Complete mitochondrial genomes of Dermacentor silvarum and comparative analyses with another hard tick Dermacentor nitens

Whole-genome sequences revealed genomic diversity and selection signatures of Dermacentor silvarum in Shaanxi, China

Dermacentor silvarum (D. silvarum) is an arthropod that feeds on blood. It is a primary tick species found in northern China that poses a significant security risk to the health and life of the host, as it has the potential to transmit a variety of pathogens to humans and animals. Through ongoing research on tick genome sequences, researchers have successfully assembled and reported reference genomes for numerous tick species. These significant advances have greatly accelerated the study of tick biology and population genomics. D. silvarum samples were obtained from the body surface of free-range goats in Yulin, Shaanxi Province, China. The whole genomes of the samples were resequenced and merged with preexisting data from the National Genomics Data Center database (project ID: PRJCA002242) to analyze the genetic structure, genetic diversity, mitochondrial genetic structure, and selection signatures of D. silvarum in the Shaanxi Province. Based on the available data, the D.silvarum species in China could be classified into two main branches. These populations exhibited low nucleotide diversity. A slight discrepancy was noted between the mitochondrial phylogenetic tree and the autosomal whole-genome phylogenetic tree of D. silvarum, consistent with a previous study. In the selected analysis of D. silvarum in the Shaanxi Province, China, genes linked to immunity, iron storage, fatty acid biosynthesis, pesticide defense, and blood digestion were identified. Leutriene A4 hydrolase (LOC119466376) was also identified, although its function remains unknown. This information is crucial for understanding the biology of D. silvarum and developing management measures.

The complete mitochondrial genome analysis of Haemaphysalis hystricis Supino, 1897 (Ixodida: Ixodidae) and its phylogenetic implications

In order to study the sequence characteristics, gene order, and codon usage of the mitochondrial genome of Haemaphysalis hystricis, and to explore its phylogenetic relationship, a total of 36 H. hystricis isolated from dogs were used as sample in this study. The mitochondrial genome of a H. hystricis was amplified with several pairs of specific primers by PCR, and was sequenced by first generation sequencing. The mitochondrial genome of H. hystricis was 14,719 bp in size, and it contained 37 genes including 13 protein coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and AT-rich region. Each PCG sequence had different lengths, the sequence longest and shortest gene were nad5 (1,652 bp) and atp8 (155 bp), respectively, among the 13 PCGs. All PCGs used ATN as their initiation codon, 10 of 13 PCGs used TAN as their termination codon, and 3 of which had incomplete termination codon (TA/T). Most of the 22 tRNAs with different sizes could form the classical cloverleaf structures expect for tRNA-Ala, tRNA-Ser1, tRNA-Ser2, and tRNA-Glu, and there were base mismatch (U-U and U-G) in all the 22 tRNAs sequences. Two rRNAs, namely rrnL and rrnS, had different lengths, rrnL located between tRNA-Leu1 and tRNA-Val, and rrnS located between tRNA-Val and tRNA-Ile, respectively. Two AT (D-loop) control areas with different lengths were in the mitochondrial genome, the NCRL was located between tRNA-Leu2 and tRNA-Cys, and the NCRS was located between rrnS and tRNA-Ile. The complete mitochondrial genome sequence of H. hystricis was AT preferences, and the gene order is the same as that of other Haemaphysalis family ticks. However, phylogenetic analysis showed that H. hystricis was most closely related to Haemaphysalis longicornis among the selected ticks. The mitochondrial genome not only enriches the genome database, provides more novel genetic markers for identifying tick species, and studying its molecular epidemiology, population genetics, systematics, but also have implications for the diagnosis, prevention, and control of ticks and tick-borne diseases in animals and humans.

Unraveling the phylogenetics of genetically closely related species, Haemaphysalis japonica and Haemaphysalis megaspinosa, using entire tick mitogenomes and microbiomes

Ticks have a profound impact on public health. Haemaphysalis is one of the most widespread genera in Asia, including Japan. The taxonomy and genetic differentiation of Haemaphysalis spp. is challenging. For instance, previous studies struggled to distinguish Haemaphysalis japonica and Haemaphysalis megaspinosa due to the dearth of nucleotide sequence polymorphisms in widely used barcoding genes. The classification of H. japonica japonica and its related sub-species Haemaphysalis japonica douglasi or Haemaphysalis jezoensis is also confused due to their high morphological similarity and a lack of molecular data that support the current classification. We used mitogenomes and microbiomes of H. japonica and H. megaspinosa to gain deeper insights into the phylogenetic relationships and genetic divergence between two species. Phylogenetic analyses of concatenated nucleotide sequences of protein-coding genes and ribosomal DNA genes distinguished H. japonica and H. megaspinosa as monophyletic clades, with further subdivision within the H. japonica clade. The 16S rRNA and NAD5 genes were valuable markers for distinguishing H. japonica and H. megaspinosa. Population genetic structure analyses indicated that genetic variation within populations accounted for a large proportion of the total variation compared to variation between populations. Microbiome analyses revealed differences in alpha and beta diversity between H. japonica and H. megaspinosa: H. japonica had the higher diversity. Coxiella sp., a likely endosymbiont, was found in both Haemaphysalis species. The abundance profiles of likely endosymbionts, pathogens, and commensals differed between H. japonica and H. megaspinosa: H. megaspinosa was more diverse.

Phylogenomics resolves the higher-level phylogeny of herbivorous eriophyoid mites (Acariformes: Eriophyoidea)

BACKGROUND

Eriophyoid mites (Eriophyoidea) are among the largest groups in the Acariformes; they are strictly phytophagous. The higher-level phylogeny of eriophyoid mites, however, remains unresolved due to the limited number of available morphological characters-some of them are homoplastic. Nevertheless, the eriophyoid mites sequenced to date showed highly variable mitochondrial (mt) gene orders, which could potentially be useful for resolving the higher-level phylogenetic relationships.

RESULTS

Here, we sequenced and compared the complete mt genomes of 153 eriophyoid mite species, which showed 54 patterns of rearranged mt gene orders relative to that of the hypothetical ancestor of arthropods. The shared derived mt gene clusters support the monophyly of eriophyoid mites (Eriophyoidea) as a whole and the monophylies of six clades within Eriophyoidea. These monophyletic groups and their relationships were largely supported in the phylogenetic trees inferred from mt genome sequences as well. Our molecular dating results showed that Eriophyoidea originated in the Triassic and diversified in the Cretaceous, coinciding with the diversification of angiosperms.

CONCLUSIONS

This study reveals multiple molecular synapomorphies (i.e. shared derived mt gene clusters) at different levels (i.e. family, subfamily or tribe level) from the complete mt genomes of 153 eriophyoid mite species. We demonstrated the use of derived mt gene clusters in unveiling the higher-level phylogeny of eriophyoid mites, and underlines the origin of these mites and their co-diversification with angiosperms.

Revealing the Diversity of the Mycobiome in Different Phases of Ticks: ITS Gene-Based Analysis

Ticks are obligate ectoparasites and vectors of a variety of pathogens in humans and animals. Certain tick-borne pathogens (TBPs) have been identified as the cause of zoonoses, posing potentially significant threats to the human health and livestock industries. Fungi are one of the major TBPs that can affect ticks and cause disease in humans. At present, there are few studies on the diversity of fungal microbial communities carried by Ixodes. Therefore, profiling tick-borne fungi will contribute to understanding the tick-fungal interaction. This study evaluated the community profile and differences in the fungal microbiome in Ixodidae collected on parasitic ticks or nonparasitic ticks in Wuwei, Gansu Province, China. The Shannon index, Simpson index, and Richness index were used to evaluate the diversity of mycobiome. Principle coordinates analysis (PCoA) was conducted to determine patterns of diversity in mycobiome. Using correlation analysis to determine the correlation of mycobiome. The results show that the high-throughput sequencing of the internal transcribed spacer gene generated 3,634,943 raw reads and 7,482 amplicon sequence variants. The dominant tick species in this region was Dermacentor nuttalli (Ixodidae). The mycobiome belonged to four classes-Dothideomycetes, Sordariomycetes, Ustilaginomycetes, and Tremellomycetes-and more than 261 genera, the most abundant genera were Cladosporium, Purpureocillium, Aureobasidium, Tranzscheliella, and Sporormiella. Alpha diversity indicated that the abundance and evenness of mycobiome were marginally higher in nonparasitic ticks than in parasitic ticks. PCoA showed that the community structures of parasitic ticks vary from nonparasitic ticks, samples from nonparasitic ticks tended to cluster more closely than those from the parasitic ticks. Correlation analysis indicated that there was a significant positive correlation or negative correlation between the mycobiome. Our results indicate that the mycobiome carried by Dermacentor nuttalli had rich diversity, and there was a significant difference in mycobiome between parasitic ticks and nonparasitic ticks. These findings may conducive to understand the complex interaction between ticks and commensal fungi and provide help for the further exploration of the behavioral characteristics of ticks and formulation of effective biological control measures.

Phylogenetic relationships of the Amblyomma cajennense complex (Acari: Ixodidae) at mitogenomic resolution

The genus Amblyomma is the third most diverse in the number of species within the Ixodidae, with practically half of its species distributed in the Americas, though there are also species occurring in Africa, Asia, and Australia. Within the genus, there are several species complexes with veterinary and public health importance. The Amblyomma cajennense complex, in the Americas, is represented by six species with a wide distribution, from Texas to northern Argentina. We combined two sequencing techniques to generate complete mitogenomes of species belonging to the Amblyomma cajennense complex: genome skimming and long-range PCRs sequencing methods. Thus, we generated seven new mitochondrial genomes for all species of the Amblyomma cajennense complex, except for Amblyomma interandinum. Genetic distances between the mitogenomes corroborate the clear differentiation between the five species of the Amblyomma cajennense complex. The phylogenetic relationships of these species had previously been evaluated by combining partial nuclear and mitochondrial genes and here these relationships are corroborated with a more robust framework of data, which demonstrates that the conjunction of mitochondrial and nuclear partial genes can resolve close relationships when entire genes or genomes are unavailable. The gene order, structure, composition, and length are stable across these mitogenomes, and they share the general characteristics of Metastriata. Future studies should increase the number of available mitogenomes for this genus, especially for those species from the Indo-Pacific region and Africa, by means of a better understanding of their relationships and evolutionary process.

Comparative analysis of the mitochondrial genome of Dermacentor steini from different regions in China

Ticks are a group of blood-sucking ectoparasites that play an important role in human health and livestock production development as vectors of zoonotic diseases. The phylogenetic tree of single genes cannot accurately reflect the true kinship between species. Based on the complete mitochondrial genome analysis one can help to elucidate the phylogenetic relationships among species. In this study, the complete mitochondrial genome of Dermacentor steini (isolate Longyan) was sequenced and compared with the mitochondrial genes of 3 other Chinese isolates (Nanchang, Jinhua and Yingtan). In Dermacentor steini 4 isolates had identical or similar mitochondrial genome lengths and an overall variation of 0.76% between sequences. All nucleotide compositions showed a distinct AT preference. The most common initiation and stop codons were ATG and TAA, respectively. Fewer base mismatches were found in the tRNA gene of D. steini (isolate Longyan), and the vicinity of the control region and tRNA gene was a hot rearrangement region of the genus Dermacentor. Maximum likelihood trees and Bayesian trees indicate that D. steini is most closely related to Dermacentor auratus. The results enrich the mitochondrial genomic data of species in the genus Dermacentor and provide novel insights for further studies on the phylogeographic classification and molecular evolution of ticks.

Complete Mitogenomes of Ticks Ixodes acutitarsus and Ixodes ovatus Parasitizing Giant Panda: Deep Insights into the Comparative Mitogenomic and Phylogenetic Relationship of Ixodidae Species

Ticks rank second in the world as vectors of disease. Tick infestation is one of the factors threatening the health and survival of giant pandas. Here, we describe the mitogenomes of Ixodes acutitarsus and Ixodes ovatus parasitizing giant pandas, and perform comparative and phylogenetic genomic analyses on the newly sequenced and other available mitogenomes of hard ticks. All six newly determined mitogenomes contain a typical gene component and share an ancient Arthropoda gene arrangement pattern. Our study suggests that I. ovatus is a species complex with high genetic divergence, indicating that different clades of I. ovatus represent distinct species. Comparative mitogenomic analyses show that the average A + T content of Ixodidae mitogenomes is 78.08%, their GC-skews are strongly negative, while AT-skews fluctuate around 0. A large number of microsatellites are detected in Ixodidae mitogenomes, and the main microsatellite motifs are mononucleotide A and trinucleotide AAT. We summarize five gene arrangement types, and identify the trnY-COX1-trnS1-COX2-trnK-ATP8-ATP6-COX3-trnG fragment is the most conserved region, whereas the region near the control region is the rearrangement hotspot in Ixodidae mitogenomes. The phylogenetic trees based on 15 genes provide a very convincing relationship (Ixodes + (Robertsicus + ((Bothriocroton + Haemaphysalis) + (Amblyomma + (Dermacentor + (Rhipicentor + (Hyalomma + Rhipicephalus))))))) with very strong supports. Remarkably, Archaeocroton sphenodonti is embedded in the Haemaphysalis clade with strong supports, resulting in paraphyly of the Haemaphysalis genus, so in-depth morphological and molecular studies are essential to determine the taxonomic status of A. sphenodonti and its closely related species. Our results provide new insights into the molecular phylogeny and evolution of hard ticks, as well as basic data for population genetics assessment and efficient surveillance and control for the giant panda-infesting ticks.

The complete mitochondrial genome of Ixodes vespertilionis (Acari: Ixodidae)

Ixodes vespertilionis is a tick parasitizing on the bodies of bats. In our study, the complete mitogenome of I. vespertilionis was determined by using Illumina sequencing technology. The mitogenome was 14,559 bp in size and was predicted to encode 37 genes including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and one control region. The gene order of the mitogenome is identical to Argasidae and non-Australasian Prostriata. The phylogenetic analysis by the Maximum-likelihood method reveals that I. vespertilionis is phylogenetically closest to Ixodes simplex. These data provide novel reference for further studies on the population genetics and phylogenetics of ticks.

Identification of tick-borne pathogens by metagenomic next-generation sequencing in Dermacentor nuttalli and Ixodes persulcatus in Inner Mongolia, China

Background

Hard ticks act as arthropod vectors in the transmission of human and animal pathogens and are widely distributed in northern China. The aim of this study is to screen the important tick-borne pathogens (TBPs) carried by hard ticks in Inner Mongolia using metagenomic next-generation sequencing (mNGS) and to estimate the risk of human infection imposed by tick bites.

Methods

The adult Dermacentor nuttalli (n = 203) and Ixodes persulcatus (n = 36) ticks feeding on cattle were collected. The pooled DNA samples prepared from these ticks were sequenced as the templates for mNGS to survey the presence of TBPs at the genus level. Individual tick DNA samples were detected by genus--specific or group-specific nested polymerase chain reaction (PCR) of these TBPs and combined with DNA sequencing assay to confirm the results of mNGS.

Results

R. raoultii (45.32%, 92/203), Candidatus R. tarasevichiae (5.42%, 11/203), Anaplasma sp. Mongolia (26.60%, 54/203), Coxiella-like endosymbiont (CLE) (53.69%, 109/203), and Babesia venatorum (7.88%, 16/203) were detected in D. nuttalli, while R. raoultii (30.56%, 11/36), Anaplasma sp. Mongolia (27.80%, 10/36), and CLE (27.80%, 10/36) were detected in I. persulcatus. The double- and triple-pathogen/endosymbiont co-infections were detected in 40.39% of D. nuttalli and 13.89% of I. persulcatus, respectively. The dual co-infection with R. raoultii and CLE (14.29%, 29/203) and triple co-infection with R. raoultii, Anaplasma sp. Mongolia, and CLE (13.79%, 28/203) were most frequent in D. nuttalli.

Conclusions

This study provides insight into the microbial diversity of D. nuttalli and I. persulcatus in Inner Mongolia, China, reporting for the first time that Candidatus R. tarasevichiae had been found in D. nuttalli in China, and for the first time in the world that Anaplasma sp. Mongolia has been detected in I. persulcatus. This study proves that various vertically transmitted pathogens co-inhabit D. nuttalli and I. persulcatus, and indicates that cattle in Inner Mongolia are exposed to several TBPs.

Graphic Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-021-04740-3.

Complete mitochondrial genome characterization and phylogenetic analyses of the main vector of Crimean-Congo haemorrhagic fever virus: Hyalomma marginatum Koch, 1844

The Mediterranean tick, Hyalomma marginatum, is the most important vector of Crimean-Congo haemorrhagic fever virus and several pathogens that cause animal and human diseases and economic losses to livestock production. Given the medical and veterinary importance of this tick species, we sequenced and characterized its mitochondrial genome (mitogenome) for the first time. We designed two new primer sets and combined long-range PCR with next generation sequencing to generate complete mitogenomes with deep coverage from 10 H. marginatum adults. The mitogenomes contained 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal subunits, two control regions, and three tick-box motifs. The nucleotide composition of the H. marginatum mitogenomes were A+T biased (79.76%) and exhibited negative AT- and GC- skews across most PCGs. All PCGs were initiated by ATK codons and two truncated termination codons were seen in the COX2 and COX3 genes. All tRNAs exhibited typical cloverleaf structures, except for tRNA^Cys and tRNA^Ser1. A total of 62 polymorphic sites defined ten unique haplotypes. Phylogenetic analyses based on the 13 PCGs of 56 tick species revealed that four Hyalomma species (H. marginatum, H. asiaticum, H. rufipes, and H. truncatum) formed a monophyletic clade with strong support. The results of this study provide a comprehensive resource for further studies on the systematics, population genetics, molecular epidemiology, and evolution of ticks.

The complete mitochondrial genome sequences of the cat flea Ctenocephalides felis felis (Siphonaptera: Pulicidae) support the hypothesis that C. felis isolates from China and USA were the same C. f. felis subspecies

The cat flea Ctenocephalides felis (Siphonaptera: Pulicidae) is the most important ectoparasite in cats and dogs worldwide. Over the years, there has been much dispute regarding the taxonomic and systematic status of C. felis. Mitochondrial (mt) genome sequences are useful genetic markers for the identification and differentiation of ectoparasites, but the mt genome of C. felis and its subspecies has not yet been entirely characterized. In the present study, the entire mt genome of C. f. felis from China was sequenced and compared with that of C. felis from the USA. Both contain 37 genes and a long non-coding region of >6 kbp. The molecular identity between the Chinese and American isolates was 99%, except for the non-coding region. The protein-coding genes showed differences at both the nucleotide (1.2%) and amino acid (1%) levels. Interestingly, the cox1 gene of the Chinese isolate had an unusual putative start codon (TTT). Taken together, our analyses strongly support the hypothesis that C. felis isolates from China and the USA were the same C. f. felis subspecies. The mt genome sequence of the C. f. felis China isolate presented in this study provides useful molecular markers to further address the taxonomy and systematics of C. felis.

The complete mitochondrial genome of Dermacentor (Indocentor) auratus (Acari, Ixodidae)

Dermacentor (Indocentor) auratus Supino, 1897 is a prominent ixodid vector of numerous pathogens of public health and veterinary importance. Using long-range PCR of two overlapping regions sequenced on an Illumina MiSeq machine, the complete mitochondrial genome of D. auratus is reported here. The resulting contigs were able to be assembled into a complete and circularised genome which had the general organisation of the mitochondrial genomes of the Metastriates. It had a total length of 14,766 bp and contained 37 genes, including 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes, as well as 2 non-coding control regions and 3 tick-boxes. The phylogenetic analysis on the whole mitogenome confirmed the position of D. auratus within the Dermacentor clade.

Characterization of the complete mitochondrial genome of Amblyomma ovale, comparative analyses and phylogenetic considerations

In this study, we sequenced two complete mitochondrial genomes of Amblyomma ovale, a tick of public health importance. Sequencing two distinct individuals, the resulting mitochondrial genomes were 14,756 and 14,760 bp in length and maintained the same gene order previously reported in Amblyomma. These were combined with RNA-seq derived mitochondrial sequences from three additional species, Amblyomma aureolatum, Amblyomma maculatum, and Amblyomma moreliae, to carry out mitogenome comparative and evolutionary analyses against all previously published tick mitochondrial genomes. We described a derivative genome rearrangement that isolates Ixodes from the remaining Ixodidae and consists of both a reverse translocation as well as an event of Tandem Duplication Random Loss. Genetic distance analyses indicated that cox2, nd1, nd5, and 16S are good candidates for future population studies in A. ovale. The phylogenetic analyses corroborated the utility of complete mitochondrial genomes as phylogenetic markers within the group. This study further supplements the genome information available for Amblyomma and facilitates future evolutionary and population genetic studies within the genus.

Microbiome analysis of the saliva and midgut from partially or fully engorged female adult Dermacentor silvarum ticks in China

Dermacentor silvarum is widely distributed in northern China and transmits several pathogens that cause diseases in humans and domestic animals. We analysed the comprehensive bacterial community of the saliva and midgut from partially and fully engorged female adult D. silvarum. Dermacentor silvarum samples were collected from Guyuan, China. Bacterial DNA was extracted from the saliva and midgut contents of partially or fully engorged female adult D. silvarum. Sequencing of the V3-V4 hypervariable regions of the 16S rRNA genes was performed using the IonS5^TMXL platform. The bacterial diversity in saliva was higher than in the midgut. The bacterial diversity of saliva from fully engorged ticks was greater than in partially engorged tick saliva. The bacterial diversity in midguts from partially engorged ticks was greater than in fully engorged tick midguts. Proteobacteria was the most dominant bacterial phylum in all of the samples. Twenty-nine bacterial genera were detected in all of the samples. Rickettsia, Anaplasma, and Stenotrophomonas were the main genera. The symbionts Coxiella, Arsenophonus, and Wolbachia were also detected in all of the samples. Eight bacterial species were identified in all of the experimental samples. Anaplasma marginale was reported for the first time in D. silvarum.

The mitochondrial genome of the ornate sheep tick, Dermacentor marginatus

The ornate sheep tick, Dermacentor marginatus, is widespread in Europe. Its vector role of various zoonotic pathogens received much attention in these regions. However, the genomic resources of the ticks are limited. In this study, the complete mitochondrial genome of a single female D. marginatus collected in Slovakia was sequenced through the Illumina HiSeq sequencing platform. The mitochondrial genome is 15,067 bp long and contains 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes. The overall G+C content is 21.6%. The gene order is identical to that of Metastriata ticks. The codon usage pattern is similar with that of other tick species. As in other ticks, two truncated tRNA genes were observed. Two control regions were found between tRNA-Leu and tRNA-Cys, tRNA-Ile and rrnS, respectively. The mitochondrial genome contains three noncoding regions, which is similar to that in D. nitens. The noncoding region located between rrnS and tRNA-Val is shorter than that of other Dermacentor species. Phylogenetic analyses indicate that D. marginatus is clustered with other Dermacentor species. These findings are helpful for exploring the systematics and evolution of ticks in the future.

Tick mitochondrial genomes: structural characteristics and phylogenetic implications

Ticks are obligate blood-sucking arachnid ectoparasites from the order Acarina, and many are notorious as vectors of a wide variety of zoonotic pathogens. However, the systematics of ticks in several genera is still controversial. The mitochondrial genome (mt-genome) has been widely used in arthropod phylogeny, molecular evolution and population genetics. With the development of sequencing technologies, an increasing number of tick mt-genomes have been sequenced and annotated. To date, 63 complete tick mt-genomes are available in the NCBI database, and these genomes have become an increasingly important genetic resource and source of molecular markers in phylogenetic studies of ticks in recent years. The present review summarizes all available complete mt-genomes of ticks in the NCBI database and analyses their characteristics, including structure, base composition and gene arrangement. Furthermore, a phylogenetic tree was constructed using mitochondrial protein-coding genes (PCGs) and ribosomal RNA (rRNA) genes from ticks. The results will provide important clues for deciphering new tick mt-genomes and establish a foundation for subsequent taxonomic research.

The Complete Mitochondrial Genome and Expression Profile of Mitochondrial Protein-Coding Genes in the Bisexual and Parthenogenetic Haemaphysalis longicornis

The tick Haemaphysalis longicornis is widely distributed in eastern Asia, New Zealand and Australia, and is well-known as a vector of multiple zoonotic pathogens. This species exhibits two reproductive strategies, bisexual and obligate parthenogenetic reproduction. Hence, in the current study, the complete mitochondrial genomes of the bisexual and parthenogenetic populations were assembled and analyzed, and the expression of the mitochondrial protein-coding genes was evaluated and compared between the two reproductive populations. The results indicated that the length of the mitochondrial genomes of the two reproductive populations is 14,694 and 14,693 bp in the bisexual and parthenogenetic populations, respectively. The AT content in the mitochondrial genome of the bisexual and obligate parthenogenetic population reached 77.22 and 77.34%, respectively. The phylogenetic tree was constructed combining 13 protein-coding genes, which showed that the genetic distance between the bisexual and parthenogenetic populations was less than that between the subspecies. The expression of the mitochondrial protein-coding genes was quantitatively analyzed at different feeding status for the bisexual and parthenogenetic populations, and the results showed significant differences in the expression patterns of these genes, suggesting that they might trigger specific energy utilization mechanisms due to their different reproductive strategies and environmental pressures.

Species delimitation of the Dermacentor ticks based on phylogenetic clustering and niche modeling

Three species belonging to the genus Dermacentor (Acari: Ixodidae), D. marginatus, D. nuttalli and D. silvarum are well known as vectors for a great variety of infection pathogens. All three of them are host ticks, which are very similar in morphology characteristics, life cycle, seasonal variation and ecological conditions, making it difficult to distinguish the three species. In the present study, these three species were delimitated based on molecular data and ecological niche. The molecular analysis showed that the three species can be distinguished by COI and ITS2 sequences. We created future potential distribution maps for the three species under climate changes with MaxEnt, which highlighted the different levels of the suitable habitats for each tick species. In addition, niche comparisons among the three species in Dermacentor were conducted, and the analysis suggested that niche overlap was relatively high with D. nuttalli and D. silvarum compared to the other species pairs, which was consistent with the molecular data. Niche equivalency and similarity test confirmed that these Dermacentor species were closely related but distinct species. In conclusion, delimitation of these three species within Dermacentor was supported by molecular phylogeny and quantitative ecological space. This study will provide deep insights into the biology, ecology, and diversification processes within Dermacentor species, and for the development of effective control for ticks.

Molecular characterization of six Hyalomma species using mitochondrial markers

Hyalomma species (Acari: Ixodidae) are vectors of several human and animal pathogens. However, due to their similar morphological properties, classification of related Hyalomma species is often challenging. Here we describe a combined approach for molecular characterization of six Hyalomma species: H. aegyptium, H. dromedarii, H. excavatum, H. impeltatum, H. marginatum and H. turanicum. This procedure was developed using a combination of PCR amplification of four molecular markers, followed by sequencing and species-specific restriction analysis. Segments from the following genes were used as markers: 12S rRNA, 16S rRNA, Cytochrome C oxidase subunit 1 (COX1), and Cytochrome B (CytB). Phylogenetic analysis based on the amplified sequences was consistent with the morphology-based classification. It revealed relative close proximity of H. excavatum, H. marginatum and H. turanicum, and close proximity of H. aegyptium and H. dromedarii to each other. H. impeltatum was examined using the COX1 and CytB markers, and in both cases was located on a separate clade from the other five species. Digestion of the amplified products using specific restriction enzymes enabled clear distinction between the six species. This report is the first to describe CytB marker sequences of the studied species, and the first to describe COX1 marker sequences of H. aegyptium, H. excavatum, H. impeltatum and H. turanicum. The information obtained in this study may therefore be useful for future combined morphological-molecular Hyalomma characterization.

Argasid and ixodid systematics: Implications for soft tick evolution and systematics, with a new argasid species list

The systematics of the genera and subgenera within the soft tick family Argasidae is not adequately resolved. Different classification schemes, reflecting diverse schools of scientific thought that elevated or downgraded groups to genera or subgenera, have been proposed. In the most recent classification scheme, Argas and Ornithodoros are paraphyletic and the placement of various subgenera remains uncertain because molecular data are lacking. Thus, reclassification of the Argasidae is required. This will enable an understanding of soft tick systematics within an evolutionary context. This study addressed that knowledge gap using mitochondrial genome and nuclear (18S and 28S ribosomal RNA) sequence data for representatives of the subgenera Alectorobius, Argas, Chiropterargas, Ogadenus, Ornamentum, Ornithodoros, Navis (subgen. nov.), Pavlovskyella, Persicargas, Proknekalia, Reticulinasus and Secretargas, from the Afrotropical, Nearctic and Palearctic regions. Hard tick species (Ixodidae) and a new representative of Nuttalliella namaqua (Nuttalliellidae), were also sequenced with a total of 83 whole mitochondrial genomes, 18S rRNA and 28S rRNA genes generated. The study confirmed the utility of next-generation sequencing to retrieve systematic markers. Paraphyly of Argas and Ornithodoros was resolved by systematic analysis and a new species list is proposed. This corresponds broadly with the morphological cladistic analysis of Klompen and Oliver (1993). Estimation of divergence times using molecular dating allowed dissection of phylogeographic patterns for argasid evolution. The discovery of cryptic species in the subgenera Chiropterargas, Ogadenus and Ornithodoros, suggests that cryptic speciation is common within the Argasidae. Cryptic speciation has implications for past biological studies of soft ticks. These are discussed in particular for the Ornithodoros (Ornithodoros) moubata and Ornithodoros (Ornithodoros) savignyi groups.

The complete mitochondrial genome of Haemaphysalis concinna (Ixodida: Ixodidae)

The complete mitochondrial genome of Haemaphysalis concinna is reported for the first time in this study. Its entire mitogenome is 14,675 bp in length, contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and two non-coding regions. Among the 13 protein-coding genes, apart from the nad1, nad4, nad4L, and nad5 gene encoded on the L-strand, the remaining protein-coding genes were encoded on the H-strand. The phylogenetic analysis by Bayesian inference method shows that Amblyomma sphenodonti and H. parva formed one clade, while H. concinna and other species of genus Haemaphysalis formed the other clade, indicating that H. concinna belong to the genus Haemaphysalis.

Mitochondrial DNA Evidence Supports the Hypothesis that Triodontophorus Species Belong to Cyathostominae

Equine strongyles, the significant nematode pathogens of horses, are characterized by high quantities and species abundance, but classification of this group of parasitic nematodes is debated. Mitochondrial (mt) genome DNA data are often used to address classification controversies. Thus, the objectives of this study were to determine the complete mt genomes of three Cyathostominae nematode species (Cyathostomum catinatum, Cylicostephanus minutus, and Poteriostomum imparidentatum) of horses and reconstruct the phylogenetic relationship of Strongylidae with other nematodes in Strongyloidea to test the hypothesis that Triodontophorus spp. belong to Cyathostominae using the mt genomes. The mt genomes of Cy. catinatum, Cs. minutus, and P. imparidentatum were 13,838, 13,826, and 13,817 bp in length, respectively. Complete mt nucleotide sequence comparison of all Strongylidae nematodes revealed that sequence identity ranged from 77.8 to 91.6%. The mt genome sequences of Triodontophorus species had relatively high identity with Cyathostominae nematodes, rather than Strongylus species of the same subfamily (Strongylinae). Comparative analyses of mt genome organization for Strongyloidea nematodes sequenced to date revealed that members of this superfamily possess identical gene arrangements. Phylogenetic analyses using mtDNA data indicated that the Triodontophorus species clustered with Cyathostominae species instead of Strongylus species. The present study first determined the complete mt genome sequences of Cy. catinatum, Cs. minutus, and P. imparidentatum, which will provide novel genetic markers for further studies of Strongylidae taxonomy, population genetics, and systematics. Importantly, sequence comparison and phylogenetic analyses based on mtDNA sequences supported the hypothesis that Triodontophorus belongs to Cyathostominae.

Genetic variation in mitochondrial genes of the tick Haemaphysalis flava collected from wild hedgehogs in China

The tick Haemaphysalis flava (Acari: Ixodidae) is an important ectoparasite, which causes direct damage to their hosts and also acts as a vector of various infectious disease agents in China. Despite its significance, the epidemiology, genetics and biology of H. flava has not been studied in detail. In the present study, the genetic variation in three mitochondrial (mt) DNA regions, namely cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 1 and 4 (nad1 and nad4), was examined in H. flava ticks collected from wild hedgehogs in China. A portion of cox1 (pcox1), nad1 (pnad1) and nad4 (pnad4) genes were PCR amplified from individual H. flava ticks and the amplicons were sequenced. The length of the sequences of pcox1, pnad1 and pnad4 were 849, 285 and 626 bp, respectively. The intra-specific sequence variation within H. flava was 0-0.4% for pcox1, 0-0.4% for pnad1 and 0-0.3% for pnad4. However, the inter-specific variation was significantly higher, 12.5-14.3%, 13.6-24.8% and 14.8-19% for pcox1, pnad1 and pnad4, respectively. Phylogenetic analysis based on Maximum likelihood (ML) method using the combined target mt gene sequences confirmed that all isolates of Haemaphysalis were H. flava. The molecular approach employed in this study provides a tool for further elucidating the molecular diversity of H. flava in China and elsewhere in Asia.