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Ixodes spp. and related ticks transmit prevalent infections, although knowledge of their biology and development of anti-tick measures have been hindered by the lack of a high-quality genome. In the present study, we present the assembly of a 2.23-Gb Ixodes scapularis genome by sequencing two haplotypes within one individual, complemented by chromosome-level scaffolding and full-length RNA isoform sequencing, yielding a fully reannotated genome featuring thousands of new protein-coding genes and various RNA species. Analyses of the repetitive DNA identified transposable elements, whereas the examination of tick-associated bacterial sequences yielded an improved Rickettsia buchneri genome. We demonstrate how the Ixodes genome advances tick science by contributing to new annotations, gene models and epigenetic functions, expansion of gene families, development of in-depth proteome catalogs and deciphering of genetic variations in wild ticks. Overall, we report critical genetic resources and biological insights impacting our understanding of tick biology and future interventions against tick-transmitted infections. A high-quality Ixodes scapularis genome contributes to improved annotations, expansion of gene families, development of proteome catalogs and the deciphering of genetic variation in wild ticks.

Borrelia burgdorferi is the causative agent of Lyme disease and is transmitted to vertebrate hosts by Ixodes spp. ticks. The spirochaete relies heavily on its arthropod host for basic metabolic functions and has developed complex interactions with ticks to successfully colonize, persist and, at the optimal time, exit the tick. For example, proteins shield spirochaetes from immune factors in the bloodmeal and facilitate the transition between vertebrate and arthropod environments. On infection, B. burgdorferi induces selected tick proteins that modulate the vector gut microbiota towards an environment that favours colonization by the spirochaete. Additionally, the recent sequencing of the Ixodes scapularis genome and characterization of tick immune defence pathways, such as the JAK–STAT, immune deficiency and cross-species interferon-γ pathways, have advanced our understanding of factors that are important for B. burgdorferi persistence in the tick. In this Review, we summarize interactions between B. burgdorferi and I. scapularis during infection, as well as interactions with tick gut and salivary gland proteins important for establishing infection and transmission to the vertebrate host.Borrelia burgdorferi has a complex life cycle with several different hosts, causing Lyme disease when it infects humans. In this Review, Fikrig and colleagues discuss how B. burgdorferi infects and interacts with its tick vector to ensure onward transmission.

In 2014, a new tick species, Ixodes inopinatus, was described, which is closely related to Ixodes ricinus. So far, I. inopinatus has been found in Tunisia, Morocco, Spain, Portugal, Romania, Austria, and southern Germany. No data is yet available regarding occurrence of I. inopinatus in northern Germany and the potential role of I. inopinatus as a vector for tick-borne pathogens. Therefore, 3845 DNA samples from Ixodes ticks collected for prevalence studies on Borrelia spp., Rickettsia spp., and Anaplasma phagocytophilum during the years 2010–2015 in the northern German cities of Hamburg and Hanover were differentiated into I. ricinus or I. inopinatus by sequencing a part of the 16S rRNA gene. In total, 4% (137/3845) of the sequenced ticks were assigned to the species I. inopinatus and 96% (3708/3845) to I. ricinus. The prevalence of Borrelia spp., Rickettsia spp., and A. phagocytophilum DNA in I. inopinatus was 34% (46/137), 46% (63/137), and 3% (4/137), respectively, whereas the prevalence of these bacteria in I. ricinus was 25% (919/3708), 47% (1729/3708), and 4% (135/3708), respectively. Compared with I. ricinus, significantly more I. inopinatus ticks tested positive for Borrelia. To the best of our knowledge, this is the first report of I. inopinatus in northern Germany. Detection of the DNA of Borrelia spp., Rickettsia spp., and A. phagocytophilum in questing I. inopinatus indicates a potential role of this tick species as a vector of these pathogens, which needs to be confirmed by transmission experiments.

Documented cases of horizontal gene transfer from bacteria to eukaryotes are rare, but now, not only is a new class of transferred genes identified, the function of one representative is also demonstrated in its new setting, where it controls bacterial growth. Bacterial genes co-opted for eukaryote immunity Eukaryotes can acquire new functions through horizontal gene transfer from bacteria but examples are rare. Here Joseph Mougous and colleagues identify a previously unknown instance of such transfer and also demonstrate the function of the transferred genes in their new setting as part of a co-opted defence system against bacterial pathogens. Specifically, they show that members of the Tae family of amidase effectors that are secreted by the type VI secretion system and target the cell wall of competing bacteria, have been transferred to eukaryotes on at least six occasions. These domesticated amidase effector ( dae ) genes acquired eukaryotic secretion signals, are expressed in recipient organisms and encode antibacterial toxins. The authors also show that in the deer tick Ixodes scapularis , a dae gene limits proliferation of Borrelia burgdorferi , the bacterium responsible for Lyme disease. Horizontal gene transfer allows organisms to rapidly acquire adaptive traits 1 . Although documented instances of horizontal gene transfer from bacteria to eukaryotes remain rare, bacteria represent a rich source of new functions potentially available for co-option 2 . One benefit that genes of bacterial origin could provide to eukaryotes is the capacity to produce antibacterials, which have evolved in prokaryotes as the result of eons of interbacterial competition. The type VI secretion amidase effector (Tae) proteins are potent bacteriocidal enzymes that degrade the cell wall when delivered into competing bacterial cells by the type VI secretion system 3 . Here we show that tae genes have been transferred to eukaryotes on at least six occasions, and that the resulting domesticated amidase effector ( dae ) genes have been preserved for hundreds of millions of years through purifying selection. We show that the dae genes acquired eukaryotic secretion signals, are expressed within recipient organisms, and encode active antibacterial toxins that possess substrate specificity matching extant Tae proteins of the same lineage. Finally, we show that a dae gene in the deer tick Ixodes scapularis limits proliferation of Borrelia burgdorferi , the aetiologic agent of Lyme disease. Our work demonstrates that a family of horizontally acquired toxins honed to mediate interbacterial antagonism confers previously undescribed antibacterial capacity to eukaryotes. We speculate that the selective pressure imposed by competition between bacteria has produced a reservoir of genes encoding diverse antimicrobial functions that are tailored for co-option by eukaryotic innate immune systems.

Background Parasites may actively seek for hosts and may use a number of adaptive strategies to promote their reproductive success and host colonization. These strategies will necessarily influence their host specificity and seasonality. Ticks are important ectoparasites of vertebrates, which (in addition to directly affecting their hosts) may transmit a number of pathogens. In Europe, three hard tick species (Ixodidae: Ixodes ariadnae , I. simplex and I. vespertilionis ) and at least two soft tick species (Argasidae: Argas transgariepinus and A. vespertilionis ) are specialized for bats. Methods Here we report data on the host range of these ticks and the seasonality of tick infestation on wild caught bats in south-east Europe. We collected 1803 ticks from 30 species of bats living in underground shelters (caves and mines) from Romania and Bulgaria. On the basis of tick–host associations, we tested several hypotheses on host–parasite evolutionary adaptations regulating host specificity, seasonality and sympatric speciation. Results We observed significant differences in host specificity and seasonality of abundance between the morphologically different bat specialist ticks ( I. simplex and I. vespertilionis ) likely caused by their host choice and their respective host-seeking behavior. The two highly generalist, but morphologically similar tick species ( I. ariadnae and I. vespertilionis ) showed temporal differences in occurrence and activity, thus exploiting significantly different host communities while occurring in geographical sympatry. Conclusions We conclude that bat-specialist ticks show a wide range of adaptations to their hosts, with differences in specificity, seasonality of occurrence, the prevalence and intensity of infestation and all these contribute to a successful division of temporal niches of ticks sharing morphologically similar hosts occurring in geographical sympatry.

Ticks and other arthropods often are hosts to nutrient providing bacterial endosymbionts, which contribute to their host's fitness by supplying nutrients such as vitamins and amino acids. It has been detected, in our lab, that Ixodes pacificus is host to Rickettsia species phylotype G021. This endosymbiont is predominantly present, and 100% maternally transmitted in I. pacificus. To study roles of phylotype G021 in I. pacificus, bioinformatic and molecular approaches were carried out. MUMmer genome alignments of whole genome sequence of I. scapularis, a close relative to I. pacificus, against completely sequenced genomes of R. bellii OSU85-389, R. conorii, and R. felis, identified 8,190 unique sequences that are homologous to Rickettsia sequences in the NCBI Trace Archive. MetaCyc metabolic reconstructions revealed that all folate gene orthologues (folA, folC, folE, folKP, ptpS) required for de novo folate biosynthesis are present in the genome of Rickettsia buchneri in I. scapularis. To examine the metabolic capability of phylotype G021 in I. pacificus, genes of the folate biosynthesis pathway of the bacterium were PCR amplified using degenerate primers. BLAST searches identified that nucleotide sequences of the folA, folC, folE, folKP, and ptpS genes possess 98.6%, 98.8%, 98.9%, 98.5% and 99.0% identity respectively to the corresponding genes of Rickettsia buchneri. Phylogenetic tree constructions show that the folate genes of phylotype G021 and homologous genes from various Rickettsia species are monophyletic. This study has shown that all folate genes exist in the genome of Rickettsia species phylotype G021 and that this bacterium has the genetic capability for de novo folate synthesis.

Multicellular animals need to control the spread of invading pathogens. This is a particular challenge for blood-feeding vectors such as ticks, which ingest large amounts of blood potentially laden with harmful microorganisms. Ticks have a basic innate immune system and protect themselves from infection through innate immune responses involving pathways such as Janus kinase (JAK) or the signalling transducer activator of transcription (STAT). Direct antimicrobial defence occurs through the rapid synthesis of numerous antimicrobial agents including antimicrobial peptides (AMPs). The tick Ixodes ricinus is one of the main vectors of the Lyme disease pathogen, the spirochete Borrelia burgdorferi sensu lato. Data suggest that the JAK/STAT signalling pathway controls the expression of AMPs and regulates the infection of the pathogen in the tick body. The innate immune system during the off-host period keeps the level of spirochete infection in check. Spirochetes may influence the innate immune response in ticks. Therefore, the aim of this study was to analyse the expression of the genes related to the JAK/STAT pathway and selected AMPs in questing ticks in which B. burgorferi s.l. was detected. In the ticks infected with spirochetes, overexpression of genes related to the JAK/STAT signalling pathway was observed in the case of STAM and SOCS genes. AMPs genes such as def1 , ric , lzs were overexpressed with different expression patterns. The results obtained suggest that AMPs may be involved in infection management in ticks.

The goal of this study was to clarify the taxonomic status of the Ixodes ricinus complex in the Southern Cone of America, by using morphological characters and molecular markers (mitochondrial 16SrDNA and cox1 genes). The morphological analysis indicates that three different taxa of the I. ricinus complex occur in this region: Ixodes pararicinus, Ixodes aragaoi, and Ixodes sp. cf. I. affinis. The most prominent diagnostic character among them is the size of scutal punctations in both male and female ticks. In the males of Ixodes sp. cf. I. affinis, the punctations on the central field and along the median marginal groove of the scutum are clearly larger than in the males of I. aragaoi and I. pararicinus, while the punctations of I. aragaoi are larger but less numerous than in I. pararicinus. The punctations in Ixodes sp. cf. I. affinis females are larger and deeper than in females of I. aragaoi and I. pararicinus, and those of I. aragaoi are slightly larger than in I. pararicinus. The length of the lateral posterior denticles of the male hypostome is comparatively longer in I. aragaoi than in the other two species, and longer in Ixodes sp. cf. I. affinis than in I. pararicinus. In the 16S analysis, I. pararicinus and I. aragaoi are monophyletic (99% and 98% bootstrap support, respectively), while Ixodes cf. I. affinis does not represent a single lineage. In the cox1 analysis, both I. pararicinus and I. aragaoi are well-defined taxa, but the bootstrap support for Ixodes sp. cf. I. affinis is low (67%). In general, there are considerable 16SrRNA differences among lineages of Ixodes sp. cf. I. affinis from different geographical areas. These results may be indicative of the existence of different species. The populations morphologically compatible with I. affinis from Argentina, Colombia, Panama, Belize, and USA should be provisionally named as Ixodes sp. cf. I. affinis until an integrative taxonomic work with further evidence redefines whether or not this taxon actually represents a species complex.

Background Ticks are obligate blood-feeding parasites associated with a huge diversity of diseases globally. The hard tick Ixodes ricinus is the key vector of Lyme borreliosis and tick-borne encephalitis in Western Eurasia. Ixodes ticks have large and repetitive genomes that are not yet well characterized. Results Here we generate two high-quality I . ricinus genome assemblies, with haploid genome assembly sizes of approximately 2.15 Gbp. We find transposable elements comprise at least 69% of the two I. ricinus genome assemblies, amongst the highest proportions found in animals. The transposable elements in ticks are highly diverse and novel, so we constructed a repeat library for ticks using our I . ricinus genome assemblies and the high-quality genome assembly of I . scapularis , another major tick vector of Lyme borreliosis. To understand the impact of transposable elements on tick genomes we compared their accumulation in the two Ixodes sister species. We find transposable elements in these two species to have distinctive post-speciation patterns, suggesting transposable elements are drivers of genome evolution in ticks. Conclusions The I . ricinus genome assemblies and our tick repeat library will be valuable resources for biological insights into these important ectoparasites. Our findings highlight that further research into the impact of transposable elements on the genomes of blood-feeding parasites is required.

This study describes the first detection of Ixodes ventalloi in Slovakia. Two engorged females of I. ventalloi were collected from Dunnocks ( Prunella modularis ) captured in eastern Slovakia. The identification of females was based on morphological and molecular 16S rRNA gene features. Phylogenetic analysis revealed a classification of the females into distinct genogroups. Moreover, comparative morphological analysis highlighted variations between the two females, particularly in the curvature of the auriculae, the shape of coxa I, and the internal spur. These findings suggest the potential for varied phenotypes of I. ventalloi correlated with their genogroups. Nonetheless, I. ventalloi population establishment within Slovakia necessitates further investigation through flagging or drag sampling.