BIOEPAR, INRA, Oniris, Université Bretagne Loire, 44307, Nantes, France.
Laboratoire d'Ecologie et Evolution des parasites, Institut de Biologie, Université de Neuchâtel, Rue Emile-Argand 11, CH-2000, Neuchâtel, Switzerland.
Parasit Vectors. 2018 Jun 26;11(1):364. doi: 10.1186/s13071-018-2932-3.
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. 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.
RNA 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.
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.
硬蜱是欧洲最重要的蜱传疾病媒介。更好地了解其基因组和转录组对于制定控制策略非常重要。以前对硬蜱的转录组学研究主要集中在特定组织中血餐期间的基因表达。为了更全面地了解血餐过程中基因表达的变化，我们对来自尼翁大学高度近交群体的若虫和成虫的整个身体进行了转录组分析。我们还分析了以前发表的 RNAseq 研究，以比较三个野生株和三个实验室株（包括尼翁株）之间的遗传变异。
从整个蜱体中提取 RNA 并对 cDNA 进行测序，产生了 162872698 对端读序列。我们的参考转录组包含 179316 个连续序列，其中 31% 使用 Trinotate 进行注释。比较了不同摄食状态（未摄食与部分摄食）的蜱之间的基因表达。我们发现，幼蜱和雌成蜱的吸血增加了与角质层相关的基因的表达。使用一组 3866 个单核苷酸多态性来计算杂合度，我们发现硬蜱的野生种群的杂合度水平明显高于三个实验室种群。
使用不同阶段和摄食条件的全蜱高通量链定向测序，我们获得了从头组装，这大大增加了硬蜱可用的基因组资源。我们的研究说明了在整个生物体的生命周期中分析转录组以获得额外的基因表达变化见解的重要性。我们对几个 RNAseq 数据集的比较表明，转录组数据具有准确描述遗传多态性以及比较不同种群或测序材料来源的强大功能。
