Abstract
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.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
Data availability
All sequence data and genome assembly data are deposited into NCBI under BioProject accession no. PRJNA678334. The assembly information is available in the following link: https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_016920785.2/. The data are also available through VEuPathDB (VectorBase release 59, 30 August 2022) using the following link: https://vectorbase.org/vectorbase/app/record/dataset/DS_bb84a3ee55. All other datasets generated and analyzed during the present study are available in the Supplementary information or the source data provided with this paper.
Code availability
All data processing and analyses were performed by existing software packages, which are either available publicly from the internet or previous publications, as detailed in the Methods and the Nature Portfolio Reporting Summary. No customized code or software was used for any aspect of data processing or analysis.
References
Parola, P. & Raoult, D. Ticks and tickborne bacterial diseases in humans: an emerging infectious threat. Clin. Infect. Dis. 32, 897–928 (2001).
Honig, V. et al. Broad-range survey of vector-borne pathogens and tick host identification of Ixodes ricinus from Southern Czech Republic. FEMS Microbiol. Ecol. 93, fix129 (2017).
Sonenshine, D. E. Range expansion of tick disease vectors in North America: implications for spread of tick-borne disease. Int. J. Environ. Res. Public Health 15, 478 (2018).
Eisen, R. J. & Eisen, L. The blacklegged tick, Ixodes scapularis: an increasing public health concern. Trends Parasitol. 34, 295–309 (2018).
Paddock, C.D., Lane, R.S., Staples, J.E. & Labruna, M.B. Changing Paradigms for Tick-borne Diseases in the Americas (National Academies of Sciences, Engineering, and Medicine, 2016).
Centers for Disease Control and Prevention. How many people get Lyme disease? https://www.cdc.gov/lyme/stats/humancases.html (CDC, 2021).
Geraci, N. S., Spencer Johnston, J., Paul Robinson, J., Wikel, S. K. & Hill, C. A. Variation in genome size of argasid and ixodid ticks. Insect Biochem. Mol. Biol. 37, 399–408 (2007).
Gulia-Nuss, M. et al. Genomic insights into the Ixodes scapularis tick vector of Lyme disease. Nat. Commun. 7, 10507 (2016).
Miller, J. R. et al. A draft genome sequence for the Ixodes scapularis cell line, ISE6. F1000Research 7, 297 (2018).
Giraldo-Calderon, G. I. et al. VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. Nucleic Acids Res. 43, D707–D713 (2015).
Jia, N. et al. Large-scale comparative analyses of tick genomes elucidate their genetic diversity and vector capacities. Cell 182, 1328–1340.e13 (2020).
Cramaro, W. J., Hunewald, O. E., Bell-Sakyi, L. & Muller, C. P. Genome scaffolding and annotation for the pathogen vector Ixodes ricinus by ultra-long single molecule sequencing. Parasit. Vectors 10, 71 (2017).
Smalley, R. T. et al. Detection of Borrelia miyamotoi and Powassan virus lineage II (deer tick virus) from Odocoileus virginianus harvested Ixodes scapularis in Oklahoma. Vector Borne Zoonotic Dis. 22, 209–216 (2022).
Matthews, B. J. et al. Improved reference genome of Aedes aegypti informs arbovirus vector control. Nature 563, 501–507 (2018).
Bickhart, D. M. et al. Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nat. Genet. 49, 643–650 (2017).
Villar, M. et al. Integrated metabolomics, transcriptomics and proteomics identifies metabolic pathways affected by Anaplasma phagocytophilum Infection in tick cells. Mol. Cell Proteom. 14, 3154–3172 (2015).
Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015).
Flynn, J. M. et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc. Natl Acad. Sci. USA 117, 9451–9457 (2020).
Pal, U., Kitsou, C., Drecktrah, D., Yas, O. B. & Fikrig, E. Interactions between ticks and lyme disease spirochetes. Curr. Issues Mol. Biol. 42, 113–144 (2021).
Kitsou, C., Fikrig, E. & Pal, U. Tick host immunity: vector immunomodulation and acquired tick resistance. Trends Immunol. 42, 554–574 (2021).
Sajid, A. et al. mRNA vaccination induces tick resistance and prevents transmission of the Lyme disease agent. Sci. Transl. Med. 13, eabj9827 (2021).
Lewis, L. A., Radulovic, Z. M., Kim, T. K., Porter, L. M. & Mulenga, A. Identification of 24h Ixodes scapularis immunogenic tick saliva proteins. Ticks Tick Borne Dis. 6, 424–434 (2015).
Narasimhan, S. et al. Immunity against Ixodes scapularis salivary proteins expressed within 24 hours of attachment thwarts tick feeding and impairs Borrelia transmission. PLoS ONE 2, e451 (2007).
Narasimhan, S. et al. A tick gut protein with fibronectin III domains aids Borrelia burgdorferi congregation to the gut during transmission. PLoS Pathog. 10, e1004278 (2014).
Yang, X., Smith, A. A., Williams, M. S. & Pal, U. A dityrosine network mediated by dual oxidase and peroxidase influences the persistence of Lyme disease pathogens within the vector. J. Biol. Chem. 289, 12813–12822 (2014).
Contreras, M., Villar, M. & de la Fuente, J. A vaccinomics approach for the identification of tick protective antigens for the control of Ixodes ricinus and Dermacentor reticulatus infestations in companion animals. Front. Physiol. 10, 977 (2019).
Machado, L. R. & Ottolini, B. An evolutionary history of defensins: a role for copy number variation in maximizing host innate and adaptive immune responses. Front. Immunol. 6, 115 (2015).
De, S. et al. Epigenetic regulation of tick biology and vectorial capacity. Trends Genet. 37, 8–11 (2021).
Kassis, J. A., Kennison, J. A. & Tamkun, J. W. Polycomb and trithorax group genes. Drosoph. Genet. 206, 1699–1725 (2017).
Beltran, S. et al. Transcriptional network controlled by the trithorax-group gene ash2 in Drosophila melanogaster. Proc. Natl Acad. Sci. USA 100, 3293–3298 (2003).
Kurtti, T. J. et al. Rickettsia buchneri sp. nov., a rickettsial endosymbiont of the blacklegged tick Ixodes scapularis. Int. J. Syst. Evol. Microbiol 65, 965–970 (2015).
Rhie, A. et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature 592, 737–746 (2021).
Nava, S., Guglielmone, A. A. & Mangold, A. J. An overview of systematics and evolution of ticks. Front. Biosci. 14, 2857–2877 (2009).
de la Fuente, J. The fossil record and the origin of ticks (Acari: Parasitiformes: Ixodida). Exp. Appl. Acarol. 29, 331–344 (2003).
Mans, B. J., Louw, A. I. & Neitz, A. W. Evolution of hematophagy in ticks: common origins for blood coagulation and platelet aggregation inhibitors from soft ticks of the genus Ornithodoros. Mol. Biol. Evol. 19, 1695–1705 (2002).
Kim, T. K. et al. Time-resolved proteomic profile of Amblyomma americanum tick saliva during feeding. PLoS Negl. Trop. Dis. 14, e0007758 (2020).
Di Venere, M. et al. Ixodes ricinus and Its endosymbiont Midichloria mitochondrii: a comparative proteomic analysis of salivary glands and ovaries. PLoS ONE 10, e0138842 (2015).
Cotte, V. et al. Differential expression of Ixodes ricinus salivary gland proteins in the presence of the Borrelia burgdorferi sensu lato complex. J. Proteom. 96, 29–43 (2014).
Iovinella, I., Ban, L., Song, L., Pelosi, P. & Dani, F. R. Proteomic analysis of castor bean tick Ixodes ricinus: a focus on chemosensory organs. Insect Biochem. Mol. Biol. 78, 58–68 (2016).
Garcia, G. R. et al. A transcriptome and proteome of the tick Rhipicephalus microplus shaped by the genetic composition of its hosts and developmental stage. Sci. Rep. 10, 12857 (2020).
Grabowski, J. M. et al. Changes in the proteome of Langat-infected Ixodes scapularis ISE6 cells: metabolic pathways associated with flavivirus infection. PLoS Negl. Trop. Dis. 10, e0004180 (2016).
de la Fuente, J. et al. Tick–pathogen interactions and vector competence: identification of molecular drivers for tick-borne diseases. Front. Cell Infect. Microbiol. 7, 114 (2017).
de la Fuente, J., Kocan, K. M. & Blouin, E. F. Tick vaccines and the transmission of tick-borne pathogens. Vet. Res. Commun. 31, 85–90 (2007).
Rodriguez-Mallon, A. Developing anti-tick vaccines. Methods Mol. Biol. 1404, 243–259 (2016).
Sprong, H. et al. ANTIDotE: anti-tick vaccines to prevent tick-borne diseases in Europe. Parasit. Vectors 7, 77 (2014).
Valle, M. R. & Guerrero, F. D. Anti-tick vaccines in the omics era. Front. Biosci. 10, 122–136 (2018).
Rego, R. O. M. et al. Counterattacking the tick bite: towards a rational design of anti-tick vaccines targeting pathogen transmission. Parasit. Vectors 12, 229 (2019).
Marques, A. R., Strle, F. & Wormser, G. P. Comparison of Lyme disease in the United States and Europe. Emerg. Infect. Dis. 27, 2017–2024 (2021).
Madison-Antenucci, S., Kramer, L. D., Gebhardt, L. L. & Kauffman, E. Emerging tick-borne diseases. Clin. Microbiol. Rev. 33, e00083-18 (2020).
Smith, A. A. et al. Cross-species interferon signaling boosts microbicidal activity within the tick vector. Cell Host Microbe 20, 91–98 (2016).
Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009).
Seppey, M., Manni, M. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation vompleteness. Methods Mol. Biol. 1962, 227–245 (2019).
Cenik, B. K. & Shilatifard, A. COMPASS and SWI/SNF complexes in development and disease. Nat. Rev. Genet. 22, 38–58 (2021).
Clavier, A., Rincheval-Arnold, A., Colin, J., Mignotte, B. & Guenal, I. Apoptosis in Drosophila: which role for mitochondria? Apoptosis 21, 239–251 (2016).
O’Rourke, J. G. et al. SUMO-2 and PIAS1 modulate insoluble mutant huntingtin protein accumulation. Cell Rep. 4, 362–375 (2013).
Wu, Q., Patocka, J. & Kuca, K. Insect antimicrobial peptides, a mini review. Toxins 10, 461 (2018).
Rytz, R., Croset, V. & Benton, R. Ionotropic receptors (IRs): chemosensory ionotropic glutamate receptors in Drosophila and beyond. Insect Biochem. Mol. Biol. 43, 888–897 (2013).
Smith, A. A. & Pal, U. Immunity-related genes in Ixodes scapularis-perspectives from genome information. Front. Cell Infect. Microbiol. 4, 116 (2014).
Shaw, D. K. et al. Vector immunity and evolutionary ecology: the harmonious dissonance. Trends Immunol. 39, 862–873 (2018).
Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549 (2018).
Stecher, G., Tamura, K. & Kumar, S. Molecular evolutionary genetics analysis (MEGA) for macOS. Mol. Biol. Evol. 37, 1237–1239 (2020).
Koci, J. et al. Antibodies against EGF-like domains in Ixodes scapularis BM86 orthologs impact tick feeding and survival of Borrelia burgdorferi. Sci. Rep. 11, 6095 (2021).
Acknowledgements
We thank K. Nassar for her assistance with the preparation of the manuscript. We thank PacBio for providing part of the reagents for DNA-seq. We deeply appreciate the assistance of I. Liachko and M. Wood with the Hi-C analyses. The present study was supported by grants from the National Institute of Allergy and Infectious Diseases (award nos. R01AI080615, R01AI116620 and P01AI138949 to U.P.) and the National Institute of Dental and Craniofacial Research (grant no. ZIA DE000751 to Y.W.).
Author information
Authors and Affiliations
Contributions
S.D., S.B.K., C.K., D.M.P. and U.P. designed research, carried out experiments, analyzed data, prepared figures and wrote part of the manuscript. S.D.F., J.C.F., V.S.R. and N.S.P. carried out experiments, analyzed data and prepared text and figures. Y.W. assisted with the MS experiments, analyzed data and prepared figures. D.A.R. supervised experiments, analyzed data and wrote part of the manuscript. T.C.G. supervised experiments, provided reagents, analyzed data and wrote part of the manuscript. U.P. conceived and designed experiments, supervised the study, prepared figures and wrote the paper with critical input from all authors. C.K. is a recipient of Blackman Postdoctoral Fellowship from Global Lyme Alliance.
Corresponding author
Ethics declarations
Competing interests
S.B.K. is an employee and shareholder of Pacific Biosciences. No other authors declare any competing interests.
Peer review
Peer review information
Nature Genetics thanks Wu-Chun Cao, Abhijeet Nayak and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Extended data
Extended Data Fig. 1 Roles of Set1 and NSD2 in tick biology.
a,b, Comparisons of the Set1 and NSD2 gene models by VectorBase (blue) and NCBI (green). Raw Iso-Seq reads are shown in the bottom (grey). c, RT-qPCR analysis of Set1 and NSD2 RNA in unfed, 8 h-, 24 h-, 48 h- and 72 h-fed ticks post placement on naïve mice. Error bars show the mean with SEM from four biological replicates. d, RT-qPCR analysis of Set1 and NSD2 RNA in 8 h-fed ticks post placement on naïve mice. Separate groups of ticks were injected with dsGFP, dsSet1, or dsNSD2. Error bars show the mean with SEM from four biological replicates (n = 4); two-tailed Mann–Whitney U-test. e, Impact of RNAi on tick engorgement time during feeding. The percentage of ticks collected after 96, 120, 144, and 168 h of tick placement on mice are shown. Error bars denote the mean with SEM from three biological replicates. f, Impact of RNAi on tick engorgement success. The total percentage of ticks collected after completion of tick feeding is shown. Error bars denote the mean with SEM from three biological replicates (n = 3); Student’s t-test. g, Impact of RNAi on tick weight. The weights of fully engorged ticks (mg) are shown, with each data point representing one nymph. Error bars denote the mean with SEM from three biological replicates of 25 ticks from each group; two-tailed Mann–Whitney U-test. h, Impact of RNAi on tick molting. The percentage of fully engorged nymphs that molted into adult ticks is shown. Error bars denote the mean with SEM from three biological replicates (n = 3); Student’s t-test.
Extended Data Fig. 2 Ash2 immunization and roles in tick biology.
a, Ash2 immunization does not affect tick feeding. The upper left panel shows the percentage of ticks collected after 96 and 120 h of feeding after placement on phosphate-buffered saline (PBS)- or Ash2-immunized mice; the upper right panel shows the total percentage of engorged ticks collected after the completion of feeding on PBS- and Ash2-immunized mice. Error bars denote the mean with SEM of three biological replicates, with 25 ticks per group (two-tailed Mann–Whitney U-test). The lower left panel denotes the weights of fully engorged ticks (mg). Each data point represents a single tick collected (n = 75) from three biological replicates; two-tailed Mann–Whitney U-test. The lower right panel shows the percentage of fully engorged nymphs that molted into adult ticks after feeding on PBS-immunized and Ash2-immunized mice. Error bars denote the mean with SEM (n = 4 biological replicates, each with 25 ticks per group); two-tailed Mann–Whitney U-test. b, Comparison of the amino acid sequences of the SPRY domains (left panel) and ZFD domains (right panel) from human, I. scapularis, D. melanogaster, A. gambiae, and A. aegypti Ash2 proteins. The human has three Ash2 protein isoforms, while the tick, Drosophila, A. gambiae, and A. aegypti each have two Ash2 isoforms. Human Ash2 isoforms do not contain any ZFDs. c, Staining of dsGFP and dsash2 groups representing 8 h-fed and 48 h-fed tick guts with anti-PH3 antibody (arrow) and DAPI. The insets show zoomed-in pictures of the tick gut cells. The PH3 positive nuclei are less apparent in Ash2-deficient tick gut. The experiment was repeated independently three times with similar results. White bar = 20 µm.
Extended Data Fig. 3 Variations in tick population genetic structures as assessed by RAD-Seq.
a,b, DAPC plot and locations of tick collection and the tick cell line. The maps were created in R scripts using open-source data for the U.S. political boundaries. c, Genetic distance tree depicts the phylogenetic relationship between ticks collected from target geographical areas and ISE6 cells.
Supplementary information
Supplementary Information
Supplementary Notes 1–7, Methods, Figs. 1–4 and Tables 1–28.
Source data
Source Data Fig. 4
Unprocessed western blot corresponding to Fig. 4f.
Source Data Fig. 7
Spreadsheet showing full list of identified proteins for Fig. 7.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
De, S., Kingan, S.B., Kitsou, C. et al. A high-quality Ixodes scapularis genome advances tick science. Nat Genet 55, 301–311 (2023). https://doi.org/10.1038/s41588-022-01275-w
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41588-022-01275-w
This article is cited by
-
Tick hemocytes have a pleiotropic role in microbial infection and arthropod fitness
Nature Communications (2024)
-
Ancient diversity in host-parasite interaction genes in a model parasitic nematode
Nature Communications (2023)
-
A longitudinal transcriptomic analysis from unfed to post-engorgement midguts of adult female Ixodes scapularis
Scientific Reports (2023)