Ixodes ricinus ticks are distributed across Europe and are a vector of tick-borne diseases. Although I. ricinus transcriptome studies have focused exclusively on protein coding genes, the last decade witnessed a strong increase in long non-coding RNA (lncRNA) research and characterization. Here, we report for the first time an exhaustive analysis of these non-coding molecules in I. ricinus based on 131 RNA-seq datasets from three different BioProjects. Using this data, we obtained a consensus set of lncRNAs and showed that lncRNA expression is stable among different studies. While the length distribution of lncRNAs from the individual data sets is biased toward short length values, implying the existence of technical artefacts, the consensus lncRNAs show a more homogeneous distribution emphasizing the importance to incorporate data from different sources to generate a solid reference set of lncRNAs. KEGG enrichment analysis of host miRNAs putatively targeting lncRNAs upregulated upon feeding showed that these miRNAs are involved in several relevant functions for the tick-host interaction. The possibility that at least some tick lncRNAs act as host miRNA sponges was further explored by identifying lncRNAs with many target regions for a given host miRNA or sets of host miRNAs that consistently target lncRNAs together. Overall, our findings suggest that lncRNAs that may act as sponges have diverse biological roles related to the tick-host interaction in different tissues.

Departamentode Genética Facultad de Ciencias Universidad de Granada Campus de Fuentenueva s n 18071 Granada Spain

Institute of Parasitology Biology Centre Czech Academy of Sciences 37005 Ceske Budejovice Czech Republic

Laboratorio de Bioinformática Centro de Investigación Biomédica PTS Instituto de Biotecnología Avda del Conocimiento s n 18016 Granada Spain

State Key Laboratory of Silkworm Genome Biology Key Laboratory of Sericultural Biology and Genetic Breeding Ministry of Agriculture Southwest University Chongqing 400715 China

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Chmelar J., Calvo E., Pedra J.H.F., Francischetti I.M.B., Kotsyfakis M. Tick Salivary Secretion as a Source of Antihemostatics. J. Proteom. 2012;75:3842. doi: 10.1016/j.jprot.2012.04.026. PubMed DOI PMC

Abbas M.N., Chlastáková A., Jmel M.A., Iliaki-Giannakoudaki E., Chmelař J., Kotsyfakis M. Serpins in Tick Physiology and Tick-Host Interaction. Front. Cell. Infect. Microbiol. 2022;12:892770. doi: 10.3389/fcimb.2022.892770. PubMed DOI PMC

Kotál J., Langhansová H., Lieskovská J., Andersen J.F., Francischetti I.M.B., Chavakis T., Kopecký J., Pedra J.H.F., Kotsyfakis M., Chmelař J. Modulation of Host Immunity by Tick Saliva. J. Proteom. 2015;128:58. doi: 10.1016/j.jprot.2015.07.005. PubMed DOI PMC

Šimo L., Kazimirova M., Richardson J., Bonnet S.I. The Essential Role of Tick Salivary Glands and Saliva in Tick Feeding and Pathogen Transmission. Front. Cell. Infect. Microbiol. 2017;7:281. doi: 10.3389/fcimb.2017.00281. PubMed DOI PMC

Chmelař J., Kotál J., Karim S., Kopacek P., Francischetti I.M.B., Pedra J.H.F., Kotsyfakis M. Sialomes and Mialomes: A Systems-Biology View of Tick Tissues and Tick–Host Interactions. Trends Parasitol. 2016;32:242–254. doi: 10.1016/j.pt.2015.10.002. PubMed DOI PMC

De La Fuente J., Villar M., Estrada-Peña A., Olivas J.A. High Throughput Discovery and Characterization of Tick and Pathogen Vaccine Protective Antigens Using Vaccinomics with Intelligent Big Data Analytic Techniques. Expert Rev. Vaccines. 2018;17:569–576. doi: 10.1080/14760584.2018.1493928. PubMed DOI

Wang H.L.V., Chekanova J.A. An Overview of Methodologies in Studying LncRNAs in the High-Throughput Era: When Acronyms ATTACK! Methods Mol. Biol. 2019;1933:1–30. doi: 10.1007/978-1-4939-9045-0_1. PubMed DOI PMC

Dempsey J.L., Cui J.Y. Long Non-Coding RNAs: A Novel Paradigm for Toxicology. Toxicol. Sci. 2017;155:3–21. doi: 10.1093/toxsci/kfw203. PubMed DOI PMC

Wang K.C., Chang H.Y. Molecular Mechanisms of Long Noncoding RNAs. Mol. Cell. 2011;43:904–914. doi: 10.1016/j.molcel.2011.08.018. PubMed DOI PMC

Mariner P.D., Walters R.D., Espinoza C.A., Drullinger L.F., Wagner S.D., Kugel J.F., Goodrich J.A. Human Alu RNA Is a Modular Transacting Repressor of MRNA Transcription during Heat Shock. Mol. Cell. 2008;29:499–509. doi: 10.1016/j.molcel.2007.12.013. PubMed DOI

Paraskevopoulou M.D., Hatzigeorgiou A.G. Analyzing MiRNA-LncRNA Interactions. Methods Mol. Biol. 2016;1402:271–286. doi: 10.1007/978-1-4939-3378-5_21. PubMed DOI

Ahmad P., Bensaoud C., Mekki I., Rehman M.U., Kotsyfakis M. Long Non-Coding RNAs and Their Potential Roles in the Vector-Host-Pathogen Triad. Life. 2021;11:56. doi: 10.3390/life11010056. PubMed DOI PMC

Kern C., Wang Y., Chitwood J., Korf I., Delany M., Cheng H., Medrano J.F., van Eenennaam A.L., Ernst C., Ross P., et al. Genome-Wide Identification of Tissue-Specific Long Non-Coding RNA in Three Farm Animal Species 06 Biological Sciences 0604 Genetics. BMC Genom. 2018;19:684. doi: 10.1186/S12864-018-5037-7/FIGURES/4. PubMed DOI PMC

Bayer-Santos E., Marini M.M., da Silveira J.F. Non-Coding RNAs in Host–Pathogen Interactions: Subversion of Mammalian Cell Functions by Protozoan Parasites. Front. Microbiol. 2017;8:474. doi: 10.3389/fmicb.2017.00474. PubMed DOI PMC

Bensaoud C., Hackenberg M., Kotsyfakis M. Noncoding RNAs in Parasite–Vector–Host Interactions. Trends Parasitol. 2019;35:715–724. doi: 10.1016/j.pt.2019.06.012. PubMed DOI

Aparicio-Puerta E., Lebrón R., Rueda A., Gómez-Martín C., Giannoukakos S., Jaspez D., Medina J.M., Zubkovic A., Jurak I., Fromm B., et al. SRNAbench and SRNAtoolbox 2019: Intuitive Fast Small RNA Profiling and Differential Expression. Nucleic Acids Res. 2019;47:W530–W535. doi: 10.1093/nar/gkz415. PubMed DOI PMC

Fromm B., Høye E., Domanska D., Zhong X., Aparicio-Puerta E., Ovchinnikov V., Umu S.U., Chabot P.J., Kang W., Aslanzadeh M., et al. MirGeneDB 2.1: Toward a Complete Sampling of All Major Animal Phyla. Nucleic Acids Res. 2021;50:D204–D210. doi: 10.1093/nar/gkab1101. PubMed DOI PMC

Vlachos I.S., Zagganas K., Paraskevopoulou M.D., Georgakilas G., Karagkouni D., Vergoulis T., Dalamagas T., Hatzigeorgiou A.G. DIANA-MiRPath v3.0: Deciphering MicroRNA Function with Experimental Support. Nucleic Acids Res. 2015;43:W460–W466. doi: 10.1093/nar/gkv403. PubMed DOI PMC

Preusse M., Theis F.J., Mueller N.S. MiTALOS v2: Analyzing Tissue Specific MicroRNA Function. PLoS ONE. 2016;11:e0151771. doi: 10.1371/JOURNAL.PONE.0151771. PubMed DOI PMC

Sonenshine E.D. Biology of Ticks. Oxford University Press; Oxford, NY, USA: 1991.

Sauer J.R., McSwain J.L., Bowman A.S., Essenberg R.C. Tick Salivary Gland Physiology. Annu. Rev. Entomol. 1995;40:245–267. doi: 10.1146/annurev.en.40.010195.001333. PubMed DOI

Narasimhan S., DePonte K., Marcantonio N., Liang X., Royce T.E., Nelson K.F., Booth C.J., Koski B., Anderson J.F., Kantor F., et al. Immunity against Ixodes Scapularis Salivary Proteins Expressed within 24 Hours of Attachment Thwarts Tick Feeding and Impairs Borrelia Transmission. PLoS ONE. 2007;2:e451. doi: 10.1371/journal.pone.0000451. PubMed DOI PMC

Francischetti I.M.B., Mather T.N., Ribeiro J.M.C. Tick Saliva Is a Potent Inhibitor of Endothelial Cell Proliferation and Angiogenesis. Thromb. Haemost. 2005;94:167–174. doi: 10.1160/TH04-09-0566. PubMed DOI PMC

Díaz-Martín V., Manzano-Román R., Oleaga A., Encinas-Grandes A., Pérez-Sánchez R. Cloning and Characterization of a Plasminogen-Binding Enolase from the Saliva of the Argasid Tick Ornithodoros Moubata. Vet. Parasitol. 2013;191:301–314. doi: 10.1016/j.vetpar.2012.09.019. PubMed DOI

Basson M.D., Sanders M.A., Gomez R., Hatfield J., VanderHeide R., Thamilselvan V., Zhang J., Walsh M.F. Focal Adhesion Kinase Protein Levels in Gut Epithelial Motility. Am. J. Physiol. Gastrointest. Liver Physiol. 2006;291:G491–G499. doi: 10.1152/ajpgi.00292.2005. PubMed DOI

Sheng H., Shao J., Townsend C.M., Evers B.M. Phosphatidylinositol 3-Kinase Mediates Proliferative Signals in Intestinal Epithelial Cells. Gut. 2003;52:1472–1478. doi: 10.1136/gut.52.10.1472. PubMed DOI PMC

Chen L., Chi H., Kinashi T. Editorial: Hippo Signaling in the Immune System. Front. Immunol. 2020;11:587514. doi: 10.3389/fimmu.2020.587514. PubMed DOI PMC

Wang Y., Malik A.B., Sun Y., Hu S., Reynolds A.B., Minshall R.D., Hu G. Innate Immune Function of the Adherens Junction Protein P120-Catenin in Endothelial Response to Endotoxin. J. Immunol. 2011;186:3180. doi: 10.4049/jimmunol.1001252. PubMed DOI PMC

Tian E., ten Hagen K.G. Recent Insights into the Biological Roles of Mucin-Type O-Glycosylation. Glycoconj J. 2009;26:325–334. doi: 10.1007/s10719-008-9162-4. PubMed DOI PMC

Gray E., Hogwood J., Mulloy B. The Anticoagulant and Antithrombotic Mechanisms of Heparin. Handb. Exp. Pharm. 2012;207:43–61. doi: 10.1007/978-3-642-23056-1_3. PubMed DOI

Li M.O., Wan Y.Y., Sanjabi S., Robertson A.K.L., Flavell R.A. Transforming Growth Factor-Beta Regulation of Immune Responses. Annu. Rev. Immunol. 2006;24:99–146. doi: 10.1146/annurev.immunol.24.021605.090737. PubMed DOI

Martínez V.G., Hernández-López C., Valencia J., Hidalgo L., Entrena A., Zapata A.G., Vicente A., Sacedón R., Varas A. The Canonical BMP Signaling Pathway Is Involved in Human Monocyte-Derived Dendritic Cell Maturation. Immunol. Cell Biol. 2011;89:610–618. doi: 10.1038/icb.2010.135. PubMed DOI

MacDonald L.A., Cohen A., Baron S., Burchfiel C.M. Respond to “Search for Preventable Causes of Cardiovascular Disease”. Am. J. Epidemiol. 2009;169:1426–1427. doi: 10.1093/aje/kwp080. PubMed DOI

Kim M., Choi S.H., Jin Y.B., Lee H.J., Ji Y.H., Kim J., Lee Y.S., Lee Y.J. The Effect of Oxidized Low-Density Lipoprotein (Ox-LDL) on Radiation-Induced Endothelial-to-Mesenchymal Transition. Int. J. Radiat. Biol. 2013;89:356–363. doi: 10.3109/09553002.2013.763193. PubMed DOI

Etebari K., Asad S., Zhang G., Asgari S. Identification of Aedes Aegypti Long Intergenic Non-Coding RNAs and Their Association with Wolbachia and Dengue Virus Infection. PLoS Negl. Trop. Dis. 2016;10:e0005069. doi: 10.1371/journal.pntd.0005069. PubMed DOI PMC

Azlan A., Obeidat S.M., Das K.T., Yunus M.A., Azzam G. Genome-Wide Identification of Aedes Albopictus Long Noncoding RNAs and Their Association with Dengue and Zika Virus Infection. PLoS Negl. Trop. Dis. 2021;15:e0008351. doi: 10.1371/journal.pntd.0008351. PubMed DOI PMC

Medina J.M., Jmel M.A., Cuveele B., Gómez-Martín C., Aparicio-Puerta E., Mekki I., Kotál J., Martins L.A., Hackenberg M., Bensaoud C., et al. Transcriptomic Analysis of the Tick Midgut and Salivary Gland Responses upon Repeated Blood-Feeding on a Vertebrate Host. Front. Cell. Infect. Microbiol. 2022;12:919786. doi: 10.3389/fcimb.2022.919786. PubMed DOI PMC

Perner J., Kropáčková S., Kopáček P., Ribeiro J.M.C. Sialome Diversity of Ticks Revealed by RNAseq of Single Tick Salivary Glands. PLoS Negl. Trop. Dis. 2018;12:e0006410. doi: 10.1371/journal.pntd.0006410. PubMed DOI PMC

Charrier N.P., Couton M., Voordouw M.J., Rais O., Durand-Hermouet A., Hervet C., Plantard O., Rispe C. Whole Body Transcriptomes and New Insights into the Biology of the Tick Ixodes Ricinus. Parasites Vectors. 2018;11:364. doi: 10.1186/s13071-018-2932-3. PubMed DOI PMC

Babraham Bioinformatics Babraham Bioinformatics—Trim Galore. [(accessed on 4 July 2018)]. Available online: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

Babraham Bioinformatics Babraham Bioinformatics—FastQC A Quality Control Tool for High Throughput Sequence Data. [(accessed on 4 July 2018)]. Available online: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Grabherr M.G., Haas B.J., Yassour M., Levin J.Z., Thompson D.A., Amit I., Adiconis X., Fan L., Raychowdhury R., Zeng Q., et al. Trinity: Reconstructing a Full-Length Transcriptome without a Genome from RNA-Seq Data. Nat. Biotechnol. 2011;29:644. doi: 10.1038/nbt.1883. PubMed DOI PMC

Fu L., Niu B., Zhu Z., Wu S., Li W. CD-HIT: Accelerated for Clustering the next-Generation Sequencing Data. Bioinformatics. 2012;28:3150–3152. doi: 10.1093/bioinformatics/bts565. PubMed DOI PMC

Li B., Dewey C.N. RSEM: Accurate Transcript Quantification from RNA-Seq Data with or without a Reference Genome. BMC Bioinform. 2011;12:323. doi: 10.1186/1471-2105-12-323. PubMed DOI PMC

Langmead B., Salzberg S.L. Fast Gapped-Read Alignment with Bowtie 2. Nat. Methods. 2012;9:357–359. doi: 10.1038/nmeth.1923. PubMed DOI PMC

Boutet E., Lieberherr D., Tognolli M., Schneider M., Bairoch A. UniProtKB/Swiss-Prot. Methods Mol. Biol. 2007;406:89–112. doi: 10.1007/978-1-59745-535-0_4. PubMed DOI

Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic Local Alignment Search Tool. J. Mol. Biol. 1990;215:403–410. doi: 10.1016/S0022-2836(05)80360-2. PubMed DOI

Medina J.M., Jmel M.A., Cuveele B., Mekki I., Kotal J., Almeida Martins L., Hackenberg M., Kotsyfakis M., Bensaoud C. IxoriDB. [(accessed on 20 August 2022)]. Available online: https://arn.ugr.es/IxoriDB.

Schmid-Hempel P. Immune Defence, Parasite Evasion Strategies and Their Relevance for ‘Macroscopic Phenomena’ Such as Virulence. Philos. Trans. R. Soc. B Biol. Sci. 2009;364:85. doi: 10.1098/rstb.2008.0157. PubMed DOI PMC

Robinson M.D., Oshlack A. A Scaling Normalization Method for Differential Expression Analysis of RNA-Seq Data. Genome Biol. 2010;11:R25. doi: 10.1186/gb-2010-11-3-r25. PubMed DOI PMC

Robinson M.D., McCarthy D.J., Smyth G.K. EdgeR: A Bioconductor Package for Differential Expression Analysis of Digital Gene Expression Data. Bioinformatics. 2010;26:139. doi: 10.1093/bioinformatics/btp616. PubMed DOI PMC

Genome sequences of four Ixodes species expands understanding of tick evolution

Recent Advances in Tick Antigen Discovery and Anti-Tick Vaccine Development

Editorial: Special Issue on the "Molecular Biology of Disease Vectors"