Whole body transcriptomes and new insights into the biology of the tick Ixodes ricinus
Abstract 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...
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doaj-7d005527983745c8b623130fca1d47ee2020-11-25T02:04:07ZengBMCParasites & Vectors1756-33052018-06-0111111510.1186/s13071-018-2932-3Whole body transcriptomes and new insights into the biology of the tick Ixodes ricinusN. Pierre Charrier0Marjorie Couton1Maarten J. Voordouw2Olivier Rais3Axelle Durand-Hermouet4Caroline Hervet5Olivier Plantard6Claude Rispe7BIOEPAR, INRA, Oniris, Université Bretagne LoireBIOEPAR, INRA, Oniris, Université Bretagne LoireLaboratoire d’Ecologie et Evolution des parasites, Institut de Biologie, Université de NeuchâtelLaboratoire d’Ecologie et Evolution des parasites, Institut de Biologie, Université de NeuchâtelBIOEPAR, INRA, Oniris, Université Bretagne LoireBIOEPAR, INRA, Oniris, Université Bretagne LoireBIOEPAR, INRA, Oniris, Université Bretagne LoireBIOEPAR, INRA, Oniris, Université Bretagne LoireAbstract 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. 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. Results RNA was extracted from whole tick bodies and the cDNA was sequenced, producing 162,872,698 paired-end reads. Our reference transcriptome contained 179,316 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. 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.http://link.springer.com/article/10.1186/s13071-018-2932-3TranscriptomicsRNA-seqIxodes ricinusExpression profilingPolymorphism |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
N. Pierre Charrier Marjorie Couton Maarten J. Voordouw Olivier Rais Axelle Durand-Hermouet Caroline Hervet Olivier Plantard Claude Rispe |
spellingShingle |
N. Pierre Charrier Marjorie Couton Maarten J. Voordouw Olivier Rais Axelle Durand-Hermouet Caroline Hervet Olivier Plantard Claude Rispe Whole body transcriptomes and new insights into the biology of the tick Ixodes ricinus Parasites & Vectors Transcriptomics RNA-seq Ixodes ricinus Expression profiling Polymorphism |
author_facet |
N. Pierre Charrier Marjorie Couton Maarten J. Voordouw Olivier Rais Axelle Durand-Hermouet Caroline Hervet Olivier Plantard Claude Rispe |
author_sort |
N. Pierre Charrier |
title |
Whole body transcriptomes and new insights into the biology of the tick Ixodes ricinus |
title_short |
Whole body transcriptomes and new insights into the biology of the tick Ixodes ricinus |
title_full |
Whole body transcriptomes and new insights into the biology of the tick Ixodes ricinus |
title_fullStr |
Whole body transcriptomes and new insights into the biology of the tick Ixodes ricinus |
title_full_unstemmed |
Whole body transcriptomes and new insights into the biology of the tick Ixodes ricinus |
title_sort |
whole body transcriptomes and new insights into the biology of the tick ixodes ricinus |
publisher |
BMC |
series |
Parasites & Vectors |
issn |
1756-3305 |
publishDate |
2018-06-01 |
description |
Abstract 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. 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. Results RNA was extracted from whole tick bodies and the cDNA was sequenced, producing 162,872,698 paired-end reads. Our reference transcriptome contained 179,316 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. 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. |
topic |
Transcriptomics RNA-seq Ixodes ricinus Expression profiling Polymorphism |
url |
http://link.springer.com/article/10.1186/s13071-018-2932-3 |
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