Abstract
BackgroundIxodes 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. Ixodes 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 laboratory strains, including the strain from Neuchâtel.ResultsRNA was extracted from whole tick bodies and the cDNA was sequenced, producing 162,872,698 paired-end reads. Our reference transcriptome contained 179,316 contigs, of which 31% were annotated using Trinotate. Gene expression was compared between ticks that differed by feeding status (unfed vs partially fed). We found that blood-feeding in nymphs and female adult ticks increased the expression of cuticle-associated genes. Using a set of 3866 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 laboratory populations.ConclusionUsing 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.
Highlights
Ixodes ricinus is the most important vector of tick-borne diseases in Europe
For the 15 different tick libraries, 88% and 91% of the reads mapped back to contigs. This good recruitment rate suggests that (i) the Trinity-produced assembly managed to capture most of the information contained by the reads, and (ii) little information was lost after eliminating the smaller class of contigs (< 300 bp)
When only considering contigs above a certain size, the number of contigs clearly tended to plateau; this plateau can already be seen for contig size > 300 bp, whereas the plateau was marked for contigs > 1000 bp
Summary
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. These studies have shown that there are thousands of transcripts that are differentially expressed with respect to the duration of the blood meal, the developmental stage (nymph versus adult), the specific tissue (salivary glands versus midgut), and other conditions [12,13,14,15,16,17,18,19] Most of these studies have focused on gene expression during the blood meal in either the nymphal tick or the adult tick, which is when pathogen transmission occurs [14]
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