Biology subjects

Sprong, H.

Publications and source records attributed to Sprong, H..

8 recordsLinked to original sources

bioRxiv2026

Optimizing genome assembly, chromosome synteny, and genetic variant discovery from Oxford Nanopore sequences of Dermacentor reticulatus ticks

Generating high-quality genome assemblies for small animals with large genomes is complex due to their small body size, DNA contamination, and repetitive elements. Ticks exemplify these complexities, while also being a global health threat to humans, domestic animals, and wildlife. Advances in long-read sequencing platforms now make it feasible to obtain large amounts of raw sequence data from individual specimens, but challenges remain. Key genome workflow challenges include error correction, assembly, transposable element annotation, and chromosome assignment and synteny. Here we examine three individual Dermacentor reticulatus ticks using deep Oxford Nanopore sequencing. Comparing and contrasting bioinformatic tools for raw read and assembly manipulation allows us to identify the parameters that provide a high-quality haploid genome assembly among 38 assemblies. We find Dorado error corrected raw read data from approximately two flow cells are needed, but limiting assembly coverage to 40x produces the highest quality assemblies. Then we examined the effects of optimal workflow parameters on downstream analyses of gene synteny and manual transposable element annotation of the three tick assemblies in comparison to an independent assembly of a fourth D. reticulatus individual from a different country. Gene synteny analysis allows chromosome assignment of scaffolds and transposable element identification was improved markedly with manual curation. Finally, we compared the genetic variation of D. reticulatus across two populations and found similar genetic diversity. Our study provides a clear workflow to obtain high-quality assemblies from Oxford Nanopore sequences and genetic characterization of a species with a large, complex, and repetitive genome.

genomics↗

bioRxiv2025

Crimean-Congo Haemorrhagic Fever Virus Circulates within Broad Ecological Networks of Ticks and Vertebrates

We produced spatial datasets of the known distribution of Orthonairovirus haemorrhagiae (formerly Crimean-Congo haemorrhagic fever virus, CCHFV) by compiling human cases, virus isolations, and serological data from humans and animals, spanning from Europe to southern Africa, with the aim on virus range modelling. Models based solely on climatic variables produced unrealistic and overly extensive predictions, overestimating suitability in northern Europe and confirming that climate alone poorly explains CCHFV range. Approaches using only tick species distributions underperformed in many parts of Africa, reflecting the complexity of vector-host interactions and the absence of a strict tick-virus association. The integration of human-biting tick distributions, livestock density, and chorotypes yielded the most robust results, accurately capturing over 90% of known occurrences, by identifying vertebrate assemblages most likely to amplify the virus while reducing dimensionality. Chorotypes, representing clusters of co-occurring hosts, enhanced model performance and improved the delineation of both the northern and African ranges limits of the virus. Our results support a generalist epidemiological model in which multiple tick species, together with a broad range of vertebrate hosts, sustain CCHFV circulation. This ecological flexibility, rather than strict vector specificity, likely explains the CCHFV wide biogeographical range and occasional lineage expansions across continents. This study provides the most comprehensive assessment to date of the abiotic and biotic determinants of the distribution of CCHFV. Although gaps remain, this study demonstrates that coupling abiotic and biotic predictors provides a more accurate and ecologically meaningful understanding of CCHFV distribution. Author SummaryCrimean-Congo haemorrhagic fever virus (CCHFV) is a tick-borne pathogen causing severe disease in humans across Africa, Asia and Europe. Understanding where the virus may circulate is crucial for anticipating outbreaks and guiding surveillance. Previous studies have mostly relied on climate-based models, assuming that temperature and humidity determine where infected ticks can prevail. However, such models often overestimate risk, predicting virus presence in regions where no cases or vectors exist. In this study, we combined climatic data with ecological information on ticks, livestock, and wildlife to create a more realistic prediction of CCHFV distribution. By incorporating host-vector interactions and vertebrate communities, our models accurately captured most known occurrences and revealed the ecological patterns underlying virus transmission. Our results suggest that CCHFV persists within broad networks of tick and vertebrate species rather than a single vector. This integrated approach offers a powerful framework to identify emerging risk areas and forms a good starting point to further improve our understanding of the ecological drivers of tickborne viral diseases.

ecology↗

bioRxiv2025

Tick Genome Assemblies: Overcoming biological limitations through advances in sequencing and assembly

Ticks are blood-feeding arthropods with approximately 1,000 species, however, only 24 species currently have a genome assembly. These genome assemblies are important resources to advance tick biology and control of tick-associated diseases. Generating tick genome assemblies is challenging due to their small body size (low DNA input), DNA contamination (from microbiota and host bloodmeals), large genome size (on average 2.4 Gbp for hard ticks), and abundant transposable elements (at least 68% of the assembly for Ixodes species). Advances in sequencing technologies have driven an increasing number of tick assemblies from 2011 to 2025. We characterize and assess the 54 tick genome assemblies within public genome databases using QUAST-LG and BUSCO compleasm. Then we evaluate the impact of biological source material and sequencing platforms on these tick genome assemblies. From the 54 tick assemblies, we identify 34 high-quality assemblies from 21 species that are suitable for downstream analyses. We recommend future tick genome assemblies use long-read sequencing platforms and Hi-C scaffolding to improve genomic resources for these unique blood-feeding parasites.

genomics↗

bioRxiv2024

Emergence and Dynamics of Usutu and West Nile Viruses in the Netherlands, 2016-2022

BackgroundMosquito-borne arboviruses, including Usutu virus (USUV) and West Nile virus (WNV), are emerging threats in Europe, with changes in climate, land use, and increased travel and trade influencing their dynamics. Understanding the emergence and establishment of these viruses in new regions is critical for informing targeted mitigation of drivers of emergence and enhancing public and wildlife health preparedness. MethodsSeven years (2016-2022) of interconnected studies were conducted in the Netherlands. Live birds were sampled by volunteer bird ringers, dead birds were referred for sampling by citizen-scientists and zoological institutions, and mosquitoes were trapped. Samples were tested for USUV and WNV using RT-PCR and screened for Orthoflavivirus antibodies using protein microarray and neutralization assays. Sequencing and phylogenetic analyses were performed. FindingsUSUV was first detected in the Netherlands in 2016, caused large outbreaks in birds until 2018, and resurged in 2022. One dominant, enzootic lineage, co-circulated alongside several limited introductions of a second lineage. A localized WNV lineage 2 outbreak occurred in live birds and mosquitoes in 2020, with another positive bird in 2022 and serological evidence of continued circulation. InterpretationWe provide the first comprehensive, multi-year documentation of two emerging arboviruses in the Netherlands. USUV was enzootically maintained over seven years and was associated with substantial bird mortality. WNV is in an early stage of establishment with no bird mortality observed. Our integrated wildlife sampling was crucial in detecting a human WNV outbreak, bringing this emerging threat to public health attention. FundingZonMw, Dutch Research Council (NWO), European Union, Government of the Netherlands

microbiology↗

bioRxiv2024

Comparative genomics of Rickettsiella bacteria reveal variable metabolic traits involved in symbiotic interactions with arthropods

Members of the Rickettsiella genus (order: Legionellales) are emerging as widespread bacteria associated with insects, arachnids, and crustaceans. While some Rickettsiella strains are highly virulent pathogens, others are maternally inherited endosymbionts that manipulate arthropod phenotypes, including the induction of defensive symbiosis and cytoplasmic incompatibility. However, the genomic diversity of Rickettsiella remains largely unexplored, and their genetic potential to induce complex phenotypes in arthropods is only partially understood. In this study, we sequenced five new Rickettsiella genomes isolated from three tick species. Through comparative genomics, we observed that Rickettsiella members share similar metabolic capabilities, and collectively lack virulence genes from pathogenic Legionellales. Additional analysis of Rickettsiella genomes revealed significant variability in metabolic properties related to endosymbiosis. Specifically, their capacity to biosynthesize certain B vitamins and heme varies, suggesting a functional role of some Rickettsiella strains in the nutrition of their arthropod hosts. Some Rickettsiella genomes harbour homologs of Wolbachia cif genes, the cause of Wolbachia-induced cytoplasmic incompatibility,, suggesting that Rickettsiella may use a similar molecular mechanism to manipulate the reproduction of their arthropod hosts. Phylogenomics further revealed that tick-borne Rickettsiella exhibit distinct evolutionary origins within the genus, indicating that Rickettsiella have undergone repeated horizontal transfers between ticks and other arthropods.

evolutionary biology↗

bioRxiv2024

Deep sequencing of 16 Ixodes ricinus ticks unveils insights into their interactions with endosymbionts.

BackgroundIxodes ricinus ticks act as vectors for numerous pathogens that present substantial health threats. Additionally, they harbour vertically transmitted symbionts, some of which have been linked to diseases. The difficulty of isolating and cultivating these symbionts has hampered our understanding of their biological role, their potential to cause disease, and their modes of transmission. To expand our understanding on the tick symbiont Midichloria mitochondrii and on Rickettsia helvetica, which has been linked to disease in humans, we utilized deep sequencing on sixteen individual adult female ticks collected from coastal dune and forested areas in the Netherlands. ResultsBy employing a combination of second and third-generation sequencing techniques, we successfully reconstructed the complete genomes of M. mitochondrii from eleven individuals, R. helvetica from eight individuals and the mitochondrial genome from all ticks. Additionally, we visualised the location of R. helvetica in tick organs and constructed genome-scale metabolic models (GEMs) of both symbionts to study their environmental dependencies. Our analysis revealed a strong cophylogeny between M. mitochondrii and mitochondrial genomes, suggesting frequent maternal transmission. In contrast, the absence of cophylogeny between R. helvetica and the mitochondrial genomes, coupled with its presence in the receptaculum seminis of I. ricinus females, raises the possibility of paternal transmission of R. helvetica. Notably, the genetic diversity of R. helvetica was found to be very low, except for the rickA virulence gene, where the presence of up to thirteen insertions of a33nt-long repeat led to significant variability. However, this variation could not account for the differences in infection prevalence observed across eight distinct locations in the Netherlands. ConclusionsBy employing deep sequencing, it becomes feasible to extract complete genomes and genetic data of symbionts directly from their host organisms. This methodology serves as a robust means to gain fresh insights into their interactions. Our observations, which suggest paternal transmission of R. helvetica, a relatively unexplored mode of transmission in ticks, require validation through experimental investigations. The genetic variations identified in the rickA virulence gene of R. helvetica have the potential to influence the infectivity and transmission dynamics of R. helvetica

microbiology↗

bioRxiv2024

The repetitive genome of the Ixodes ricinus tick reveals transposable elements have driven genome evolution in ticks

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. Here we generate two high-quality I. ricinus genome assemblies, with haploid genome sizes of approximately 2.15 Gbp. We find transposable elements comprise at least 69% of the two I. ricinus genomes, 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 genomes and the genome 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 be drivers of genome evolution in ticks. The I. ricinus genome assemblies and our tick repeat library will be valuable resources for biological insights into this important ectoparasite. Our findings highlight that further research into the impact of transposable elements on the genomes of blood-feeding parasites is required.

genomics↗

bioRxiv2023

Genome dynamics across the evolutionary transition to endosymbiosis

Endosymbiosis - where a microbe lives and replicates within a host - is an important contributor to organismal function that has accelerated evolutionary innovations and catalysed the evolution of complex life. The evolutionary processes associated with transitions to endosymbiosis, however, are poorly understood. Here, we use comparative genomics of the genus Arsenophonus to reveal the complex processes that occur on evolution of an endosymbiotic lifestyle. We compared the genomes of 38 strains spanning diverse lifestyles from environmentally acquired infections to obligate inter-dependent endosymbionts. We observed recent endosymbionts had larger genome sizes than closely related environmentally acquired strains, consistent with evolutionary innovation and rapid gain of new function. Increased genome size was a consequence of prophage and plasmid acquisition including a cargo of type III effectors, and concomitant loss of CRISPR-Cas genome defence systems enabling mobile genetic element expansion. Persistent endosymbiosis was also associated with loss of type VI secretion, likely reflecting reduced microbe-microbe competition. Thereafter, the transition to stable endosymbiosis and vertical inheritance was associated with the expected relaxation of purifying selection, pseudogenisation of genes and reduction of metabolism, leading to genome reduction. However, reduced %GC that is typically considered a progressive linear process was observed only in obligate interdependent endosymbionts. We argue that a combination of the need for rapid horizontal gene transfer-mediated evolutionary innovation together with reduced phage predation in endosymbiotic niches drives loss of genome defence systems and rapid genome expansion upon adoption of endosymbiosis. These remodelling processes precede the reductive evolution traditionally associated with adaptation to endosymbiosis.

genomics↗