus with an Illumina platform and compared it with the mt genomes of other closely related species. The circular mt genome was 13,735 bp in size with 36 genes. All genes are transcribed in the same direction and the mt gene arrangement is identified as a GA3 pattern, that is the most common pattern of gene arrangement observed in nematodes to date. Phylogenetic analysis using concatenated amino acid sequences of 12 protein-coding genes supported the hypothesis that S. dentatus was closely related to the family Chabertiidae. Our results provided insights into the phylogenetic relationship of the family Syngamidae within the superfamily Strongyloidea.

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.

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.

Newly discovered cichlid fish biodiversity threatened by hybridization with non-native species

Invasive freshwater fishes are known to readily hybridize with indigenous congeneric species, driving loss of unique and irreplaceable genetic resources. Here we reveal that newly discovered (2013-2016) evolutionarily significant populations of Korogwe tilapia (Oreochromis korogwe) from southern Tanzania are threatened by hybridization with the larger invasive Nile tilapia (Oreochromis niloticus). We use a combination of morphology, microsatellite allele frequencies and whole genome sequences to show that O. korogwe from southern lakes (Nambawala, Rutamba and Mitupa) are distinct from geographically disjunct populations in northern Tanzania (Zigi River and Mlingano Dam). We also provide genetic evidence of O. korogwe × niloticus hybrids in three southern lakes and demonstrate heterogeneity in the extent of admixture across the genome. Finally, using the least admixed genomic regions we estimate that the northern and southern O. korogwe populations most plausibly diverged ~140,000 years ago, suggesting that the geographical separation of the northern and southern groups is not a result of a recent translocation, and instead these populations represent independent evolutionarily significant units. We conclude that these newly discovered and phenotypically unique cichlid populations are already threatened by hybridization with an invasive species, and propose that these irreplaceable genetic resources would benefit from conservation interventions.

Evaluation and utility of mitochondrial ribosomal genes for molecular systematics of parasitic nematodes

BACKGROUND

Molecular advances have accelerated our understanding of nematode systematics and taxonomy. However, comparative analyzes between various genetic markers have led to discrepancies in nematode phylogenies. This study aimed to evaluate the suitability of using mitochondrial 12S and 16S ribosomal RNA genes for nematode molecular systematics.

METHODS

To study the suitability of mitochondrial 12S and 16S ribosomal RNA genes as genetic markers for nematode molecular systematics, we compared them with the other commonly used genetic markers, nuclear internal transcribed spacer 1 and 2 regions, nuclear 18S and 28S ribosomal RNA genes, and mitochondrial cytochrome c oxidase subunit 1 gene. After that, phylum-wide primers for mitochondrial 12S and 16S ribosomal RNA genes were designed, and parasitic nematodes of humans and animals from 75 taxa with 21 representative species were inferred through phylogenetic analyzes. Phylogenetic analyzes were carried out using maximum likelihood and Bayesian inference algorithms.

RESULTS

The phylogenetic relationships of nematodes based on the mitochondrial 12S rRNA gene supported the monophyly of nematodes in clades I, IV, and V, reinforcing the potential of this gene as a genetic marker for nematode systematics. In contrast, the mitochondrial 16S rRNA gene only supported the monophyly of clades I and V, providing evidence that the 12S rRNA gene is more suitable for nematode molecular systematics. In this study, subclades of clade III containing various nematode families were not monophyletic when the 16S or 12S rRNA gene was used as the genetic marker. This is similar to the phylogenetic relationship revealed by previous studies using whole mitochondrial genomes as genetic markers.

CONCLUSIONS

This study supports the use of the 12S rRNA gene as a genetic marker for studying the molecular systematics of nematodes to understand intra-phyla relationships. Phylum-wide primers for nematodes using mitochondrial ribosomal genes were prepared, which may enhance future studies. Furthermore, sufficient genetic variation in the mitochondrial 12S and 16S rRNA genes between species also allowed for accurate taxonomy to species level, revealing the potential of these two genes as genetic markers for DNA barcoding.

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.

Morphological and Molecular Characteristics of the Gastro-Intestinal Nematode Parasite Ascaridia columbae Infecting the Domestic Pigeon Columba livia domestica in Saudi Arabia

BACKGROUND

Parasitism is a complex problem that is often ignored in companion animals, including birds, unless it develops into a severe clinical disorder. The present study was, therefore, aimed to investigate the presence of the gastrointestinal nematode infecting the domestic pigeon and provide a complete morphological description and clarify its taxonomic position through phylogenetic analysis of the ITS1-5.8s-ITS2 rDNA gene region.

MATERIALS AND METHODS

During the current study, a total of twenty-six domestic pigeons, Columba livia domestica, were collected and internal organs examined for helminth detection. Using light and scanning electron microscopy, the recovered parasite species are studied. In addition, the selected gene region was obtained and sequenced using appropriate primers that aid in the formation of the phylogenetic dendrogram for the recovered parasite species with others retrieved from GenBank.

RESULTS

Morphological examination showed that this nematode parasite belongs to the Ascaridiidae family within the genus Ascaridia. The material was assigned to the previously described Ascaridia columbae by providing all the characteristic features as the presence of a mouth opening surrounded by three tri-lobed lips; each lip has two triangular teeth with a spoon-like structure, cephalic papillae and amphidal pores on lips surface, presence of lateral cuticular alae and pre-cloacal sucker, 10 pairs of caudal papillae, and two equal spicules in male worms. The morphological investigations of this species were supplemented by molecular analysis of ITS1-5.8s-ITS2 rDNA gene region. The data showed that the present A. coulmbae is deeply embedded in the Ascaridia genus with a 74-99% sequence similarity to other species in the Chromadorea class. Ascaridiidae appears as monophyly and represented as a sister group to Heterakidae. The ascaridiid species examined belong to the Ascaridia genus and displaced a close relationship with the previously described A. coulmbae (gb| KF147909.1, gb| AJ001509.1, gb| KC905082.1, gb| JQ995321.1, gb| JX624729.1) as putative sister taxa.

CONCLUSION

The present study revealed that the species Ascaridia is the first account of this genus as an endoparasite from the domestic pigeon inhabiting Saudi Arabia. Therefore, the combination of morphological and molecular studies helps to identify this species correctly and identified as Ascaridia columbae.

Molecular Identification and Phylogenetic Analysis of Heterakis dispar Isolated from Geese

Purpose

Heterakidosis is a common parasitic infection caused in domestic birds by Heterakis species: Heterakis gallinarum, H. isolonche, and H. dispar. Among them, the best described species is H. gallinarum, noted mainly in gallinaceous birds. In waterfowl, H. dispar is the predominant species. The variations in morphology and host specificity qualify H. dispar as a different species, but the phylogenetic relationships between heterakids were unclear for a long time, because of a lack of H. dispar sequences.

Methods

The authors provided the molecular data for H. dispar and analyzed the obtained sequences of the partial 18S rRNA gene and region ITS1-5.8SrRNA-ITS2 with the homological sequences.

Results

The 18S rRNA PCR product of H. dispar was about 800 bp, and the ITS-5.8S-ITS2 PCR product was about 920 bp, noticeably smaller size compared to H. gallinarum product. The BLAST analysis of H. dispar 18S sequence showed a 99% similarity with the sequences of Heterakis gallinarum and Ascaridia galli, 98% with A. nymphii, but only 94% with the sequence of Heterakis sp. Our ITS sequence of H. dispar was almost identical to the H. isolonche isolate, there is only one nucleotide of difference among the 943 sites analyzed. It also showed a lower similarity to the ITS sequences of H. gallinarum (88%), H. spumosa (87%), and H. dahomensis (87%).

Conclusions

In our phylogenetic analysis, it is the first attempt at the reconstruction of relationships within this superfamily Heterakoidea based on 18S rDNA and ITS region.

Genomic Analyses Identify Novel Molecular Signatures Specific for the Caenorhabditis and other Nematode Taxa Providing Novel Means for Genetic and Biochemical Studies

The phylum Nematoda encompasses numerous free-living as well as parasitic members, including the widely used animal model Caenorhabditis elegans, with significant impact on human health, agriculture, and environment. In view of the importance of nematodes, it is of much interest to identify novel molecular characteristics that are distinctive features of this phylum, or specific taxonomic groups/clades within it, thereby providing innovative means for diagnostics as well as genetic and biochemical studies. Using genome sequences for 52 available nematodes, a robust phylogenetic tree was constructed based on concatenated sequences of 17 conserved proteins. The branching of species in this tree provides important insights into the evolutionary relationships among the studied nematode species. In parallel, detailed comparative analyses on protein sequences from nematodes (Caenorhabditis) species reported here have identified 52 novel molecular signatures (or synapomorphies) consisting of conserved signature indels (CSIs) in different proteins, which are uniquely shared by the homologs from either all genome-sequenced Caenorhabditis species or a number of higher taxonomic clades of nematodes encompassing this genus. Of these molecular signatures, 39 CSIs in proteins involved in diverse functions are uniquely present in all Caenorhabditis species providing reliable means for distinguishing this group of nematodes in molecular terms. The remainder of the CSIs are specific for a number of higher clades of nematodes and offer important insights into the evolutionary relationships among these species. The structural locations of some of the nematodes-specific CSIs were also mapped in the structural models of the corresponding proteins. All of the studied CSIs are localized within the surface-exposed loops of the proteins suggesting that they may potentially be involved in mediating novel protein-protein or protein-ligand interactions, which are specific for these groups of nematodes. The identified CSIs, due to their exclusivity for the indicated groups, provide reliable means for the identification of species within these nematodes groups in molecular terms. Further, due to the predicted roles of these CSIs in cellular functions, they provide important tools for genetic and biochemical studies in Caenorhabditis and other nematodes.

Prevalence, Morphological and Molecular Phylogenetic Analyses of the Rabbit Pinworm, Passalurus ambiguus Rudolphi 1819, in the Domestic Rabbits Oryctolagus cuniculus

INTRODUCTION

Passalurus ambiguus, a pinworm nematode parasite, infects domestic and wild rabbits, hares, and rodents worldwide.

MATERIALS AND METHODS

The current parasitological study was performed during January-December 2016, to investigate helminth parasites infecting the domestic rabbit species Oryctolagus cuniculus at the Department of Animal Production, Faculty of Agriculture, Cairo University, Cairo, Egypt.

RESULTS

Of the twenty rabbit specimens examined for gastrointestinal nematodes, 75% were infected with adult oxyurid species, which were morphologically characterized using light and scanning electron microscopy studies. The oxyurid species had a triangular mouth opening surrounded by simple lips with four cephalic papillae and a pair of lateral amphidial pores with three teeth-like structures, an esophagus divided into a cylindrical corpus and globular bulb supported internally with tri-radiate valvular apparatus, and four caudal papillae distributed on the posterior end of males with a single short protruding spicule and ovijector apparatus opening ventrally by the vulva, surrounded by protruded lips in female worms. The species were compared morphometrically with other Passalurus species described previously; light differences were found in different body part sizes. Molecular characterization based on 18 small subunit (SSU) rDNA sequences showed ~ 85% similarity with other Chromadorea species. A preliminary genetic comparison between the 18S rDNA sequences of the isolated parasite and those of other oxyurid species suggested that it belonged to Passalurus ambiguus. The 18S rDNA sequence of the parasite was deposited in GenBank (accession no., MG310151.1).

CONCLUSION

The 18S rDNA gene of P. ambiguus was shown to yield a unique genetic sequence that confirms its taxonomic position within the Oxyuridae family.

Design, synthesis and biological evaluation of imidazo[1,2-a]pyridine analogues or derivatives as anti-helmintic drug

The Albendazole was used as the lead compound, which was modified by structural transformation and with alkyl groups. A total of 18 compounds (4a-4r) were designed and synthesized. The in vitro experiment results showed that compounds 4e, 4f, 4k, 4l, 4q and 4r had good inhibitory effect on egg and imago of roundworm. IC₅₀ of compound 4l to anti-egg of roundworm was 0.65 ± 0.01 μmol/L and to anti-imago of roundworm was 1.04 ± 0.01 μmol/L. At the same time, it showed that compound 4l had the best effect in vivo, and the rate of anti-helmintic could reach more than 99%. The results of acute toxicity tests indicated that these compounds were with LD₅₀ > 2100 mg/kg by oral administration, so they were low toxicity compounds. In a word, compound 4l was most likely to be a new anti-helmintic drug through screening in vitro and in vivo.

The mitochondrial genomes of the mesozoans Intoshia linei, Dicyema sp. and Dicyema japonicum

The Dicyemida and Orthonectida are two groups of tiny, simple, vermiform parasites that have historically been united in a group named the Mesozoa. Both Dicyemida and Orthonectida have just two cell layers and appear to lack any defined tissues. They were initially thought to be evolutionary intermediates between protozoans and metazoans but more recent analyses indicate that they are protostomian metazoans that have undergone secondary simplification from a complex ancestor. Here we describe the first almost complete mitochondrial genome sequence from an orthonectid, Intoshia linei, and describe nine and eight mitochondrial protein-coding genes from Dicyema sp. and Dicyema japonicum, respectively. The 14,247 base pair long I. linei sequence has typical metazoan gene content, but is exceptionally AT-rich, and has a unique gene order. The data we have analysed from the Dicyemida provide very limited support for the suggestion that dicyemid mitochondrial genes are found on discrete mini-circles, as opposed to the large circular mitochondrial genomes that are typical of the Metazoa. The cox1 gene from dicyemid species has a series of conserved, in-frame deletions that is unique to this lineage. Using cox1 genes from across the genus Dicyema, we report the first internal phylogeny of this group.

According to mitochondrial DNA evidence, Parascaris equorum and Parascaris univalens may represent the same species

Parascarosis is caused mainly by parasitic infections with Parascaris equorum and Parascaris univalens, the most common ascarid nematodes, in the small intestine of equines. Parascarosis often causes severe illness and even death in foals and yearlings. In this study, we obtained the complete sequence of the P. equorum mitochondrial (mt) genome and compared its organization and structure with that of P. equorum Japan isolate (nearly complete), and the complete mtDNA sequences of P. univalens Switzerland and USA isolates. The complete mtDNA genome of P. equorum China isolate is 13,899 base pairs (bp), making it the smallest of the four genomes. All four Parascaris mt genomes are circular, and all genes are transcribed in the same direction. The P. equorum mtDNA genome consists of 12 protein-coding genes, two ribosomal RNA genes, 22 transfer (t) RNA genes and one non-coding region, which is consistent with P. equorum Japan isolate and P. univalens Switzerland isolate but distinct from P. univalens USA isolate, which has 20 tRNA genes. Differences in nucleotide sequences of the four entire mt genomes range from 0.1–0.9%, and differences in total amino acid sequences of protein-coding genes are 0.2–2.1%. Phylogenetic analyses showed that the four Parascaris species clustered in a clade, indicating that P. equorum and P. univalens are very closely related. These mt genome datasets provide genetic evidence that P. equorum and P. univalens may represent the same species, which will be of use in further studies of the taxonomy, systematics and population genetics of ascarids and other nematodes.

New record of Ascaridia nymphii (Secernentea: Ascaridiidae) from macaw parrot, Ara chloroptera, in China

Present study was performed to identify the species of ascarids from macaw parrot, Ara chloroptera, in China. Total 6 ascarids (3 males and 3 females) were collected in the feces of 3 macaws at Guangzhou Zoo in Guangdong Province, China. Their morphological characteristics with dimensions were observed under a light microscope, and their genetic characters were analyzed with the partial 18S rDNA, ITS rDNA and nad4 gene sequences, respectively. Results showed that all worms have no interlabia but male worms have two alate spicules, well-developed precloacal sucker and a tail with ventrolateral caudal alae and 11 pairs of papillae. The partial 18S rDNA, ITS rDNA and nad4 sequences were 831bp, 1015bp and 394bp in length, respectively. They showed the highest similarity of 99.8% (18S rDNA) with Ascaridia nymphii, 93.8% identities (ITS rDNA) with A. columbae and 98.5% to 99.5% identities (nad4) with Ascaridia sp. from infected parrot. All Ascaridia nematodes from the macaws were clustered into one clade and formed monophyletic group of Ascaridia with A. columbae and A. galli in two phylogenetic trees. It is observed that the combining morphological and sequencing data from three loci, the present Ascaridia species was identified as Ascaridia nymphii, which is the first record of A. nymphii from macaw parrot in China.

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.

Characterization of the complete mitochondrial genome of Ortleppascaris sinensis (Nematoda: Heterocheilidae) and comparative mitogenomic analysis of eighteen Ascaridida nematodes

Ortleppascaris sinensis (Nematoda: Ascaridida) is a dominant intestinal nematode of the captive Chinese alligator. However, the epidemiology, molecular ecology and population genetics of this parasite remain largely unexplored. In this study, the complete mitochondrial (mt) genome sequence of O. sinensis was first determined using a polymerase chain reaction (PCR)-based primer-walking strategy, and this is also the first sequencing of the complete mitochondrial genome of a member of the genus Ortleppascaris. The circular mitochondrial genome (13,828 bp) of O. sinensis contained 12 protein-coding, 22 transfer RNA and 2 ribosomal RNA genes, but lacked the ATP synthetase subunit 8 gene. Finally, phylogenetic analysis of mtDNAs indicated that the genus Ortleppascaris should be attributed to the family Heterocheilidae. It is necessary to sequence more mtNDAs of Ortleppascaris nematodes in the future to test and confirm our conclusion. The complete mitochondrial genome sequence of O. sinensis reported here should contribute to molecular diagnosis, epidemiological investigations and ecological studies of O. sinensis and other related Ascaridida nematodes.

Genetic variation in mitochondrial cox2 of Heterakis gallinarum from poultry in Sichuan, China

Heterakis gallinarum is one of the common parasitic nematodes found in the caecum of poultry. To investigate the genetic diversity and genetic structure of the H. gallinarum population in Sichuan, we amplified and sequenced the complete mitochondrial (mt) cytochrome c oxidase subunit II (cox2) gene of 59 H. gallinarum isolates from seven different geographical regions, then analyzed their genetic polymorphisms. All cox2 genes of the 59 H. gallinarum isolates were 696 bp in length, with an average A + T content of 67.1%. Fifty-nine sequences contained 34 variable sites, and were classified into 23 haplotypes (HS1-HS23). The values of haplotype diversity (Hd) and nucleotide diversity (π) were 0.688 and 0.00288, respectively. Based on values of F_ST and Nm (F_ST = 0.01929, Nm = 12.71), there was a frequent gene flow but no significant genetic differentiation observed among the populations. The network map showed that the most prominent haplotype was HS1, and the other haplotypes (HS2-HS23) were centered on HS1 with a star-like topology, indicating that H. gallinarum had previously experienced a population expansion. To our knowledge, this is the first research on the population genetics of H. gallinarum based on mitochondrial cox2.

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.

Procamallanus spiculogubernaculus Agarwal, 1958 (Nematoda: Camallanidae) from Stinging catfish, Heteropneustes fossilis in India: morphological characterization and molecular data

The nematode, Procamallanus spiculogubernaculus Agarwal, 1958 was found from the Stinging catfish, Heteropneustes fossilis (Bloch, 1794) from Ghazipur, Delhi, India. Morphological characterization, including scanning electron microscope observation supplemented with DNA sequences is provided. Specimens recently found are characterized by the presence of an unlined buccal capsule having a small basal ring, esophagus muscular and glandular, vulva position is slightly post-equatorial, tail conical, long, and ending in three digit-like processes, phasmids present at about mid-length and cloaca located at the posterior end. In this study the species P. spiculogubernaculus is validated on the basis of molecular data after 47 years from its original description. In the scanning electron microscope examination, the topology of mouth and sensory pits in anterior portion, while the phasmids and digit like processes in posterior portion is clearly observed. Molecular data of the 18S ribosomal RNA and mitochondrial cytochrome c oxidase subunit 1 (cox1) gene were analyzed. Molecular phylogenetic analyses supported the validity of Procamallanus spiculogubernaculus and confirmed the paraphyletic status of the members of Procamallanus, Spirocamallanus, Camallanus and Paracamallanus. Taxonomic status of members of the family Camallanidae are briefly discussed along with the results of the systematic evaluation of P. spiculogubernaculus based on molecular data.

Complete mitochondrial genomes of Gnathostoma nipponicum and Gnathostoma sp., and their comparison with other Gnathostoma species

Gnathostomiasis is a foodborne zoonotic parasitosis caused by Gnathostoma nematodes. It has caused significant public problems worldwide, but its molecular biology is limited. The purpose of this study was to decode the complete mitochondrial (mt) genomes of Gnathostoma nipponicum and Gnathostoma sp., and compare their mt sequences with other Gnathostoma species. The complete mt genome sequences were amplified by long-range PCR and determined by subsequent primer walking. The complete mt genomes of G. nipponicum and Gnathostoma sp. were 14,093bp and 14,391bp, respectively. Both of the two mt genomes contain 12 protein-coding genes (PCGs), 2 ribosomal RNA genes and 22 transfer RNA genes. The gene order and transcription direction are the same as G. spinigerum and G. doloresi. The sequence difference across the entire mt genomes varied from 14.4% to 18.2% between G. nipponicum, Gnathostoma sp., G. spinigerum and G. doloresi of Japan and China isolates. Phylogenetic analyses by Bayesian inference (BI) using concatenated amino acid sequences of 12 PCGs showed that G. nipponicum and Gnathostoma sp. are two distinctive species of Gnathostoma, and G. nipponicum are more closely related to Gnathostoma sp. than to G. spinigerum. The mtDNA datasets provide abundant resources of novel markers, which can be used for the studies of molecular epidemiology and diagnosis of Gnathostoma spp.

Mitochondrial Phylogenomics yields Strongly Supported Hypotheses for Ascaridomorph Nematodes

Ascaridomorph nematodes threaten the health of humans and other animals worldwide. Despite their medical, veterinary and economic importance, the identification of species lineages and establishing their phylogenetic relationships have proved difficult in some cases. Many working hypotheses regarding the phylogeny of ascaridomorphs have been based on single-locus data, most typically nuclear ribosomal RNA. Such single-locus hypotheses lack independent corroboration, and for nuclear rRNA typically lack resolution for deep relationships. As an alternative approach, we analyzed the mitochondrial (mt) genomes of anisakids (~14 kb) from different fish hosts in multiple countries, in combination with those of other ascaridomorphs available in the GenBank database. The circular mt genomes range from 13,948-14,019 bp in size and encode 12 protein-coding genes, 2 ribosomal RNAs and 22 transfer RNA genes. Our analysis showed that the Pseudoterranova decipiens complex consists of at least six cryptic species. In contrast, the hypothesis that Contracaecum ogmorhini represents a complex of cryptic species is not supported by mt genome data. Our analysis recovered several fundamental and uncontroversial ascaridomorph clades, including the monophyly of superfamilies and families, except for Ascaridiidae, which was consistent with the results based on nuclear rRNA analysis. In conclusion, mt genome analysis provided new insights into the phylogeny and taxonomy of ascaridomorph nematodes.

The complete mitochondrial genomes of Gnathostoma doloresi from China and Japan

Gnathostoma doloresi is one of the neglected pathogens causing gnathostomiasis. Although this zoonotic parasite leads to significant socioeconomic concerns globally, little is known of its genetics and systematics. In the present study, we sequenced and characterized the complete mitochondrial (mt) genomes of G. doloresi isolates from China and Japan. The lengths of the mt genomes of the G. doloresi China and Japan isolates are 13,809 and 13,812 bp, respectively. Both mt genomes encode 36 genes, including 12 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. The gene order, transcription direction, and genome content are identical with its congener G. spinigerum. Phylogenetic analyses based on concatenated amino acid sequences of 12 PCGs by Bayesian inference (BI) indicated that G. doloresi are closely related to G. spinigerum. Our data provide an invaluable resource for studying the molecular epidemiology, phylogenetics, and population genetics of Gnathostoma spp. and should have implications for further studies of the diagnosis, prevention, and control of gnathostomiasis in humans and animals.

Molecular and ultrastructure characterization of two nematodes (Thelandros scleratus and Physalopteroides dactyluris) based on ribosomal and mitochondrial DNA sequences

The phylogenetic relationships of the nematode species Thelandros scleratus (Oxyurida: Pharyn-godonidae) and Physalopteroides dactyluris (Spirurida: Physalopteridae) were analyzed using the ribosomal 18S rRNAand the mitochondrial cytochrome C oxidase subunit genes. The nematodes were recovered from Brook's house gecko, Hemidactylus brooki (Reptilia: Gekkonidae) from Hast-inapur, Meerut (U.P.), India. The results demonstrated that T. scleratus shows 100% similarity with another sequence available from the same species and a close relationship (98-99%) with species of Parapharyngodon in both 18S rRNAand cox 1 regions. Regarding the nematode Physalopteroides. analysis showed a close phylogenetic relationship between P. dactyluris and several species of Phy-saloptera. This is the first sequence of 18S available for any species of the genus Physalopteroides

Comparative analyses of the complete mitochondrial genomes of the two murine pinworms Aspiculuris tetraptera and Syphacia obvelata

Pinworms Aspiculuris tetraptera and Syphacia obvelata are important parasitic nematodes of laboratory mice, rat and other rodents. However, the mitochondrial (mt) genome of these parasites have not been known yet. In the present study, the complete mt genomes of A. tetraptera and S. obvelata were sequenced, which were 13,669 bp and 14,235 bp in size, respectively. Both genomes included 12 protein-coding genes, two rRNA genes, 22 tRNA genes and one non-coding region. The mt genomes of A. tetraptera and S. obvelata preferred bases A and T, with the highest for T and the lowest for C. The mt gene arrangements of the two pinworms were the same as that of the GA8 type. Phylogenetic analysis using mtDNA data revealed that the Bayesian inference (BI) trees contained two big branches: species from Oxyuridomorpha, Rhabditomorpha and Ascaridomorpha formed one branch, and those from Spiruromorpha formed another branch with high statistical support. The two murine pinworms A. tetraptera and S. obvelata have closer relationship than to other pinworms. This study provides a foundation for studying the population genetics, systematics and molecular phylogeny of pinworms.

Mitochondrial genomes of Heterakis gallinae and Heterakis beramporia support that they belong to the infraorder Ascaridomorpha

Heterakis gallinae and Heterakis beramporia are the most prevalent nematode infecting native chicken breed, causing major economic losses. In the present study, the complete mitochondrial genomes (mt) of H. gallinae and H. beramporia were amplified by long-PCR and then sequenced. The complete mt genomes of H. gallinae and H. beramporia were 13,973bp and 14,012bp in size, respectively. Both mt genomes contain 12 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. All genes are transcribed in the same direction and the gene arrangement is identical to Ascaridia spp. Phylogenetic analysis based on the 12 protein-coding genes revealed that the family Heterakidae (represented by H. gallinae and H. beramporia) was more closely related to the infraorder Ascaridomorpha than it was to the infraorder Oxyuridomorpha. The present study determined the complete mt genome sequences for two Heterakis species, providing useful markers for studying the systematics, population genetics, and molecular epidemiology of these Heterakis parasites.

Mitogenomics reveals high synteny and long evolutionary histories of sympatric cryptic nematode species

Species with seemingly identical morphology but with distinct genetic differences are abundant in the marine environment and frequently co-occur in the same habitat. Such cryptic species are typically delineated using a limited number of mitochondrial and/or nuclear marker genes, which do not yield information on gene order and gene content of the genomes under consideration. We used next-generation sequencing to study the composition of the mitochondrial genomes of four sympatrically distributed cryptic species of the Litoditis marina species complex (PmI, PmII, PmIII, and PmIV). The ecology, biology, and natural occurrence of these four species are well known, but the evolutionary processes behind this cryptic speciation remain largely unknown. The gene order of the mitochondrial genomes of the four species was conserved, but differences in genome length, gene length, and codon usage were observed. The atp8 gene was lacking in all four species. Phylogenetic analyses confirm that PmI and PmIV are sister species and that PmIII diverged earliest. The most recent common ancestor of the four cryptic species was estimated to have diverged 16 MYA. Synonymous mutations outnumbered nonsynonymous changes in all protein-encoding genes, with the Complex IV genes (coxI-III) experiencing the strongest purifying selection. Our mitogenomic results show that morphologically similar species can have long evolutionary histories and that PmIII has several differences in genetic makeup compared to the three other species, which may explain why it is better adapted to higher temperatures than the other species.