Large-Scale Comparative Analyses of Tick Genomes Elucidate Their Genetic Diversity and Vector Capacities.

Among arthropod vectors, ticks transmit the most diverse human and animal pathogens, leading to an increasing number of new challenges worldwide. Here we sequenced and assembled high-quality genomes of six ixodid tick species and further resequenced 678 tick specimens to understand three key aspects of ticks: genetic diversity, population structure, and pathogen distribution. We explored the genetic basis common to ticks, including heme and hemoglobin digestion, iron metabolism, and reactive oxygen species, and unveiled for the first time that genetic structure and pathogen composition in different tick species are mainly shaped by ecological and geographic factors. We further identified species-specific determinants associated with different host ranges, life cycles, and distributions. The findings of this study are an invaluable resource for research and control of ticks and tick-borne diseases.

PREDAC-CNN: predicting antigenic clusters of seasonal influenza A viruses with convolutional neural network.

Vaccination stands as the most effective and economical strategy for prevention and control of influenza. The primary target of neutralizing antibodies is the surface antigen hemagglutinin (HA). However, ongoing mutations in the HA sequence result in antigenic drift. The success of a vaccine is contingent on its antigenic congruence with circulating strains. Thus, predicting antigenic variants and deducing antigenic clusters of influenza viruses are pivotal for recommendation of vaccine strains. The antigenicity of influenza A viruses is determined by the interplay of amino acids in the HA1 sequence. In this study, we exploit the ability of convolutional neural networks (CNNs) to extract spatial feature representations in the convolutional layers, which can discern interactions between amino acid sites. We introduce PREDAC-CNN, a model designed to track antigenic evolution of seasonal influenza A viruses. Accessible at http://predac-cnn.cloudna.cn, PREDAC-CNN formulates a spatially oriented representation of the HA1 sequence, optimized for the convolutional framework. It effectively probes interactions among amino acid sites in the HA1 sequence. Also, PREDAC-CNN focuses exclusively on physicochemical attributes crucial for the antigenicity of influenza viruses, thereby eliminating unnecessary amino acid embeddings. Together, PREDAC-CNN is adept at capturing interactions of amino acid sites within the HA1 sequence and examining the collective impact of point mutations on antigenic variation. Through 5-fold cross-validation and retrospective testing, PREDAC-CNN has shown superior performance in predicting antigenic variants compared to its counterparts. Additionally, PREDAC-CNN has been instrumental in identifying predominant antigenic clusters for A/H3N2 (1968-2023) and A/H1N1 (1977-2023) viruses, significantly aiding in vaccine strain recommendation.

Drug-Embedded Nanovesicles Assembled from Peptide-Decorated Hyaluronic Acid for Rheumatoid Arthritis Synergistic Therapy.

Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease that causes endless pain and poor quality of life in patients. Usage of a lubricant combined with anti-inflammatory therapy is considered a reasonable and effective approach for the treatment of RA. Herein, inspired by glycopeptides, a peptide-decorated hyaluronic acid was synthesized, and the grafted Fmoc-phenylalanine-phenylalanine-COOH (FmocFF) peptide self-assembled with ß-sheet conformations could induce the folding of polymer molecular chains to form a vesicle structure in aqueous solution. The hydrophobic anti-inflammatory drug curcumin (Cur) could be embedded in the vesicle walls through π-π interactions with the FmocFF peptide. Furthermore, the inflammation suppression function of the Cur-loaded vesicles both in vitro and in vivo was demonstrated to be an effective treatment for RA therapy. This work proposes new insights into the folding and hierarchical assembly of glycopeptide mimics, providing an efficient approach for constructing intelligent platforms for drug delivery, disease therapy, and diagnostic applications.

The genome-wide characterization and associated cold-tolerance function of the superoxide dismutase in the cold response of the tick Haemaphysalis longicornis.

Accumulating evidence suggests that superoxide dismutase (SOD) is the first line of antioxidant defense in organisms and plays an important role in scavenging reactive oxygen species produced during environmental stress. However, limited information is available regarding the response of SOD genes to cold stress in ticks. Therefore, in the present study, SOD genes were cloned and identified from the genome of Haemaphysalis longicornis, and the function of SOD during the cold response was further explored. Seven SOD genes were characterized: HlCCS1, HlCCS2, HlMSD, HlCSD1, HlCSD2, HlCSD3, and HlCSD4. Bioinformatics analysis showed that HlCCS1 and HlCCS2 are copper chaperones of SODs. HlCSD1-HlCSD4 belong to the Cu/Zn SOD, whereas HlMSD belongs to the Mn SOD gene family. Fluorescence quantitative PCR showed that the expression of HlCCS2, HlMSD, and HlCSD1-3 was upregulated, whereas HlCCS1 and HlCSD4 were downregulated during the cold response of H. longicornis. Western blotting confirmed changes in the relative expression of HlCSD3 and HlMSD in H. longicornis after cold treatment. Mortality of H. longicornis increased significantly after dsRNA injection of HlCCS2, HlMSD, HlCSD1, and HlCSD3. The above results show that SODs have different regulatory functions during the cold response in H. longicornis, and there might be an interaction between treatment temperature and duration. Furthermore, the results lay a foundation for subsequent research on the molecular mechanism of cold tolerance in H. longicornis and shed light on the population distribution and diffusion limit of ticks.

The new Haemaphysalis longicornis genome provides insights into its requisite biological traits.

Ticks are a large group of blood-feeding arthropods that transmit multiple human and animal pathogens and are hence of importance to public health. The tick Haemaphysalis longicornis is associated with the transmission of multiple human pathogens in Asia, and recently found invading to the United States. Here, we report the sequencing, assembly and annotation of the 3.16 gigabase genome of this species, which is larger than the previous assembled one. The present Haemaphysalis longicornis genome was characterized by 6519 scaffolds, 24,189 protein-coding genes and a high proportion of simple sequence repeats (54.72%). By genomic assembly and comparative genomic analysis, we characterized the key genes that play essential roles in iron metabolism, detoxification, and freeze tolerance of H. longicornis. Furthermore, a total of 79 endogenous viral elements were identified within the genome, which might have had a considerable impact on its evolution. Decoding the H. longicornis genome not only provides insight into the genetic underpinnings of specific biological processes but also offers the basis for the subsequent integrated control of ticks and tick-borne diseases.

Effects of temperature on cathepsin B, cathepsin D and acid phosphatase during embryo development of the hard tick Haemaphysalis longicornis.

The effects of temperature on the expression patterns and enzyme activity of cathepsin B (HlCatB), cathepsin D (HlCatD) and acid phosphatase (HlACP) during the embryo development of Haemaphysalis longicornis (bisexual population) were investigated in this study. Eggs were exposed to 20 °C (low temperature), 26 °C (normal temperature), and 30 °C (high temperature) immediately after laying, and collected on odd days of embryo development to measure HlCatB, HlCatD and HlACP gene expression using quantitative real-time PCR, as well as three enzyme activities using spectrophotometry. Then the associations between mRNA expression levels of three enzymes and their enzyme activities were assessed. Compared with normal temperature, the mRNA expression peaks of HlCatB were higher and appeared later at low and high temperatures and the activity of HlCatB increased on most days of embryonic development at high temperature. As for HlCatD, the expression peak appeared later at low temperature, but earlier at high temperature. The activity peaks of HlCatD were lower and appeared earlier at low and high temperatures. As for HlACP, the expression peak was higher and appeared later at low temperature, whereas it formed no prominent peak at high temperature. The activity peak of HlACP was higher at low temperature, but lower at high temperature. The linear regression analysis showed that activities of three enzymes were associated with their mRNA expression levels (P < 0.05). Three enzymes are involved in the embryo adaptation to temperature stress. Moreover, the mRNA expression level may be another factor affecting its enzyme activity.

Mechanism of the toxic effects of tetracycline on blood meal digestion in Haemaphysalis longicornis.

The extensive utilization of antibiotics in the field of animal husbandry gives rise to various concerns pertaining to the environment and human health. Here, we demonstrate that the administration of tetracycline impedes blood meal digestion in the tick Haemaphysalis longicornis. Tissue sectioning, 16S rRNA high-throughput sequencing, and transcriptome sequencing of the midgut were employed to elucidate the mechanism underlying tetracycline toxicity. The treatment group consisted of engorged female ticks that were subjected to tetracycline microinjections (75 µg per tick), whereas the control group received sterile water injections. On days 2 and 4 following the injections, the tick body weight changes were assessed and the midguts were dissected and processed. Change in tick body weight in tetracycline-treated group was less than in the control group. In tetracycline-treated ticks, midgut epithelial cells were loosely connected and blood meal digestion was impaired compared to the control group. There was no significant change in midgut bacterial diversity after tetracycline treatment. On day 2 following treatment, the relative abundance of Escherichia-Shigella was significantly decreased, whereas the relative abundance of Allorhizobium was significantly increased compared to the control group. On day 4 following treatment, the relative abundance of Escherichia-Shigella, Allorhizobium, Ochrobactrum, and Acidibacter decreased significantly, whereas the relative abundance of Paraburkholderia and Pelomonas increased significantly. Tetracycline treatment also affected midgut gene expression, producing a cumulative effect wherein the differentially expressed genes (DEGs) were mostly down-regulated. KEGG enrichment pathway analysis revealed that on day 2 the up-regulated DEGs were significantly enriched in 21 pathways, including apoptosis and phagosome. Comparatively, the down-regulated DEGs were significantly enriched in 26 pathways, including N-glycan biosynthesis, lysosome, and autophagy. In contrast, on day 4 the up-regulated DEGs were significantly enriched in 10 pathways including aminoacyl-tRNA biosynthesis, ribosome biogenesis, RNA transport, and DNA replication, whereas the down-regulated differential genes were significantly enriched in 11 pathways including lysosome, peroxisome, N-glycan biosynthesis, and fatty acid synthesis. This indicates that tetracycline injection inhibited blood meal digestion by affecting midgut digestive cells, gut flora diversity, and gene expression. These findings could contribute to tick control by inhibiting blood meal digestion.

Proteomic analysis suggests that monoterpenes in lemongrass disrupt Ca2+ homeostasis in Haemaphysalis longicornis leading to mitochondrial depolarization and cytotoxicity.

Complex mixtures of bioactive ingredients in plant essential oils present complex chemistries which involve different modes of action. An increasing body of scientific reports has recently focused on the acaricidal activities of plant essential oils attributed to their monoterpene components, but information about their underlying molecular mechanism of action is scarce. Here, after the chemical analysis of lemongrass oil, a proteomic analysis of the ovary, salivary gland, and midgut of Haemaphysalis longicornis exposed to Cymbopogon citratus (lemongrass) essential oil was performed via data-independent acquisition mass spectrometry (DIA-MS) technology to further elucidate the molecular mechanisms involved. Pathway analysis reveals the activation of metabolic pathways mediated by oxidoreductases and transferases. Furthermore, the upregulation of various calcium-associated proteins and the upregulation of cytochrome c1, cytochrome c oxidase polypeptide IV, and programmed cell death protein 6-like isoform X1 suggest a cytotoxic mode of action via the formation of reactive oxygen species (ROS), mitochondrial Ca2+ overload, mitochondrial uncoupling, and depolarization, and ATP depletion leading to either apoptotic or necrotic death. Morphological alterations observed after the RNAi of a major detoxification enzyme (glutathione S-transferase) merit further investigation. Hence, the cytotoxic mode of action exhibited by C. citratus oil could be vital for the development of eco-friendly acaricide.

Hemocompatibility Multi-in-One Hydrogel Coating with ROS-Triggered Inflammation Suppression and Anti-Infection Properties for Blood-Contacting Device.

In traditional blood-contacting medical devices, infection and thrombosis are easily formed on the surface of the materials. In addition, inflammation is also a clinical complication that cannot be ignored. More importantly, there is a mutually promoting relationship between the inflammatory response and the infection as well as thrombosis. In this work, we propose a self-adaptive anti-inflammatory coating strategy combined with anti-infection and anticoagulant capacity, which was accomplished based on nano-Ag particles and dexamethasone (Dex)-loaded hydrogel coating. The coating loaded with nano-Ag endows it with good bactericidal performance, including Gram-positive and Gram-negative bacteria. As an anti-inflammatory drug, Dex was grafted onto hydrogel coating by a reactive oxygen species (ROS)-cleavable thioketal (TK) bond and released upon the trigger of an inflammatory environment, blocking further inflammatory cascade, providing self-adaptive anti-inflammatory properties, and avoiding side effects of the drug. It was demonstrated that the coating worked as a precise strategy to resist coagulation, infection, and inflammation, provided a new perspective for designing clinical complication-conformable coatings, and had great application prospects on blood-contacting medical devices.

The regulatory strategy of proteins in the mouse kidney during Babesia microti infection.

Babesia is a protozoan that mainly parasitizes mammalian red blood cells. It causes damage to multiple organs of the host, even threatening the life of the host when the infection is severe. This study found that the mouse kidney was injured after Babesia infection, leading to changes such as ischaemia and an abnormal morphology of renal and epithelial cells. Serum tests showed that indices reflecting renal abnormalities (including serum creatinine, uric acid, and bilirubin) appeared to be abnormal. To further explore the molecular mechanism underlying kidney injury and self-healing in infected hosts, we employed a data-independent acquisition (DIA) proteomics method to investigate large-scale B. microti infection-induced changes in protein expression and phosphorylation in mouse kidneys. This study identified and analysed the reasons for the obvious changes in kidney injury-related proteins, repair-related proteins, immune-related proteins, and lipid metabolism-related proteins. The results provide a strong theoretical basis for effective treatments of the kidney disease caused by Babesia infection.

The toxicity of the monoterpenes from lemongrass is mitigated by the detoxifying symbiosis of bacteria and fungi in the tick Haemaphysalis longicornis.

The entry mode of terpenes into the atmosphere is via volatilization of hydrocarbons from foliage over heavily forested areas besides entering the environment through surface water runoff. Some monoterpenes in essential oils are phytotoxins, acting as plant chemical defenses against bacteria or fungi infections and plant-eating insects. For organisms to survive, their enzymatic systems are activated in response to an assault by potentially harmful compounds. Certain bacterial and fungal genera have developed special abilities to transform toxic terpenes into less toxic derivatives. Here, we investigated the response of the bacterial and fungal community in Haemaphysalis longicornis exposed to Cymbopogon citratus (lemongrass) essential oil (EO) and citronellal. Sequencing of bacterial 16S rRNA and fungal ITS1 regions on an Illumina NovaSeq PE250 sequencing platform was performed for H. longicornis tick samples treated with 15 and 20 mg/mL of lemongrass essential oil and citronellal. The diversity recorded in samples treated with C. citratus EO was higher in comparison to those treated with citronellal but significantly lower in the control samples as reflected by the Shannon diversity index. All major H. longicornis bacterial phyla, including Proteobacteria (93.81 %), Firmicutes (2.58 %), and Bacteroidota (0.99 %) were detected. A switch of dominance from Coxiella to Pseudomonas, which has high biotransformation capacity, was observed in the bacterial community, whereas the phylum Ascomycota (Genera: Aspergillus, Archaeorhizomyces, Alternaria, and Candida) dominated in the fungal community indicating detoxifying symbiosis. Other significantly abundant bacterial genera include Ralstonia, Acinetobacter, Vibrio, and Pseudoalteromonas, while Ganoderma and Trichosporon (yeasts) spp. represented the fungi Basidiomycota. This study expanded the understanding of enzymatic modification of phytotoxic substances by microorganisms, which could provide deeper insights into the mitigation of harmful phytotoxins and the synthesis of eco-friendly derivatives for the control of ticks.

DNA Methylation Variation Is a Possible Mechanism in the Response of Haemaphysalis longicornis to Low-Temperature Stress.

Ticks are notorious ectoparasites and transmit the greatest variety of pathogens than any other arthropods. Cold tolerance is a key determinant of tick abundance and distribution. While studies have shown that DNA methylation is one of the important epigenetic regulations found across many species and plays a significant role in their response to low-temperature stress, its role in the response of ticks to low-temperature stress remains unexplored. Herein, we explored the DNA methylation profile of the tick, Haemaphysalis longicornis, exposed to low-temperature stress (4 °C) using whole-genome bisulfite sequencing (WGBS). We found that approximately 0.95% and 0.94% of the genomic C sites were methylated in the control and low-temperature groups, respectively. Moreover, the methylation level under the CG context was about 3.86% and 3.85% in the control and low-temperature groups, respectively. In addition, a total of 6087 differentially methylated regions (DMRs) were identified between the low-temperature and control groups, including 3288 hypermethylated and 2799 hypomethylated DMRs. Further, Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of differentially methylated genes revealed that most of the DMGs were significantly enriched in binding and RNA transport pathways. Taken together, this research confirmed, for the first time, the whole genome DNA methylation profile of H. longicornis and provided new insights into the DNA methylation changes relating to low-temperature stress in H. longicornis, as well as provided a foundation for future studies on the epigenetic mechanism underlying the responses of ticks to abiotic stress.

Bacterial microbiota analysis demonstrates that ticks can acquire bacteria from habitat and host blood meal.

Ticks have a diversity of habitats and host blood meals. Whether and how factors such as tick developmental stages, habitats and host blood meals affect tick bacterial microbiota is poorly elucidated. In the present study, we investigated the bacterial microbiotas of the hard tick Haemaphysalis longicornis, their blood meals and habitats using 16S rRNA gene high-throughput sequencing. The bacterial richness and diversity in ticks varied depending on the tick developmental stage and feeding status. Results showed that fed ticks present a higher bacterial richness suggesting that ticks may acquire bacteria from blood meals. The significant overlap of the bacteria of fed ticks and the host blood also supports this possibility. Another possibility is that blood meals can stimulate the proliferation of certain bacteria. However, most shared bacteria cannot transmit throughout the tick life cycle, as they were not present in tick eggs. The most shared bacteria between ticks and habitats are members of the genera Staphylococcus, Pseudomonas, Enterobacter, Acinetobacter and Stenotrophomonas, suggesting that these environmental bacteria cannot be completely washed away and can be acquired by ticks. The predominant proportion of Coxiella in fed females further demonstrates that this genus is involved in H. longicornis physiology, such as feeding activity and nutritional provision. These findings further reveal that the bacterial composition of ticks is influenced by a variety of factors and will help in subsequent studies of the function of these bacteria.

Redescription and molecular characterization of the tick Argas japonicus Yamaguti, Clifford & Tipton, 1968 (Ixodida: Argasidae).

Species of the genus Argas are parasites that transmit pathogens, eubacteria, and viruses. Argas japonicus Yamaguti, Clifford & Tipton, 1968 was described based on specimens collected from Japan and Korea. Recently, A. japonicus was reported in different areas of China, suggesting that it may be widely distributed. Here, we have redescribed the female, male, and nymphal stages of A. japonicus and provided scanning electron microscope images based on specimens collected in Neimenggu, China. In addition, we compared four A. japonicus individuals with Argas 16S rDNA and cytochrome c oxidase subunit 1 sequences obtained from GenBank.

Chemical composition of essential oils from Thymus mongolicus, Cinnamomum verum, and Origanum vulgare and their acaricidal effects on Haemaphysalis longicornis (Acari: Ixodidae).

Chemical acaricides are mainly used in traditional tick control, which leads to the emergence of tick resistance and concurrently results in environmental pollution. In the present study, the chemical constituents of essential oils (EOs) from Thymus mongolicus, Cinnamomum verum, and Origanum vulgare was analyzed, and their potential application was evaluated to control the vector tick Haemaphysalis longicornis, which is widely distributed over vast areas of Eurasia, Australia, and New Zealand. Gas chromatography-mass spectrometry analysis revealed that the phenols thymol and carvacrol accounted for 34.66% and 75.72% of the EOs of T. mongolicus and O. vulgare, respectively, whereas trans-cinnamaldehyde (49.42%) was the main constituent of C. verum EO. Immersion tests showed that the EOs of C. verum and O. vulgare had significant acaricidal activity against larval H. longicornis, with the 50% lethal concentration (LC50) being 16.07 and 18.02 mg/mL, respectively, and the 95% lethal concentration (LC95) being 120.37 and 130.09 mg/mL, respectively. The EOs of O. vulgare and T. mongolicus showed significant acaricidal activity against unfed adult H. longicornis, with LC50 being 43.50 and 44.21 mg/mL, respectively, and LC95 being 113.66 and 137.99 mg/mL, respectively. The fumigant toxicity test showed significant acaricidal activity of the three EOs against both unfed and engorged nymphal and adult H. longicornis. Enzyme assays revealed that the EOs of both C. verum and O. vulgare significantly inhibited glutathione S-transferase activity (P < 0.05). In contrast, the activities of carboxylesterase and multifunction oxidases were significantly inhibited by EOs extracted from all three plants (P < 0.05). Taken together, these findings suggest that plant EOs may serve as an environment-friendly alternative for synthetic acaricides in future tick control.

A retrospective review on ixodid tick resistance against synthetic acaricides: implications and perspectives for future resistance prevention and mitigation.

The ending of the nineteenth-century was characterized by an escalation of ticks and tick-borne diseases that resulted in the death of many cattle. This necessitated the search for an effective means of tick control. Arsenicals were introduced in Australia in 1895, and arsenic-based dipping vats went on to be used for about 40 years until resistance was found in ticks and more effective alternatives - chemical acaricides - were developed after World War II. However, the development of resistance by ticks, environmental persistence, and mammalian toxicity militated against the sustained use of subsequent chemical acaricides. Furthermore, the development of resistance is a phenomenon that would always evolve, and the multiple mechanisms underlying the synthetic acaricides resistance are of great importance for future integrated control of ticks and tick-borne diseases. Hence, this study retrospectively reviewed the development of synthetic acaricides and the underlying mechanisms of tick resistance against synthetic acaricides in the hope of providing the implications and perspectives for resistance prevention and mitigation for future tick control.

Transcriptome profile of Haemaphysalis longicornis (Acari: Ixodidae) exposed to Cymbopogon citratus essential oil and citronellal suggest a cytotoxic mode of action involving mitochondrial Ca2+ overload and depolarization.

Haemaphysalis longicornis is an ixodid tick species of medical and veterinary importance. Investigation into the acaricidal activities of botanicals have increased recently but information about their molecular mechanism of action is scarce. Here, RNA-seq analysis of the ticks exposed to Cymbopogon citratus essential oil and citronellal was performed and the responsive genes were identified. More than 6.39 G clean reads with Q20 ≥ 94.88% were obtained for each H. longicornis sample, with an average GC content of 50.94%. Using the Trinity method, 166,710 unigenes with a mean length of 869 bp and a maximum contig length of 29,156 bp were obtained. The upregulation of genes was concentration-dependent in most of the treated groups. Many genes responsive to C. citratus oil and citronellal were stress-related and they include genes associated with adrenergic signaling/calcium channels, cGMP-PKG signaling, apoptosis, focal adhesion, ECM-receptor interaction, ubiquitin-mediated proteolysis, mTOR signaling pathway, and longevity regulating pathway. The upregulation of genes (CACNAID, ADCY9, TPM1, and MYH6) associated with calcium channels suggests a neurotoxic mode of action, whereas, the upregulation of apoptosis-associated genes (CYC, DRONC, CASP7, CASP9, BCL2L1, bcl-xL, etc.) suggests a cytotoxic mode of action. The metabolism of C. citratus essential oil generates oxidative stress which increases the intra-mitochondrial free Ca2+ and triggers the formation of reactive oxygen species (ROS) that culminates to mitochondrial depolarization, ATP depletion, and either necrotic or apoptotic death. The neurotoxic and cytotoxic effects exhibited by the monoterpenes in H. longicornis is vital and could be exploited for the advancement of acaricide development and eco-friendly tick control.

Comprehensive dynamic analysis of proteins in the spermatheca of female Haemaphysalis longicornis after copulation.

Ticks are obligate blood-sucking parasitic arthropods. When sucking the blood of hosts, they can also transmit a variety of pathogens to hosts that severely endanger the health of humans and animals. The spermatheca is an organ for the storage and protection of sperm and an important component of the reproductive system of female ticks. The spermatheca content changes dramatically over time after copulation. In particular, some proteins and polypeptide substances can influence the physiological functions of female ticks and promote blood feeding and egg laying by female ticks. To investigate the molecular mechanisms underlying the productive process of Haemaphysalis longicornis, data-independent acquisition (DIA) quantitative proteomics technology was used to perform in-depth research of the dynamic changes in all proteins in the spermatheca of ticks within a short time after copulation to look for key proteins in the spermatheca contents after copulation that affect the reproduction of female ticks in order to provide meaningful information for the comprehensive prevention and control of ticks.

Precise annotation of tick mitochondrial genomes reveals multiple copy number variation of short tandem repeats and one transposon-like element.

BACKGROUND: In the present study, we used long-PCR amplification coupled with Next-Generation Sequencing (NGS) to obtain complete mitochondrial (mt) genomes of individual ticks and unprecedently performed precise annotation of these mt genomes. We aimed to: (1) develop a simple, cost-effective and accurate method for the study of extremely high AT-content mt genomes within an individual animal (e.g. Dermacentor silvarum) containing miniscule DNA; (2) provide a high-quality reference genome for D. silvarum with precise annotation and also for future studies of other tick mt genomes; and (3) detect and analyze mt DNA variation within an individual tick. RESULTS: These annotations were confirmed by the PacBio full-length transcriptome data to cover both entire strands of the mitochondrial genomes without any gaps or overlaps. Moreover, two new and important findings were reported for the first time, contributing fundamental knowledge to mt biology. The first was the discovery of a transposon-like element that may eventually reveal much about mechanisms of gene rearrangements in mt genomes. Another finding was that Copy Number Variation (CNV) of Short Tandem Repeats (STRs) account for mitochondrial sequence diversity (heterogeneity) within an individual tick, insect, mouse or human, whereas SNPs were not detected. The CNV of STRs in the protein-coding genes resulted in frameshift mutations in the proteins, which can cause deleterious effects. Mitochondria containing these deleterious STR mutations accumulate in cells and can produce deleterious proteins. CONCLUSIONS: We proposed that the accumulation of CNV of STRs in mitochondria may cause aging or diseases. Future tests of the CNV of STRs hypothesis help to ultimately reveal the genetic basis of mitochondrial DNA variation and its consequences (e.g., aging and diseases) in animals. Our study will lead to the reconsideration of the importance of STRs and a unified study of CNV of STRs with longer and shorter repeat units (particularly polynucleotides) in both nuclear and mt genomes.

Community structure and diversity of the microbiomes of two microhabitats at the root-soil interface: implications of meta-analysis of the root-zone soil and root endosphere microbial communities in Xiong'an New Area.

The diversity of the microbial compositions of the root-zone soil (the rhizosphere-surrounding soil) and root endosphere (all inner root tissues) of Pinus tabulaeformis Carr. and Ginkgo biloba L. were evaluated in Xiong'an New Area using high-throughput sequencing; the influence of the soil edaphic parameters on microbial community compositions was also evaluated. Our results showed that both the taxonomic and phylogenetic diversities of the root endosphere were lower than those of the root-zone soil, but the variation in the endosphere microbial community structure was remarkably higher than that of the root-zone soil. Spearman correlation analysis showed that the soil organic matter, total nitrogen, total phosphate, total potassium, ratio of carbon to nitrogen, and pH significantly explained the α-diversity of the bacterial community and that total nitrogen differentially contributed to the α-diversity of the fungal community. Variation partitioning analysis showed that plant species had a greater influence on microbial composition variations than did any other soil property, although soil chemical parameters explained more variation when integrated. Together, our results suggest that both plant species and soil chemical parameters played a critical role in shaping the microbial community composition.