Whole body transcriptomes and new insights into the biology of the tick Ixodes ricinus

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.Electronic supplementary materialThe online version of this article (10.1186/s13071-018-2932-3) contains supplementary material, which is available to authorized users.

Catalogue of stage-specific transcripts in Ixodes ricinus and their potential functions during the tick life-cycle

“…Functional classification of most typical transcription was linked to cuticle formation and chitin metabolism as well as to the activation of blood-meal processing enzymes, all in response to a blood meal. These findings were anticipated and are in line with previous observations [30,31,33,75].…”

“…Several transcriptomic studies were focusing on molecules that might directly influence feeding, such as haem utilization in ticks [27] or arthropod proteases, both being essential factors enabling a haematophagous life strategy [28]. Transcriptional regulation of the entire life-cycle, controlling tick ontogenesis and development has not been fully covered to date and existing research has only focused on a specific organ [29] or a life stage [30].…”

“…More specifically, expression analyses using tick haemocytes, the main actors in tick immunity, can unveil the character of the immunity barrier for tick-borne pathogens [29]. Organism-level transcriptomes of feeding stages, on the other hand, can provide a picture of global changes induced by a blood meal [30] , hence a more thorough description of factors driving tick developmental processes throughout its life-cycle will be instrumental in understanding the process of hostseeking and blood-feeding as an integral event in tick development.…”

De Novo Assembly and Analysis of Transcriptome of the Dermacentor Marginatus Genes Differentially Expressed After Blood Feeding and Long-term Starvation

“…Up to 55 unigenes on carbohydrate metabolism were differentially expressed (35 in F tick group, 9 in H tick group and 11 in M tick group), covering biological process such as carbohydrate phosphorylation, protein glycosylation, glycogen catabolic process, galactose metabolic process. The results indicated that the up-regulated unigenes encoding carbohydrate-metabolizing enzymes were similar with the genes identi ed in the transcriptomes of Ixodes ricinus [67], Haemaphysalis ava [31], Dermacentor variabilis [68], and in Argasidae of Ornithodoros moubata [41] and Ornithodoros erraticus [60]. According to the annotations, the up-regulated unigenes were associated with the metabolism and transport of several carbohydrates including glucose, fructose, mannose, galactose, maltose, idose, malate and chitin (Table 4).…”

Hard ticks as research resources for vector biology: from genome to whole-body level

“…ncbi.nlm.nih.gov/genbank/) or the web sites of each publication (for example: https://parasitesandvectors. biomedcentral.com/articles/10.1186/s13071-018-2932-3 (Charrier et al, 2018). Among tick species shown in Fig.…”