RT Journal Article SR Electronic T1 Whole body transcriptomes and new insights into the biology of the tick Ixodes ricinus JF bioRxiv FD Cold Spring Harbor Laboratory SP 244830 DO 10.1101/244830 A1 N. Pierre Charrier A1 Marjorie Couton A1 Maarten J. Voordouw A1 Olivier Rais A1 Axelle Durand-Hermouet A1 Caroline Hervet A1 Olivier Plantard A1 Claude Rispe YR 2018 UL http://biorxiv.org/content/early/2018/01/09/244830.abstract AB Background Ixodes ricinus is the most important vector of tick-borne-diseases in Europe. A better knowledge of its genome and transcriptome is important for developing control strategies. Previous transcriptomic studies of I. ricinus have focused on gene expression during the blood meal in specific tissues. To obtain a broader picture of changes in gene expression during the blood meal, our study analysed the transcriptome at the level of the whole body for both nymphal and adult ticks. I. ricinus ticks from a highly inbred colony at the University of Neuchâtel were used. We also analysed previously published RNAseq studies to compare the genetic variation between three wild strains and three lab strains, including the strain from Neuchâtel.Results RNA was extracted from whole tick bodies and the cDNA was sequenced, producing 162,872,698 paired-end reads. Our reference transcriptome contained 179,682 contigs, of which 31% were annotated using Trinotate. Gene expression was compared between ticks that differed with respect to stage (nymph, adult), sex (female, male), and feeding status (unfed, partially fed). We found that blood feeding in nymphs and female adult ticks increased the expression of cuticle-associated genes. Using a set of 5,422 single nucleotide polymorphisms to calculate the heterozygosity, we found that the wild tick populations of I. ricinus had much higher levels of heterozygosity than the three lab populations.Conclusion Using high throughput strand-oriented sequencing for whole ticks in different stages and feeding conditions, we obtained a de novo assembly that significantly increased the genomic resources available for I. ricinus. Our study illustrates the importance of analysing the transcriptome at the level of the whole body to gain additional insights into how gene expression changes over the life cycle of an organism. Our comparison of several RNAseq datasets shows the power of transcriptomic data to accurately characterize genetic polymorphism and for comparing different populations or sources of sequencing material.