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Article

Bioinformatic Analysis of Ixodes ricinus Long Non-Coding RNAs Predicts Their Binding Ability of Host miRNAs

1
Departamentode Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071 Granada, Spain
2
Laboratorio de Bioinformática, Centro de Investigación Biomédica, PTS, Instituto de Biotecnología, Avda. del Conocimiento s/n, 18016 Granada, Spain
3
State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing 400715, China
4
Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 Ceske Budejovice, Czech Republic
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editor: Tamir Tuller
Int. J. Mol. Sci. 2022, 23(17), 9761; https://doi.org/10.3390/ijms23179761
Received: 24 July 2022 / Revised: 22 August 2022 / Accepted: 24 August 2022 / Published: 28 August 2022
(This article belongs to the Special Issue Molecular Biology of Disease Vectors)
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. View Full-Text
Keywords: Ixodes ricinus; ectoparasite-host interactions; host immunity; RNA-sequencing; lncRNA Ixodes ricinus; ectoparasite-host interactions; host immunity; RNA-sequencing; lncRNA
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MDPI and ACS Style

Medina, J.M.; Abbas, M.N.; Bensaoud, C.; Hackenberg, M.; Kotsyfakis, M. Bioinformatic Analysis of Ixodes ricinus Long Non-Coding RNAs Predicts Their Binding Ability of Host miRNAs. Int. J. Mol. Sci. 2022, 23, 9761. https://doi.org/10.3390/ijms23179761

AMA Style

Medina JM, Abbas MN, Bensaoud C, Hackenberg M, Kotsyfakis M. Bioinformatic Analysis of Ixodes ricinus Long Non-Coding RNAs Predicts Their Binding Ability of Host miRNAs. International Journal of Molecular Sciences. 2022; 23(17):9761. https://doi.org/10.3390/ijms23179761

Chicago/Turabian Style

Medina, José María, Muhammad Nadeem Abbas, Chaima Bensaoud, Michael Hackenberg, and Michail Kotsyfakis. 2022. "Bioinformatic Analysis of Ixodes ricinus Long Non-Coding RNAs Predicts Their Binding Ability of Host miRNAs" International Journal of Molecular Sciences 23, no. 17: 9761. https://doi.org/10.3390/ijms23179761

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