Integration of Ixodes ricinus genome sequencing with transcriptome and proteome annotation of the naïve midgut.
BACKGROUND
In Europe, Ixodes ricinus ticks are the most important vectors of diseases threatening humans, livestock, wildlife and companion animals. Nevertheless, genomic sequence information is missing and functional annotation of transcripts and proteins is limited. This lack of information is restricting studies of the vector and its interactions with pathogens and hosts. Here we present and integrate the first analysis of the I. ricinus genome with the transcriptome and proteome of the unfed I. ricinus midgut.


METHODS
Whole genome sequencing was performed on I. ricinus ticks and the sequences were de novo assembled. In parallel, I. ricinus ticks were dissected and the midgut transcriptome sequenced. Both datasets were integrated by transcript discovery analysis to identify putative genes and genome contigs were screened for homology. An alignment-based and a motif-search-based approach were combined for the annotation of the midgut transcriptome. Additionally, midgut proteins were identified and annotated by mass spectrometry with public databases and the in-house built transcriptome database as references and results were cross-validated.


RESULTS
The de novo assembly of 1 billion DNA sequences to a reference genome of 393 Mb length provides an unprecedented insight into the I. ricinus genome. A homology search revealed sequences in the assembled genome contigs homologous to 89% of the I. scapularis genome scaffolds indicating coverage of most genome regions. We identified moreover 6,415 putative genes. More than 10,000 transcripts from naïve midgut were annotated with respect of predicted function and/or cellular localization. By combining an alignment-based with a motif-search-based annotation approach, we doubled the number of annotations throughout all functional categories. In addition, 574 gel spots were significantly identified by mass spectrometry (p<0.05) and 285 distinct proteins expressed in the naïve midgut were annotated functionally and/or for cellular localization. Our systems approach reveals a midgut metabolism of the unfed tick that is prepared to sense and process an anticipated blood meal.


CONCLUSIONS
This multiple-omics study vastly extends the publicly available DNA and RNA databases for I. ricinus, paving the way for further in-depth analysis of the most important European disease vector and its interactions with pathogens and hosts.
Department of Infection and Immunity, Luxembourg Institute of Health (former Centre de Recherche Public de la Santé)/Laboratoire National de Santé, Luxembourg, Luxembourg. wibke.jochum@LiH.lu.
Wibke J
WJ
Cramaro
Department of Infection and Immunity, Luxembourg Institute of Health (former Centre de Recherche Public de la Santé)/Laboratoire National de Santé, Luxembourg, Luxembourg. dominique.revets@LiH.lu.
Dominique
D
Revets
Department of Infection and Immunity, Luxembourg Institute of Health (former Centre de Recherche Public de la Santé)/Laboratoire National de Santé, Luxembourg, Luxembourg. oliver.hunewald@LiH.lu.
Oliver E
OE
Hunewald
Department of Infection and Immunity, Luxembourg Institute of Health (former Centre de Recherche Public de la Santé)/Laboratoire National de Santé, Luxembourg, Luxembourg. regina.brunnhoefer@LiH.lu.
Regina
R
Sinner
Department of Infection and Immunity, Luxembourg Institute of Health (former Centre de Recherche Public de la Santé)/Laboratoire National de Santé, Luxembourg, Luxembourg. anna.reye@web.de.
Anna L
AL
Reye
Department of Infection and Immunity, Luxembourg Institute of Health (former Centre de Recherche Public de la Santé)/Laboratoire National de Santé, Luxembourg, Luxembourg. claude.muller@LiH.lu.
Claude P
CP
Muller
D000818:Animals; D049750:Genome, Insect / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D018884:Ixodes / Q000235:genetics*; D020543:Proteome; D017422:Sequence Analysis, DNA; D059467:Transcriptome
D020543:Proteome