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Background  Global warming and other ecological changes have facilitated the expansion of  Ixodes ricinus  tick populations.  Ixodes ricinus  is the most important carrier of vector-borne pathogens in Europe, transmitting viruses, protozoa and bacteria, in particular  Borrelia burgdorferi  ( sensu lato ), the causative agent of Lyme borreliosis, the most prevalent vector-borne disease in humans in the Northern hemisphere. To faster control this disease vector, a better understanding of the  I. ricinus  tick is necessary. To facilitate such studies, we recently published the first reference genome of this highly prevalent pathogen vector. Here, we further extend these studies by scaffolding and annotating the first reference genome by using ultra-long sequencing reads from third generation single molecule sequencing. In addition, we present the first genome size estimation for  I. ricinus  ticks and the embryo-derived cell line IRE/CTVM19.    Results  235,953 contigs were integrated into 204,904 scaffolds, extending the currently known genome lengths by more than 30% from 393 to 516 Mb and the N50 contig value by 87% from 1643 bp to a N50 scaffold value of 3067 bp. In addition, 25,263 sequences were annotated by comparison to the tick’s North American relative  Ixodes scapularis . After (conserved) hypothetical proteins, zinc finger proteins, secreted proteins and P450 coding proteins were the most prevalent protein categories annotated. Interestingly, more than 50% of the amino acid sequences matching the homology threshold had 95–100% identity to the corresponding  I. scapularis  gene models. The sequence information was complemented by the first genome size estimation for this species. Flow cytometry-based genome size analysis revealed a haploid genome size of 2.65Gb for  I. ricinus  ticks and 3.80 Gb for the cell line.    Conclusions  We present a first draft sequence map of the  I. ricinus  genome based on a PacBio-Illumina assembly. The  I. ricinus  genome was shown to be 26% (500 Mb) larger than the genome of its American relative  I. scapularis . Based on the genome size of 2.65 Gb we estimated that we covered about 67% of the non-repetitive sequences. Genome annotation will facilitate screening for specific molecular pathways in  I. ricinus  cells and provides an overview of characteristics and functions.    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-017-2008-9) contains supplementary material, which is available to authorized users.

Genome scaffolding and annotation for the pathogen vector Ixodes ricinus by ultra-long single molecule sequencing